WO2018178265A1 - Immunogenic composition, use and method of treatment - Google Patents

Immunogenic composition, use and method of treatment Download PDF

Info

Publication number
WO2018178265A1
WO2018178265A1 PCT/EP2018/058131 EP2018058131W WO2018178265A1 WO 2018178265 A1 WO2018178265 A1 WO 2018178265A1 EP 2018058131 W EP2018058131 W EP 2018058131W WO 2018178265 A1 WO2018178265 A1 WO 2018178265A1
Authority
WO
WIPO (PCT)
Prior art keywords
immunogenic composition
immunogenic
use
seq id
treatment
Prior art date
Application number
PCT/EP2018/058131
Other languages
French (fr)
Inventor
Catherine COHET
Jeanne-Marie Josephine DEVASTER
David Mayhew
Bruce Miller
Ruth Tal-Singer
Vincent Weynants
Thomas Wilkinson
Original Assignee
Glaxosmithkline Intellectual Property Development Limited
Glaxosmithkline Biologicals Sa
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority to US201762479562P priority Critical
Priority to US62/479,562 priority
Application filed by Glaxosmithkline Intellectual Property Development Limited, Glaxosmithkline Biologicals Sa filed Critical Glaxosmithkline Intellectual Property Development Limited
Publication of WO2018178265A1 publication Critical patent/WO2018178265A1/en

Links

Classifications

    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL, OR TOILET PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K39/02Bacterial antigens
    • A61K39/104Pseudomonadales, e.g. Pseudomonas
    • A61K39/1045Moraxella
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL, OR TOILET PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL, OR TOILET PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K39/02Bacterial antigens
    • A61K39/102Pasteurellales, e.g. Actinobacillus, Pasteurella; Haemophilus
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL, OR TOILET PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K2039/55Medicinal preparations containing antigens or antibodies characterised by the host/recipient, e.g. newborn with maternal antibodies
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL, OR TOILET PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K2039/555Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
    • A61K2039/55511Organic adjuvants
    • A61K2039/55555Liposomes; Vesicles, e.g. nanoparticles; Spheres, e.g. nanospheres; Polymers
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL, OR TOILET PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K2039/70Multivalent vaccine
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00Drugs for disorders of the respiratory system

Abstract

The present invention relates to immunogenic compositions comprising an immunogenic polypeptide from Haemophilus influenzae or an immunogenic fragment thereof and/or an immunogenic polypeptide from Moraxella catarrhalis or an immunogenic fragment thereof, for use in the treatment or prevention of a recurrence of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) resulting from a bacterial infection in a subject.

Description

IMMUNOGENIC COMPOSITION, USE AND METHOD OF TREATMENT Technical Field

The present invention relates to the field of immunogenic compositions and the use of such compositions in medicine. More particularly, it relates to immunogenic compositions comprising an immunogenic polypeptide from Haemophilus influenzae or an immunogenic fragment thereof and/or an immunogenic polypeptide from Moraxella catarrhalis or an immunogenic fragment thereof, for use in the treatment or prevention of a recurrence of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection jn a subject.

Background to the Invention

Chronic Obstructive Pulmonary Disease (COPD) is a chronic inflammatory disorder resulting in irreversible decline in lung function as a consequence of inhalation of tobacco smoke or other irritants. Chronic obstructive pulmonary disease (COPD) is recognised as encompassing several conditions (airflow obstruction, chronic bronchitis, bronchiolitis or small airways disease and emphysema) that often coexist (Wilson et al., Eur. Respir. J. 2001; 17: 995-1007). Patients suffer exacerbations of their condition that are usually associated with increased breathlessness, and often have increased cough that may be productive of mucus or purulent sputum (Wilson, Eur Respir J 2001 17:995-1007). COPD is defined physiologically by the presence of irreversible or partially reversible airway obstruction in patients with chronic bronchitis and/or emphysema (Standards for the diagnosis and care of patients with chronic obstructive pulmonary disease. American Thoracic Society. Am J Respir Crit Care Med. 1995 Nov; 152(5 Pt 2):S77-121).

COPD is a major cause of morbidity and mortality worldwide. Approximately one in 20 deaths in 2005 in the US had COPD as the underlying cause. (Drugs and Aging 26:985-999 (2009)). It is projected that in 2020 COPD will rise to the fifth leading cause of disability adjusted life years, chronic invalidating diseases, and to the third most important cause of mortality (Lancet 349: 1498-1504 (1997)). The course of COPD is characterized by progressive worsening of airflow limitation and a decline in pulmonary function. COPD may be complicated by frequent and recurrent acute exacerbations (AE), which are associated with enormous health care expenditure and high morbidity. (Proceedings of the American Thoracic Society 4:554-564 (2007)). One study suggests that approximately 50% of acute exacerbations of symptoms in COPD are caused by non-typeable Haemophilus influenzae, Moraxella catarrhalis, Streptococcus pneumoniae, and Pseudomonas aeruginosa. (Drugs and Aging 26:985-999 (2009)). Haemophilus influenzae (H. influenzae) is found in 20-30% of exacerbations of COPD; Streptococcus pneumoniae, in 10-15% of exacerbations of COPD; and Moraxella catarrhalis, in 10-15% of exacerbations of COPD. (New England Journal of Medicine 359:2355-2365 (2008)). Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis have been shown to be the primary pathogens in acute exacerbations of bronchitis in Hong Kong, South Korea, and the Phillipines, while Klebsiella spp., Pseudomonas aeruginosa and Acinetobacter spp. constitute a large proportion of pathogens in other Asian countries/regions including Indonesia, Thailand, Malaysia and Taiwan (Respirology, (2011) 16, 532-539; doi: 10.1111/j.1440.1843.2011.01943.x). In Bangladesh, 20% of patients with COPD showed positive sputum culture for Pseudomonas, Klebsiella, Streptococcus pneumoniae and Haemophilus influenzae, while 65% of patients with AECOPD (acute exacerbation of COPD) showed positive cultures for Pseudomonas, Klebsiella, Acinetobacter, Enterobacter, Moraxella catarrhal 'is and combinations thereof. (Mymensingh Medical Journal 19:576-585 (2010)). However, it has been suggested that the two most important measures to prevent COPD exacerbation are active immunizations and chronic maintenance of pharmacotherapy. (Proceedings of the American Thoracic Society 4:554-564 (2007)).

One of the difficulties in treating and managing COPD is the heterogeneity of this complex disease in terms of severity, progression, exercise tolerance, and nature of symptoms. This complexity is also evident in acute exacerbations of COPD (AECOPD), which are transient and apparently stochastic periods of increased COPD symptoms requiring additional medical treatment and often hospitalization (Sethi et al., N Eng J Med 2008;359:2355-65). Known subtypes of exacerbations are defined by the nature of key triggers including bacterial or viral infections, and/or high eosinophil levels, and these events are typically treated with a combination of antibiotics and steroids in a non-specific manner (Bafadhel et al., Am J Respir Crit Care Med 2011;184:662).

There exists a need for improved uses of immunogenic compositions and methods for the prevention and/or treatment of AECOPD.

Summary of the Invention

According to the present invention, it has been surprisingly found that bacterial exacerbations are more likely to be repeated in subsequent exacerbations within a subject and that this finding can be used to determine appropriate treatments for a given subject (e.g. a COPD patient).

Accordingly, there is provided in one aspect of the present invention an immunogenic composition comprising an immunogenic polypeptide from Haemophilus influenzae or an immunogenic fragment thereof and/or an immunogenic polypeptide from Moraxella catarrhalis or an immunogenic fragment thereof, for use in the treatment or prevention of a recurrence of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection in a subject.

In another aspect of the present invention there is provided an immunogenic composition comprising an immunogenic polypeptide from Haemophilus influenzae or an immunogenic fragment thereof and/or an immunogenic polypeptide from Moraxella catarrhalis or an immunogenic fragment thereof, for use in a method of treating or preventing a recurrence of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) resulting from a bacterial infection in a subject, wherein the method comprises identifying that the subject has previously had an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection and then administering the immunogenic composition to the subject.

In another aspect of the present invention there is provided the use of an immunogenic composition comprising an immunogenic polypeptide from Haemophilus influenzae or an immunogenic fragment thereof and/or an immunogenic polypeptide from Moraxella catarrhalis or an immunogenic fragment thereof, in the manufacture of a medicament for the treatment or prevention of a recurrence of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection in a subject. In another aspect of the present invention there is provided the use of an immunogenic composition comprising an immunogenic polypeptide from Haemophilus influenzae or an immunogenic fragment thereof and/or an immunogenic polypeptide from Moraxella catarrhalis or an immunogenic fragment thereof, in the manufacture of a medicament for use in a method of treating or preventing a recurrence of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection in a subject, wherein the method comprises identifying that the subject has previously had an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection and then administering the immunogenic composition to the subject.

In another aspect of the present invention there is provided a method of treatment or prevention of a recurrence of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection in a subject at risk of developing an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) recurrence, said method comprising administering to said subject, a therapeutically effective amount of an immunogenic composition comprising an immunogenic polypeptide from Haemophilus influenzae or an immunogenic fragment thereof and/or an immunogenic polypeptide from Moraxella catarrhalis or an immunogenic fragment thereof.

In another aspect of the present invention there is provided a method of treatment or prevention of a recurrence of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection in a subject at risk of developing an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) recurrence, said method comprising administering to said subject, a therapeutically effective amount of an immunogenic composition comprising an immunogenic polypeptide from Haemophilus influenzae or an immunogenic fragment thereof and/or an immunogenic polypeptide from Moraxella catarrhalis or an immunogenic fragment thereof, wherein the method comprises identifying that the subject has previously had an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection and then administering the immunogenic composition to the subject.

Detailed Description

Terminology

A "subject" as used herein is a mammal, including humans, non-human primates, and non-primate mammals such as members of the rodent genus (including but not limited to mice and rats) and members of the order Lagomorpha (including but not limited to rabbits). In one embodiment, the subject is a human.

As used herein, "adjuvant" means a compound or substance that, when administered to a subject in conjunction with a vaccine, immunotherapeutic, or other antigen- or immunogen- containing composition, increases or enhances the subject's immune response to the administered antigen or immunogen (as compared to the immune response that would be obtained in the absence of adjuvant).

As used herein, the term "immunogenic fragment" is a portion of an antigen smaller than the whole, that is capable of eliciting a humoral and/or cellular immune response in a host animal, e.g. human, specific for that fragment. Fragments of a protein can be produced using techniques known in the art, e.g. recombinantly, by proteolytic digestion, or by chemical synthesis. Internal or terminal fragments of a polypeptide can be generated by removing one or more nucleotides from one end (for a terminal fragment) or both ends (for an internal fragment) of a nucleic acid which encodes the polypeptide.

As used herein, the term "conservative amino acid substitution" involves substitution of a native amino acid residue with a non-native residue such that there is little or no effect on the size, polarity, charge, hydrophobicity, or hydrophilicity of the amino acid residue at that position, and without resulting in decreased immunogenicity. For example, these may be substitutions within the following groups: valine, glycine; glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid; asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. Conservative amino acid modifications to the sequence of a polypeptide (and the corresponding modifications to the encoding nucleotides) may produce polypeptides having functional and chemical characteristics similar to those of a reference polypeptide.

As used herein "signal peptide" refers to a short (less than 60 amino acids, for example, 3 to 60 amino acids) polypeptide present on precursor proteins (typically at the N terminus), and which is typically absent from the mature protein. The signal peptide (sp) is typically rich in hydrophobic amino acids. The signal peptide directs the transport and/or secretion of the translated protein through the membrane. Signal peptides may also be called targeting signals, transit peptides, localization signals, or signal sequences. For example, the signal sequence may be a co-translational or post-translational signal peptide.

Chronic obstructive pulmonary disease (COPD) is a lung disease characterized by chronic obstruction of lung airflow that interferes with normal breathing and is not fully reversible.

A COPD diagnosis is confirmed by a simple test called spirometry, which measures how deeply a person can breathe and how fast air can move into and out of the lungs. Such a diagnosis should be considered in any patient who has symptoms of cough, sputum production, or dyspnea (difficult or labored breathing), and/or a history of exposure to risk factors for the disease. Where spirometry is unavailable, the diagnosis of COPD should be made using all available tools. Clinical symptoms and signs, such as abnormal shortness of breath and increased forced expiratory time, can be used to help with the diagnosis. A low peak flow is consistent with COPD, but may not be specific to COPD because it can be caused by other lung diseases and by poor performance during testing. Chronic cough and sputum production often precede the development of airflow limitation by many years, although not all individuals with cough and sputum production go on to develop COPD.

An acute exacerbation of COPD (AECOPD) is an acute event characterised by a worsening of the patient's respiratory symptoms that is beyond normal day-to-day variations. Typically an

AECOPD leads to a change in medication.

For the purposes of this invention, "treatment of a recurrence of an acute exacerbation of

COPD" means ameliorating, stabilising, reducing or eliminating the increased symptoms that are a feature of an acute exacerbation in a subject, wherein the subject has experienced one or more past exacerbations of the same phenotype (e.g. bacterial phenotype associated with a bacterial infection by Haemophilus influenza (e.g. non-typeable H. influenzae (NTHi) and/or Moraxella catarrhalis). As used herein, the phrase "prevention of a recurrence of an acute exacerbation of COPD" means preventing, reducing the incidence or frequency, or reducing the severity of future acute exacerbations of a particular phenotype (e.g. bacterial phenotype associated with a bacterial infection by Haemophilus influenza (e.g. non-typeable H. influenzae (NTHi) and/or Moraxella catarrhalis)) in a subject who has experienced one or more past exacerbations of the same phenotype. In one embodiment, an immunogenic composition according to the present invention is for the reduction of the frequency of acute exacerbations of chronic obstructive pulmonary disease (AECOPD) in a subject. In another embodiment, an immunogenic composition according to the present invention is for the reduction of the frequency of acute exacerbations of chronic obstructive pulmonary disease (AECOPD) resulting from a bacterial infection in a subject.

In one embodiment, an immunogenic composition according to the present invention is for the prevention of a recurrence of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) resulting from a bacterial infection in a subject.

In a further embodiment, an immunogenic composition according to the present invention is for the treatment of a recurrence of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) resulting from a bacterial infection in a subject.

Description of Figures

Figure 1: Flow chart of subject enrollment, sputum sampling, and selection samples for microbiome analysis for AERIS

Figure 2: Microbiome differences in disease severity and stable or exacerbation visits (A) The Shannon diversity index and relative abundances of bacteria labeled at the phylum and genus level of samples grouped by COPD disease severity. Significant differences in relative abundances between groups are labeled with arrows indicating the relative change in abundance; *P<0.05. (B) The same alpha diversity and relative abundances grouped by stable or exacerbation status. (C) Paired analysis of changes in relative abundances of key genera between matched stable and subsequent exacerbation events; *P<0.05.

Figure 3: Lung microbiome stability (A) Weighted UniFrac distances measured within and between subjects and comparing stable and exacerbation events; ***P<0.001, ****P<0.0001. (B) Unweighted UniFrac distances measured within and between subjects and comparing stable and exacerbation events; ****P<0.0001. (C) Weighted UniFrac distances for all within subject samples as a function of exacerbation frequency defined by number of exacerbation event and the fraction of samples within an individual taken during an exacerbation. (D) Paired weighted UniFrac distances between exacerbation sample and its previous stable sample from that subject. Exacerbation subtypes labelled as B-Bacterial, V-Viral, E-Eosinophilic, Other, or mixed, *P<0.05. Figure 4: Markov chain analysis of transitions between exacerbation states (A) Markov chain analysis from longitudinal exacerbation sampling within individuals identifies non-random transition probabilities for bacterial and eosinophilic exacerbations, but not viral. The size of each node is proportional to abundance of that exacerbation type and the width of the edges are proportional to the transition probabilities. (B) Markov chain analysis of the bacterial exacerbation identifies significantly different transition probabilities for bacterial exacerbations which were positive and negative for the presence of H. influenzae.

Figure 5: ABCD Assessment Tool for COPD

COPD is characterised by progressive worsening of airflow limitation and a decline in pulmonary function. The disease is complicated by acute exacerbations (AECOPD), which are transient and apparently stochastic periods of increased COPD symptoms requiring additional medical treatment and often hospitalisation. The present inventors have now surprisingly found that an understanding of a subject's exacerbation history (i.e. previous exacerbation phenotype) can be used to guide future therapeutic strategies. Clinical data from a previous exacerbation can be used to inform the likely phenotype of the next acute exacerbation, enabling administration of preventative/prophylactic treatment and/or a more rapid administration of appropriate therapy on presentation of an acute exacerbation.

The present inventors have found, in particular, that bacterial exacerbations are more likely to be repeated in subsequent exacerbations within a subject (e.g. a COPD patient). Thus, COPD patients with a documented history of one or more bacterial exacerbations represent a high-risk sub-population of COPD patients that would benefit from preventive therapy with an immunogenic composition.

As used herein, the term "bacterial exacerbation" refers to an exacerbation associated with a positive bacterial pathogen on routine culture (Haemophilus influenza, Moraxella catarrhalis, Streptococcus pneumoniae, Staphylococcus aureus or Pseudomonas aeruginosa) or a total aerobic CFU count greater than or equal to 107 cells. In one embodiment, the bacterial exacerbation is associated with a positive bacterial culture for

a) Haemophilus influenza (e.g. non-typeable H. influenzae (NTHi));

b) Moraxella catarrhalis; or

c) Haemophilus influenzae (e.g. non-typeable H. influenzae (NTHi)) and Moraxella catarrhalis

In one aspect there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection is defined by:

a) a positive bacterial pathogen on culture of an induced or spontaneous sputum sample obtained from a subject; and/or

b) a total aerobic CFU count greater than or equal to 107 cells; and/or

c) the presence of increased sputum purulence.

In a further aspect there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection is defined by a positive bacterial pathogen on culture of an induced or spontaneous sputum sample obtained from a subject.

In a further aspect there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection is defined by a total aerobic CFU count greater than or equal to 107 cells.

In a further aspect, the bacterial infection is present in the lung(s) of a subject.

In a further aspect there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the bacterial infection occurred in the presence of Haemophilus influenza (e.g. non-typeable H. influenzae (NTHi)) and/or Moraxella catarrhalis. In one aspect, the bacterial infection occurred in the presence of Haemophilus influenza (e.g. non-typeable H. influenzae (NTHi)). In another aspect, the bacterial infection occurred in the presence of Moraxella catarrhalis.

In one aspect there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the subject is at risk for developing an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) resulting from a bacterial infection.

In particular, the present inventors found that a significant decrease in entropy of the microbiome (Shannon diviersity index; Pad] < 0.05) and an increase in the relative abundance of Proteobacteria, such as Haemophilus, is associated with an increase in disease severity. Furthermore, Moraxella showed a significant increase in exacerbation (P = 0.0153). Thus, in one aspect there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the subject has a decreased entropy of the lung microbiome as measured according to the Shannon diversity index (Padj < 0.05) compared to a measurement taken during a previous acute exacerbation in COPD (AECOPD) in the same subject. In another aspect, there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the subject has a Shannon diversity index less than 3.0.

In another aspect there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the subject has an increased abundance of Proteobacteria, e.g. Haemophilus and/or Moraxella.

The present inventors assessed the contribution of changes in the COPD airway microbiome to the incidence of AECOPD in patients aged 40-85 years with a confirmed diagnosis of COPD, categorised as moderate, severe, or very severe according to the Global Initiative for Chronic Obstructive Lung Disease (GOLD) classification.

The Global Strategy for the Diagnosis, Management and Prevention of COPD prepared by GOLD state that COPD should be considered in any patient with dyspnea, chronic cough or sputum production, and/or a history of exposure to risk factors for the disease, such as tobacco smoking, occupation, or pollutants. A spirometry assessment, measuring airflow limitation, is required to establish diagnosis. The classification of airflow limitation severity in COPD outlined in the GOLD strategy is shown in Table 1.

Table 1. Classification of airflow limitation severity in COPD (Based on post-bronchodilator FEVi) In patients with FEVi/FVC < 0.70 GOLD 1 Mild FEVi > 80% predicted

GOLD 2 Moderate 50% < FEVi < 80% predicted

GOLD 3 Severe 30% < FEVi < 50% predicted

GOLD 4 Very Severe FEVi < 30% predicted

COPD assessment also includes analysis of patient symptoms, and this can be performed using comprehensive disease-specific health status questionnaires such as the Chronic Respiratory Questionnaire (CRQ) and St. George's Respiratory Questionnaire (SGRQ). For routine practice the COPD Assessment Test (CAT™) and The COPD Control Questionnaire (The CCQ©) have been developed. The CAT™ and CCQ® tests do not categorise patients for the purpose of treatment, however for the SRGQ assessment a symptom score > 25 may be used as the threshold for considered regular treatment for breathlessness. The equivalent threshold for the CAT™ is 10. A simple assessment of breathlessness is the Modified British Medical Research Council (mMRC) Questionnaire.

According to the GOLD strategy, of the patients classified at the GOLD 2 (moderate) stage, approximately 20% may experience frequent exacerbations requiring antibiotic and/or systemic corticosteroid therapy in addition to regular maintenance therapy. The risk of exacerbations is significantly higher for patients classified as GOLD 3 (severe) and GOLD 4 (very severe).

The "ABCD" assessment tool is further used to understand a COPD patient's severity of disease. This assessment combines the patient's spirometry analysis with their exacerbation history and symptom assessment to give a spirometric grade combined with an "ABCD" group. The ABCD assessment tool is shown in Figure 5.

In another aspect there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the subject has GOLD 2 (moderate), GOLD 3 (severe) or GOLD 4 (very severe) COPD status.

In one aspect there is provided an immunogenic composition, use or method of treatment or prevention according to the present invention, wherein the subject is an adult aged 40-85 years old.

In another aspect there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the subject is a tobacco smoker.

In one aspect, the present invention provides an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the subject has experienced at least one (e.g. 2 or more, 3 or more) episodes of acute exacerbation in chronic obstructive pulmonary disease (AECOPD) resulting from a bacterial infection. In another aspect, the present invention provides an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the subject has experienced at least one (e.g. 2 or more, 3 or more) episodes of acute exacerbation in chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection within a period of 12 months.

In a further aspect there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the subject has experienced at least one (e.g. 2 or more, 3 or more) episodes of acute exacerbation in chronic obstructive pulmonary disease (AECOPD) resulting from a bacterial infection in the preceding 12 months.

The present inventors also found that in patients with bronchiectasis, a substantial increase in Haemophilus was observed which was evident in both stable and exacerbation events. Bronchiectasis is a condition in which an area of the bronchial tubes is permanently and abnormally widened (dilated), with accompanying infection. Types include cylindrical, follicular, fusiform, saccular, and varicose, named according to the nature of the dilatations. Examination of the walls of the bronchial tubes reveals destruction of the normal structural elements, with replacement by scar tissue. Pus collects within the bronchi, and the normal flow of oxygen into the lungs, and carbon dioxide out of the lungs (air exchange) is impaired. The bronchi show signs of inflammation, with swelling and invasion by a variety of immune cells. The inflamed areas show signs of increased growth of blood vessels. The area of the lung which should be served by a diseased bronchial tube is also prone to inflammation and infection. The most immediate symptom is persistent coughing with sputum production.

Thus, in another aspect there is provided an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the subject has bronchiectasis.

The present invention also provides an immunogenic composition for use, use of an immunogenic composition or method of treatment or prevention according to the present invention, wherein the subject has experienced an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) resulting from a bacterial infection and failed to achieve resolution of symptoms after antibiotic therapy.

Immunogenic proteins and immunogenic fragments

Identity between polypeptides may be calculated by various algorithms. For example, the Needle program, from the EMBOSS package (Free software; EMBOSS: The European Molecular Biology Open Software Suite (2000). Trends in Genetics 16(6): 276—277) and the Gap program from the GCG® package (Accelrys Inc.) may be used. This Gap program is an implementation of the Needleman-Wunsch algorithm described in: Needleman, S. B. and Wunsch, C. D. (1970) J. Mol. Biol. 48, 443-453. The BLOSUM62 scoring matrix has been used, and the gap open and extension penalties were respectively 8 and 2.

Looking at the computed alignment, identical residues between two compared sequences can be observed. A percentage of identity can be computed by (1) calculating the number of identities divided by the length of the alignment, multiplied by 100 (for example, for the Needle program analysis), (2) calculating the number of identities divided by the length of the longest sequence, multiplied by 100, (3) calculating the number of identities divided by the length of the shortest sequence, multiplied by 100, or (4) calculating the number of identities divided by the number of aligned residues, multiplied by 100 (a residue is aligned if it is in front of another) (for example, for the Gap program analysis).

In one embodiment, sequence identity is calculated over the full length of the reference sequence (e.g. SEQ ID NO. 1 to 21 of the present invention). The immunogenic polypeptides and immunogenic fragments the invention may be derived from an amino acid sequence at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a reference sequence (e.g. SEQ ID NO. 1 to 21 of the present invention) which has been modified by the deletion and/or addition and/or substitution of one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 amino acids). Amino acid substitution may be conservative or non- conservative. In one aspect, amino acid substitution is conservative. Substitutions, deletions, additions or any combination thereof may be combined in a single variant so long as the variant is an immunogenic polypeptide.

Immunogenic polypeptides from non-typeable H. influenzae (NTHi) and immunogenic fragments

In one aspect of the invention, the immunogenic composition comprises an immunogenic polypeptide from non-typeable H. influenzae (NTHi) or an immunogenic fragment thereof. In another aspect of the invention, the immunogenic composition comprises an immunogenic fragment of a polypeptide from non-typeable H. influenzae (NTHi).

In one aspect of the invention, the immunogenic composition comprises Protein D or an immunogenic fragment thereof, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to Protein D sequence.

Protein D may be as described in W091/18926. In an embodiment, the immunogenic composition of the invention comprises protein D from Haemophilus influenzae (PD), for example, protein D sequence from Figure 9 (Figure 9a and 9b together, 364 amino acids) of EP 0594610 (SEQ ID NO: 1). Inclusion of this protein in the immunogenic composition may provide a level of protection against Haemophilus influenzae related otitis media (Pyrmula et al Lancet 367; 740-748 (2006)). Protein D may be used as a full length protein or as a fragment (for example, Protein D may be as described in WO0056360). For example, a protein D sequence may comprise (or consist) of the protein D fragment described in EP0594610 which begins at the sequence SSHSSNMANT (SerSerHisSerSerAsnMetAlaAsnThr) (SEQ ID NO. 3), and lacks the 19 N-terminal amino acids from Fig 9 of EP0594610, optionally with the tripeptide MDP from NS1 fused to the N-terminal of said protein D fragment (348 amino acids) (SEQ ID NO: 2). In one aspect, the protein D or fragment of protein D is unlipidated.

In one aspect of the invention, the immunogenic composition comprises Protein D or an immunogenic fragment thereof, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to SEQ ID NO. 1. Immunogenic fragments of Protein D comprise immunogenic fragments of at least 7, 10, 15, 20, 25, 30 or 50 contiguous amino acids of SEQ ID NO. 1. The immunogenic fragments may elicit antibodies which can bind SEQ ID NO. 1. In another aspect of the invention, the immunogenic composition comprises Protein D or an immunogenic fragment thereof, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to SEQ ID NO. 2.

In one aspect of the invention, the immunogenic composition comprises Protein E or an immunogenic fragment thereof, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to Protein E sequence. In another aspect of the invention, the immunogenic composition comprises an immunogenic fragment of Protein E, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to Protein E sequence. Protein E (PE) is an outer membrane lipoprotein with adhesive properties. It plays a role in the adhesion/invasion of non-typeable Haemophilus influenzae (I THi) to epithelial cells. (J. Immunology 183: 2593-2601 (2009); The Journal of Infectious Diseases 199:522-531 (2009), Microbes and Infection 10:87-96 (2008)). It is highly conserved in both encapsulated Haemophilus influenzae and non-typeable H. influenzae and has a conserved epithelial binding domain. (The Journal of Infectious Diseases 201:414-419 (2010)). Thirteen different point mutations have been described in different Haemophilus species when compared with Haemophilus influenzae Rd as a reference strain. Its expression is observed on both logarithmic growing and stationary phase bacteria. (WO2007/084053).

Protein E is also involved in human complement resistance through binding vitronectin. (Immunology 183: 2593-2601 (2009)). PE, by the binding domain PKRYARSVRQ YKILNCANYH LTQVR (SEQ ID NO. 1, corresponding to amino acids 84-108 of SEQ ID NO. 4), binds vitronectin which is an important inhibitor of the terminal complement pathway. (J. Immunology 183:2593- 2601 (2009)).

As used herein "Protein E", "protein E", "Prot E", and "PE" mean Protein E from H. influenzae. Protein E may consist of or comprise the amino acid sequence of SEQ ID NO. 4 (corresponding to SEQ ID NO. 4 of WO2012/139225A1): (MKKIILTLSL GLLTACSAQI QKAEQNDVKL APPTDVRSGY IRLVKNVNYY IDSESIWVDN QEPQIVHFDA WNLDKGLYV YPEPKRYARS VRQYKILNCA NYHLTQVRTD FYDEFWGQGL RAAPKKQKKH TLSLTPDTTL YNAAQIICAN YGEAFSVDKK) as well as sequences with at least or exactly 75%, 77%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identity, over the entire length, to SEQ ID NO. 4. In an aspect of the invention, the immunogenic composition comprises Protein E or an immunogenic fragment thereof, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to SEQ ID NO. 4. Immunogenic fragments of Protein E comprise immunogenic fragments of at least 7, 10, 15, 20, 25, 30 or 50 contiguous amino acids of SEQ ID NO. 4. The immunogenic fragments may elicit antibodies which can bind SEQ ID NO. 4.

In another aspect of the invention, the immunogenic composition comprises an immunogenic fragment of Protein E, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to SEQ ID NO. 5 (corresponding to Seq ID No. 125 of WO2012/139225A1): SEQ ID NO. 5: Amino acids 20-160 of Protein E

I QKAEQNDVKL APPTDVRSGY IRLVKNVNYY IDSESIWVDN QEPQIVHFDA WNLDKGLYV YPEPKRYARS VRQYKILNCA NYHLTQVRTD FYDEFWGQGL RAAPKKQKKH TLSLTPDTTL YNAAQIICAN YGEAFSVDKK

In one aspect of the invention, the immunogenic composition comprises PilA or an immunogenic fragment thereof, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to PilA sequence. In another aspect of the invention, the immunogenic composition comprises an immunogenic fragment of PilA, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to PilA sequence.Pilin A (PilA) is likely the major pilin subunit of H. influenzae Type IV Pilus (Tfp) involved in twitching motility (Infection and Immunity, 73: 1635-1643 (2005)). NTHi PilA is a conserved adhesin expressed in vivo. It has been shown to be involved in NTHi adherence, colonization and biofilm formation. (Molecular Microbiology 65: 1288-1299 (2007)).

As used herein "PilA" means Pilin A from H. influenzae. PilA may consist of or comprise the protein sequence of SEQ ID NO. 6 (corresponding to SEQ ID NO. 58 of WO2012/139225A1) (MKLTTQQTLK KGFTLIELMI VIAIIAILAT lAIPSYQNYT KKAAVSELLQ ASAPYKADVE LCVYSTNETT NCTGGKNGIA ADITTAKGYV KSVTTSNGAI TVKGDGTLAN MEYILQATGN AATGVTWTTT CKGTDASLFP ANFCGSVTQ) as well as sequences with 80% to 100% identity to SEQ ID NO. 6. For example, PilA may be at least 80%, 85%, 90%, 95%, 97% or 100% identical to SEQ ID NO. 6. In an aspect of the invention, the immunogenic composition comprises comprises PilA or an immunogenic fragment thereof, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to Seq ID NO. 6.

For example, immunogenic fragments of PilA comprise immunogenic fragments of at least 7, 10, 15, 20, 25, 30 or 50 contiguous amino acids of SEQ ID NO. 6. The immunogenic fragments may elicit antibodies which can bind SEQ ID NO. 6.

In another aspect of the invention, the immunogenic composition comprises an immunogenic fragment of PilA, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to SEQ ID NO. 7 (corresponding to Seq ID No. 127 of WO2012/139225A1):

SEQ ID NO. 7 Amino acids 40-149 of PilA from H. influenzae strain 86-028NP

T KKAAVSELLQ ASAPYKADVE LCVYSTNETT NCTGGKNGIA ADITTAKGYV KSVTTSNGAI TVKGDGTLAN MEYILQATGN AATGVTWTTT CKGTDASLFP ANFCGSVTQ.

Protein E and Pilin A may be presented as a fusion protein (PE-PilA). In another aspect of the invention, the immunogenic composition comprises Protein E and PilA, wherein Protein E and PilA are present as a fusion protein, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to LVL- 735 SEQ ID NO. 8 (corresponding to Seq ID No. 194 of WO2012/139225A1). SEQ ID NO. 8: LVL735 (protein): (pelB sp)(ProtE aa 20-160)(GG)(PNA aa40-149):

MKYLLPTAAA GLLLLAAQPA MAIQKAEQND VKLAPPTDVR SGYIRLVKNV NYYIDSESIW VDNQEPQIVH FDAWNLDKG LYVYPEPKRY ARSVRQYKIL NCANYHLTQV RTDFYDEFWG QGLRAAPKKQ KKHTLSLTPD TTLYNAAQII CANYGEAFSV DKKGGTKKAA VSELLQASAP YKADVELCVY STNETTNCTG GKNGIAADIT TAKGYVKSVT TSNGAITVKG DGTLANMEYI LQATGNAATG VTWTTTCKGT DASLFPANFC GSVTQ

In another aspect of the invention, the immunogenic composition comprises Protein E and PilA, wherein Protein E and PilA are present as a fusion protein, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to LVL-735, wherein the signal peptide has been removed, SEQ ID NO. 9 (Coresponding to Seq ID No. 219 of WO2012/139225A1).

SEQ ID NO. 9: PE-PilA fusion protein without signal peptide

IQKAEQND VKLAPPTDVR SGYIRLVKNV NYYIDSESIW VDNQEPQIVH FDAWNLDKG LYVYPEPKRY ARSVRQYKIL NCANYHLTQV RTDFYDEFWG QGLRAAPKKQ KKHTLSLTPD TTLYNAAQII CANYGEAFSV DKKGGTKKAA VSELLQASAP YKADVELCVY STNETTNCTG GKNGIAADIT TAKGYVKSVT TSNGAITVKG DGTLANMEYI LQATGNAATG VTWTTTCKGT DASLFPANFC GSVTQ

The immunogenicity of Protein E (PE) and Pilin A (PilA) polypeptides may be measured as described in WO2012/139225A1; the contents of which are incorporated herein by reference. Immunogenic polypeptides from Moraxella catarrhal is and Immunogenic Fragments In one aspect of the invention, the immunogenic composition comprises an immunogenic polypeptide from M. catarrhalis or an immunogenic fragment thereof.

In another aspect of the invention, the immunogenic composition comprises UspA2 or an immunogenic fragment thereof.

In one aspect of the invention, the immunogenic composition comprises UspA2 or an immunogenic fragment thereof, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to UspA2 sequence. In another aspect of the invention, the immunogenic composition comprises an immunogenic fragment of UspA2, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to UspA2 sequence.

Ubiquitous surface protein A2 (UspA2) is a trimeric autotransporter that appears as a lollipop-shared structure in electron micrographs (Hoiczyk et al. EMBO J. 19: 5989-5999 (2000)). It is composed of a N-terminal head, followed by a stalk which ends by an amphipathic helix and a C-terminal membrane domain. (Hoiczyk et al. EMBO J. 19: 5989-5999 (2000)). UspA2 contains a very well conserved domain (Aebi et al., Infection & Immunity 65(11) 4367-4377 (1997)), which is recognized by a monoclonal antibody that was shown protective upon passive transfer in a mouse Moraxella catarrhalis challenge model (Helminnen et al. J Infect Dis. 170(4): 867-72 (1994)).

UspA2 has been shown to interact with host structures and extracellular matrix proteins like fibronectin (Tan et al., J Infect Dis. 192(6): 1029-38 (2005)) and laminin (Tan et al., J Infect Dis. 194(4): 493-7 (2006)), suggesting it can play a role at an early stage of Moraxella catarrhalis infection.

UspA2 also seems to be involved in the ability of Moraxella catarrhalis to resist the bactericidal activity of normal human serum. (Attia AS et al. Infect Immun 73(4): 2400-2410 (2005)). It (i) binds the complement inhibitor C4bp, enabling Moraxella catarrhalis to inhibit the classical complement system, (ii) prevents activation of the alternative complement pathway by absorbing C3 from serum and (iii) interferes with the terminal stages of the complement system, the Membrane Attack Complex (MAC), by binding the complement regulator protein vitronectin, (de Vries et al., Microbiol Mol Biol Rev. 73(3): 389-406 (2009)).

As used herein "UspA2" means Ubiquitous surface protein A2 from Moraxella catarrhalis.

UspA2 may consist of or comprise the amino acid sequence of SEQ ID NO: 10 from ATCC 25238:

MKTMKLLPLKIAVTSAMIIGLGAASTANAQAKNDITLEDLPYLIKKIDQNELEADIGDIT ALEKYLALSQYGNILALEELNKALEELDEDVGWNQNDIANLEDDVETLTKNQNALAEQGE AIKEDLQGLADFVEGQEGKILQNETSIKKNTQRNLVNGFEIEKNKDAIAKNNESIEDLYD FGHEVAESIGEIHAHNEAQNETLKGLITNSIENTNNITKNKADIQALENNWEELFNLSG RLIDQKADIDNNINNIYELAQQQDQHSSDIKTLKKNVEEGLLELSGHLIDQKTDIAQNQA NIQDLATYNELQDQYAQKQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDA LNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINN IYELAQQQDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKL ITANKTAIDANKASADTKFAATADAITKNGNAITKNAKSITDLGTKVDGFDSRVTALDTK VNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRV NPNLAFKAGAAINTSGNKKGSYNIGVNYEF (SEQ ID NO: 1)

as well as sequences with at least or exactly 63%, 66%, 70%, 72%, 74%, 75%, 77%, 80%, 84%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identity, over the entire length, to SEQ ID NO: 10.

UspA2 as described in SEQ ID NO: 10 contains a signal peptide (for example, amino acids 1 to 29 of SEQ ID NO: 10), a laminin binding domain (for example, amino acids 30 to 177 of SEQ ID NO: 10), a fibronectin binding domain (for example, amino acids 165 to 318 of SEQ ID NO: 10) (Tan et al. JID 192: 1029-38 (2005)), a C3 binding domain (for example, amino acids 30 to 539 of SEQ ID NO: 10 (WO2007/018463), or a fragment of amino acids 30 to 539 of SEQ ID NO: 10, for example, amino acids 165 to 318 of SEQ ID NO: 1 (Hallstrom T et al. J. Immunol. 186: 3120-3129 (2011)), an amphipathic helix (for example, amino acids 519 to 564 of SEQ ID NO: 10 or amino acids 520-559 of SEQ ID NO: 10, identified using different prediction methods) and a C terminal anchor domain (for example, amino acids 576 to 630 amino acids of SEQ ID NO: 10 (Brooks et al., Infection & Immunity, 76(11), 5330-5340 (2008)).

In an embodiment, an immunogenic fragment of UspA2 contains a laminin binding domain and a fibronectin binding domain. In an additional embodiment, an immunogenic fragment of UspA2 contains a laminin binding domain, a fibronectin binding domain and a C3 binding domain. In a further embodiment, an immunogenic fragment of UspA2 contains a laminin binding domain, a fibronectin binding domain, a C3 binding domain and an amphipathic helix. UspA2 amino acid differences have been described for various Moraxella catarrhalis species. See for example, J Bacteriology 181(13):4026-34 (1999), Infection and Immunity 76(ll):5330-40 (2008) and PLoS One 7(9):e45452 (2012).

UspA2 may consist of or comprise an amino acid sequence that differs from SEQ ID NO. 10 at any one or more amino acid selected from the group consisting of: AA (amino acid) 30 to 298, AA 299 to 302, AA 303 to 333, AA 334 to 339, AA 349, AA 352 to 354, AA 368 to 403, AA 441, AA 451 to 471, AA 472, AA474 to 483, AA 487, AA 490, AA 493, AA 529, AA 532 or AA 543. UspA2 may consist of or comprise an amino acid sequence that differs from SEQ ID NO: 10 in that it contains an amino acid insertion in comparison to SEQ ID NO. 10. UspA2 may consists of or comprise an amino acid sequence that differs from SEQ ID NO. 10 at any one of the amino acid differences in SEQ ID NO: 22 through SEQ ID NO: 58. For example, SEQ ID NO. 10 may contain K instead of Q at amino acid 70, Q instead of G at amino acid 135 and/or D instead of N at amino acid 216. Table 1: UspA2 amino acid sequences from 38 strains of Moraxalla catarrhalis (SEQ ID NO: 10 and SEQ ID NO: 22 - SEQ ID NO: 58).

Figure imgf000016_0001
FDGRVTALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVA IGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (613 aa)

American MKTMKLLPLKIAV SALI IGLGAASTANAQQQLQTETFLPNFLSNDNYDLTDPFYHNMILGDTA 2912 LLDKQDGSQPQLKFYSNDKDSVPDSLLFSKLLHEQQLNGFKKGD I IPLDKDGKPVYQVDYKLD

GKGKKQKRRQVYSVTTKTATDDDVNSAYSRGILGKVDDLDDEMNFLNHDITSLYDVTANQQDAI

(SEQ ID KDLKKGVKGLNKELKELDKEVGVLSRDIGSLNDDVAQNNESIEDLYDFSQEVADSIGEIHAHNK NO: 23) AQNETLQDLITNSVENTNNITKNKADIQALENNWEELFNLSGRLIDQKADLTKDIKTLESNVE

EGLLELSGHLIDQKADIAKNQADIAQNQANIQDLAAYNELQDAYAKQQTEAIDALNKASSENTQ NIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSD IKTLAKASAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAIDENKASADTK FAATADAI KNGNAI KNAKSI DLGTKVDGFDSRVTALDTKVNAFDGRI ALDSKVENGMAAQ AALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGV NYEF (644 aa)

American MKTMKLLPLKIAVTSALIVGLGAASTANAQLVERFFPNIFLDKPLAKQHYHNVWGDTSIVSDL 2908 QSNSDQLKFYSDDEGLVPDSLLFNKMLHEQLLNGFKEGD I IPLDENGKPVYKVDYKLDGKEPR

KVYSVTTKIATAEDVATSSYANGIQKDIDDLYDFDHQVTERLTQHGKTIYRNGERILANEESVQ

(SEQ ID YLNKEVQNNIEHIYELAQQQDQHSSDIKTLESNVEKGLLELSGHLIDQKADLTKDIKTLESNVE NO : 24) EGLLDLSGRLIDQKADLTKDIKTLESNVEEGLLDLSGRLIDQKADIAQNQANIQDLAAYNELQD

QYAQKQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIAKNQA DIANNINNIYELAQQQDQHSSDIKTLAKASAANTNRIATAELGIAENKKDAQIAKAQANANKTA IDENKASADTKFAATADAI KNGNAI KNAKSITDLGTKVDGFDSRVTALDTKVNAFDGRITAL DSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTS GNKKGSYNIGVNYEF (591 aa)

Finnish MKTMKLLPLKIAVTSAMI IGLGAASTANAQQQQQQQQQQQSRTEIFFPNIFFNENHDELDDAYH 307 NI ILGDTALLDKQDGSQPQLKFYSNDKDSVPDSLLFSKLLHEQQLNGFKKGDTI IPLDKDGKPV

YQVDYKLDGKGKKQKRRQVYSVTTKTATDDDVNSAYSRGILGKVDDLDDEMNFLNHDITSLYDV

(SEQ ID TANQQDAIKGLKKGVKGLNKELKELDKEVGVLSRDIGSLNDDVAQNNESIEDLYDFSQEVADSI NO: 25) GEIHAHNKAQNETLQDLITNSVENTNNITKNKADIQALENNWEELFNLSGRLIDQKADLTKDI

KTLESNVEEGLLELSGHLIDQKADIAKNQADIAQNQANIQDLAAYNELQDAYAKQQTEAIDALN KASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTE AIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAKNKAD ADASFETLTKNQNTLIEKDKEHDKLITANKTAIDENKASADTKFAATADAITKNGNAITKNAKS ITDLGTKVDAFDGRVTALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAAL GGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (687 aa) Finnish MKTMKLLPLKIAVTSAMIVGLGMASTANAQQQKSPKTETFLPNIFFNEYADDLDTLYHNMILGD 353 TAI HDDQYKFYADDATEVPDSLFFNKILHDQLLYGFKEGDKI IPLDENGKPVYKLDKRLENGV

QKTVYSVTTKTATADDVNSAYSRGIQGDIDDLYEANKENVNRLIEHGDKIFANEESVQYLNREV

(SEQ ID QNNIENIHELAQQQDQHSSDIKTLKKNVEKDLLDLSGRLIAQKEDIAQNQTDIQDLATYNELQD NO : 26) QYAQKQTEAIDALNKASSENTQNIAKNSNHIKTLENNIEEGLLELSGHLIDQKADLTKDIKALE

SNVEEGLLDLSGRLIDQKADIAQNQANIQDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIE DLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSE NTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTKN QNTLIEKDKEHDKLI ANKTAIDANKASADTKFAATADAITKNGNAITKNAKSITDLGTKVDGF DGRVTALDTKVNALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYG SKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (683 amino acids)

Finnish MKTMKLLPLKIAVTSAMMVGLGMASTANAQQQKSPKTEIFLPNLFDNDNTELTDPLYHNMILGN 358 TALLTQENQYKFYADDGNGVPDSLLFNKILHDQLLHGFKEGGTI IPLDENGKPVYKLDSIVEQG

KTKTVYSVTTKTATADDVNSAYSRGIQGDIDDLYEANKENVNRLIEHGDKIFANEESVQYLNRE

(SEQ ID VQNNIENIHELAQQQDQHSSDIKTLKKNVEKDLLDLSGRLIAQKEDIAQNQTDIQDLATYNELQ NO : 27) DQYAQKQTEAIDALNKASSENTQNIAKNSNHIKTLENNIEEGLLELSGHLIDQKADLTKDIKAL

ESNVEEGLLDLSGRLIDQKADIAQNQANIQDLAAYNELQDAYAKQQTEAIDALNKASSENTQNI EDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASS ENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTK NQNTLIEKDKEHDKLITANKTAIDANKASADTKFAATADAITKNGNAITKNAKSITDLGTKVDG FDGRVTALDTKVNALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGY GSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (684 amino acids)

Finnish MKTMKLLPLKIAVTSAMI IGLGAASTANAQQQQKTKTEVFLPNLFDNDYYDLTDPLYHSMILGD 216 TATLFDQQDNSKSQLKFYSNDKDSVPDSLLFSKLLHEQQLNGFKAGDTI IPLDKDGKPVYTQDT

RTKDGKVETVYSVTTKIATQDDVEQSAYSRGIQGDIDDLYDINREVNEYLKATHDYNERQTEAI

(SEQ ID DALNKASSANTDRIDTAEERIDKNEYDIKALESNVGKDLLDLSGRLIAQKEDIDNNINHIYELA NO : 28) QQQDQHSSDIKTLKNNVEEGLLELSGHLIDQKADLTKDIKTLENNIEEGLLELSGHLIDQKADL

TKDIKTLENNIEEGLLELSGHLIDQKADIAQNQANIQDLAAYNELQDQYAQKQTEAIDALNKAS SENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAID ALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKVSAANTDRIAKNKADADA SFETLTKNQNTLIEKDKEHDKLITANKTAIDANKASADTKFAATADAITKNGNAITKNAKSITD LGTKVDGFDGRVTALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGY GSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (684 amino acids) Dutch H2 MKTMKLLPLKIAVTSAMMVGLGMASTANAQQQKSPKTEIFLPNLFDNDNTELTDPLYHNMILGN TALLTQENQYKFYADDGNGVPDSLLFNKILHDQLLHGFKKGD I IPLDENGKPVYKLDSIVEQG

(SEQ ID KTKTVYSVTTKTATADDVNSAYSRGIQGDIDDLYEANKENVNRLIEHGDKIFANEESVQYLNRE NO : 29) VQNNIENIYELVQQQDQHSSDIKTLKKNVEKDLLDLSGRLIAQKEDIAQNQTDIQDLATYNELQ

DQYAQKQTEAIDALNKASSENTQNIAKNSNHIKTLENNIEEGLLELSGHLIDQKADLTKDIKAL ESNVEEGLLDLSGRLIDQKADIAQNQANIQDLAAYNELQDAYAKQQTEAIDALNKASSENTQNI EDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASS ENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTK NQNTLIEKDKEHDKLI ANKTAIDANKASADTKFAATADAI KNGNAI KNAKSI DLGTKVDG FDGRVTALDTKVNALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGY GSKSAVAIGAGYRVNPNLAFKAGAAIN SGNKKGSYNIGVNYEF (684 amino acids)

Dutch F10 MKTMKLLPLKIAV SAMI IGLGAASTANAQLAEQFFPNIFSNHAPVKQHYHNVWGD SIVENL

QDSDDTQLKFYSNDEYSVPDSLLFNKMLHEQQLNGFKKGD I IPLDENGKPVYKVDYKLDGQEP

(SEQ ID RRVYSVTTKIATQDDVDNSPYSRGIQGDIDDLYEANKENVNRLIEHGDKIFANEESVQYLNKEV NO: 30) QNNIENIYELAQQQDQHSSDIKTLKKNVEEGLLELSGHLIDQKADLTKDIKTLESNVEEGLLEL

SGHLIDQKADIAKNQADIAQNQANIQDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLA AYNELQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAK ASAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLI ANKTAIDANKASADTKFAATAD AITKNGNAITKNAKSITDLGTKVDAFDGRVTALDTKVNAFDGRITALDSKVENGMAAQAALSGL FQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF

(574 amino acids)

Norwegian MKTMKLLPLKIAVTSALIVGLGAASTANAQQQPQTETFFPNIFFNENHDALDDVYHNMILGDTA 1 ITQDNQYKFYADAISEVPDSLLFNKILHDQQLNGFKEGDTI IPLDENGKPVYKLDEKVENGVKK

SVYSVTTKTATRADVEQSAYSRGIQGDIDDLYEANKENVNRLIEHGDKIFANEESVQYLNKEVQ

(SEQ ID NNIENIHELAQQQDQHSSDIKTLKKNVEEGLLELSGHLIDQKADLTKDIKTLESNVEEGLLDLS NO: 31) GRLLDQKADIAQNQANIQDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDA

YAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAY NELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNI AKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTKNQNTLI EKDKEHDKLITANKTAIDANKASADTKFAATADAITKNGNAITKNAKSITDLGTKVDAFDGRVT ALDTKVNALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAV AIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (678 amino acids)

Norwegian MKTMKLLPLKIAVTSAMIVGLGAASTANAQQQQQPRTETFFPNIFFNENHDALDDVYHNMILGD 13 TAITQDNQYKFYADAISEVPDSLLFNKILHDQQLNGFKEGDTI IPLDENGKPVYKLDEKVENGV KKSVYSVTTKTATRADVEQSAYSRGIQGDIDDLYEANKENVNRLIEHGDKIFANEESVQYLNRE

(SEQ ID

VQNNIENIHELAQQQDQHSSDIKTLKKNVEKDLLDLSGRLIAQKEDIAQNQTDIQDLATYNELQ NO: 32)

DQYAQKQTEAIDALNKASSENTQNIAKNSNHIKTLENNIEEGLLELSGHLIDQKADLTKDIKTL ENNIEEGLLELSGHLIDQKADLTKDIKALESNVEEGLLDLSGRLLDQKADIAQNQANIQDLAAY NELQDQYAQKQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNI AKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTKNQNTLI EKDKEHDKLI ANKTAIDTNKASADTKFAATADAI KNGNAI KNAKSI DLGTKVDGFDGRVT ALDTKVNALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAV AIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (678 amino acids)

Norwegian MKTMKLLPLKIAVTSALIVGLGAASTANAQLVERFFPNIFLDKPLAKQHYHNVWGDTSIVSDL 33 QSNSDQLKFYSDDEGLVPDSLLFNKMLHEQLLNGFKEGD I IPLDENGKPVYKVDYKLDGKEPR

KVYSVTTKIATAEDVATSSYANGIQKDIDDLYDFDHQVTERLTQHGKTIYRNGERILANEESVQ

(SEQ ID YLNKEVQNNIEHIYELAQQQDQHSSDIKTLESNVEKGLLELSGHLIDQKADLTKDIKTLENNVE NO: 33) EGLLDLSGRLIDQKADIAQNQANIQDLAAYNELQDQYAQKQTEAIDALNKASSENTQNIEDLAA

YNELQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKA SAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLI ANKTAIDTNKASADTKFAATADA ITKNGNAITKNAKSITDLGTKVDGFDSRVTALDTKVNALDTKVNALDTKVNAFDGRITALDSKV ENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKK GSYNIGVNYEF (587 amino acids)

Norwegian MKTMKLLPLKIAVTSAMIVGLGAASTANAQQQQQPRTETFFPNIFFNENHDALDDVYHNMILGD 25 TAITQDNQYKFYADAISEVPDSLLFNKILHDQQLNGFKEGDTI IPLDENGKPVYKLDEKVENGV

KKSVYSVTTKTATRADVEQSAYSRGIQGDIDDLYEANKENVNRLIEHGDKIFANEESVQYLNRE

(SEQ ID VQNNIENIHELAQQQDQHSSDIKTLKKNVEKDLLDLSGRLIAQKEDIAQNQTDIQDLATYNELQ NO: 34) DQYAQKQTEAIDALNKASSENTQNIAKNSNHIKTLENNIEEGLLELSGHLIDQKADLTKDIKTL

ENNIEEGLLELSGHLIDQKADLTKDIKALESNVEEGLLDLSGRLLDQKADIAQNQANIQDLAAY NELQDQYAQKQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNI AKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTKNQNTLI EKDKEHDKLITANKTAIDTNKASADTKFAATADAITKNGNAITKNAKSITDLGTKVDGFDGRVT ALDTKVNALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAV AIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (678 amino acids)

Norwegian MKTMKLLPLKIAVTSALIVGLGAASTANAQVRDKSLEDIEALLGKIDISKLEKEKKQQTELQKY 27 LLLSQYANVLTMEELNKNVEKNTNSIEALGYEIGWLENDIADLEEGVEELTKNQNTLIEKDEEH

DRLIAQNQADIKTLENNWEELFNLSDRLIDQEADIAKNNASIEELYDFDNEVAERIGEIHAYT

(SEQ ID EEVNKTLEKLITNSVKNTDNIDKNKADIQALENNVEEGLLELSGHLIDQKADLTKDIKALESNV NO: 35) EEGLLDLSGRLLDQKADIAKNQADIAQNQTDIQDLAAYNELQDQYAQKQTEAIDALNKASSENT QNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNK ASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKVSAANTDRIAKNKADADASFET LTKNQNTLIEKDKEHDKLI ANKTAIDANKASADTKFAATADAI KNGNAI KNAKSI DLGTK VDGFDSRVTALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKS AVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (616 amino acids)

Norwegian MKTMKLLPLKIAVTSALIVGLGAASTANAQATETFLPNLFDNDYTETTDPLYHGMILGNTAITQ 36 DTQYKFYAENGNEVPDSLFFNKILHDQQLNGFKEGD I IPLDENGKPVYKLDEI ENGVKRKVY

SVTTKTATREDVEQSAYSRGIQGDIDDLYEANKENVNRLIEHGDKIFANEESVQYLNKEVQNNI

(SEQ ID ENIHELAQQQDQHSSDIKTLKKNVEEGLLELSGHLIDQKADLTKDIKALESNVEEGLLDLSGHL NO: 36) IDQKADLTKDIKALESNVEEGLLDLSGRLLDQKADIAKNQADIAQNQTDIQDLAAYNELQDQYA

QKQTEAIDALNKASSENTQNIEDLAAYNELQDQYAQKQTEAIDALNKASSENTQNIEDLAAYNE LQDQYAQKQTEAIDALNKASSENTQNIEDLAAYNELQDQYAQKQTEAIDALNKASSENTQNIAK NQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTKNQNTLIEK DKEHDKLI ANKTAIDANKASADTKFAATADAITKNGNAITKNAKSITDLGTKVDGFDGRVTAL DTKVNALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVAI GAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (676 amino acids)

BC5SV MKTMKLLPLKIAVTSALIVGLGAASTANAQNGTSTKLKNLKEYAQYLDNYAQYLDDDIDDL

DKEVGELSQNIAKNQANIKDLNKKLSRDIDSLREDVYDNQYEIVNNQADIEKNQDDIKELE

(SEQ ID

NNVGKELLNLSGRLLDQKADIDNNINNIYELAQQQDQHSSDIKTLKKNVEEGLLELSGHLI NO: 37)

DQKSDIAQNQTDIQDLATYNELQDQYAQKQTEAIDALNKASSENTQNIEDLAAYNELQDAY AKQQTEAIDALNKASSENTQNIQDLAAYNELQDAYAKQQTEAI DALNKASSENTQNIEDLA AYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSE NTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQ DQHSSDIKTLAKASAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAID ANKASADTKFAATADAITKNGNAITKNAKSITDLGTKVDAFDGRVTALDTKVNAFDGRITA LDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAA INTSGNKKGSYNIGVNYEF (629 amino acids)

Norwegian MKTMKLLPLKIAVTSAMIVGLGMASTANAQQQRSPKTETFLPNIFFNEYADDLDTLYHNMI 14 LGDTAITHDDQYKFYADDATEVPDSLFFNKILHDQLLYGFKEGDKI I PLDENGKPVYKLDK

RLDNGVQKTVYSVTTKTATADDVNSAYSRGIQGDI DDLYEANKENVNRLIEHGDKIFANEE

(SEQ ID

SVQYLNKEVQNNIENIHELAQQQDQHSSDIKTLKKNVEEGLLELSGHLIDQKTDIAQNQTD NO: 38)

IQDLATYNELQDQYAQKQTEAIDALNKASSENTQNIAKNSNRIKALENNIEEGLLELSGHL IDQKADLTKDIKALESNVEEGLLDLSGRLIDQKADIAQNQANIQDLAAYNELQDAYAKQQT EAI DALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNEL QDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKAS AANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAIDANKASADTKFAATA DAITKNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNALDTKVNAFDGRITALDSKVEN GMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNK KGSYNIGVNYEF (683 amino acids)

Norwegian MKTMKLLPLKIAVTSAMIVGLGAASTANAQAQSNRSLDQVQALLRGI DETKIKKEIQQSQQ

PELNKYLTFNQLANALNIEELNNNVQKNTQRLDSAATLYGDLSKTVPKSIKENKESIKENK

3

ESIKENKESIKENKESIKENKESIKENKESITTLTRKSFQNQVDIVRNNASIEDLYAYGQE

(SEQ ID VAKSIGEIHAYTEEVNKTLENLITNSVENTNNITKNKADIQALENNVVEELFNLSGRLIDQ NO: 39) KADIDNNINNIYELAQQQDQHSSDIKTLKKNVEEGLLELSGHLI DQKADLTKDIKTLESNV

EEGLLDLSGRLLDQKADIAQNQANIQDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIE DLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAI DALNKA SSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELA QQQDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKT VIDANKASADTKFAATADAITKNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNALDTK VNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVN PNLAFKAGAAINTSGNKKGSYNIGVNYEF (700 amino acids)

Finnish MKTMKLLPLKIAVTSALIVGLGAASTANAQATETFLPNLFDNDYIETTDPLYHGMILGNTA

ITQDTQYKFYAENGNEVPDSLFFNKILHDQQLNGFKEGDTI IPLDENGKPVYKLDEITENG

414

VKRKVYSVTTKTATREDVEQSAYSRGIQGDI DDLYEANKENVNRLIEHGDKIFANEESVQY

(SEQ ID LNKEVQNNIENIHELAQQQDQHSSDIKTLKKNVEEGLLELSGHLIDQKADLTKDIKTLENN NO : 40) VEEGLLELSGHLIDQKADLTKDIKALESNVEEGLLDLSGRLLDQKADIAKNQADIAQNQTD

IQDLAAYNELQDQYAQKQTEAIDALNKASSENTQNIEDLAAYNELQDQYAQKQTEAIDALN KASSENTQNIEDLAAYNELQDQYAQKQTEAI DALNKASSENTQNIEDLAAYNELQDQYAQK QTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRI AKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAIDANKASADTKFAATADAITKNG NAITKNAKSITDLGTKVDGFDGRVTALDTKVNALDTKVNAFDGRITALDSKVENGMAAQAA LSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIG VNYEF (676 amino acids)

Japanese MKTMKLLPLKIAVTSAMI IGLGAASTANAQLAEQFFPNI FSNHAPVKQHYHNVWGDTSIV

ENLQDSDDTQLKFYSNDEYSVPDSLLFNKMLHEQQLNGFKKGDTI IPLDENGKPVYKVDYK

Z7476

LDGQEPRRVYSVTTKIATQDDVDNSPYSRGIQGDI DDLYEANKENVNRLIEHGDKIFANEE SVQYLNKEVQNNIENIYELAQQQDQHSSDIKTLKKNVEEGLLELSGRLIDQKADIAQNQAN IQDLAAYNELQDQYAQKQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALN

(SEQ ID

KASSENTQNIEDLAAYNELQDAYAKQQTEAI DALNKASSENTQNIEDLAAYNELQDAYAKQ NO : 41)

QTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYN ELQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAK VSAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAIDANKASADTKFAA TADAITKNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNAFDGRITALDSKVENGMAAQ AALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYN IGVNYEF (678 amino acids)

Belgian MKTMKLLPLKIAVTSAMI IGLGAASTANAQSRDRSLEDIQDSI SKLVQDDINTLKQDQQKM

NKYLLLNQLANTLITDELNNNVIKNTNSIEALGDEIGWLENDIADLEEGVEELTKNQNTLI

Z7530

EKDEEHDRLIAQNQADIQTLENNWEELFNLSGRLIDQEADIAKNNASIEELYDFDNEVAE

(SEQ ID RIGEIHAYTEEVNKTLENLITNSVKNTDNIDKNKADIDNNINHIYELAQQQDQHSSDIKTL NO: 42) KNNVEEGLLELSGHLIDQKADLTKDIKALESNVEEGLLDLSGRLLDQKADLTKDIKALESN

VEEGLLDLSGRLLDQKADIAQNQTDIQDLAAYNELQDQYAQKQTEAI DALNKASSENTQNI EDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSS DIKTLAKASAANTNRIATAELGIAENKKDAQIAKAQANANKTAIDENKASADTKFAATADA ITKNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNAFDGRITALDSKVENGMAAQAALS GLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVN YEF (613 amino acids)

German MKTMKLLPLKIAVTSALIVGLGAASTANAQATNKDITLEDVLKSIEEIDPYELRDYIEYPT

AIERFLLLSQYGNTLTLEEFDNDIELLDQDVEDLEESVTELAKNQNSLIEQGEAIKEDLQG

Z8063

LADFVERQEDKILQNETSIKKNTQRNLVNGFEIEKNKDAIAKNNESIEDLYDFGHEVAKSI

(SEQ ID GEIHAHNEAQNETLKDLITNSVKNTDNITKNKADIQALESNVEKGLLELSGHLIDQKADID NO: 43) NNINNIHELAQQQDQHSSDIKTLKKNVEEGLLELSGHLIDQKSDIAQNQANIQDLATYNEL

QDQYAQKQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAI DALNKASSENTQNI AKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTKNQN TLIEKDKEHDKLITANKTAIDANKASADTKFAATADAITKNGNAITKNAKSITDLGTKVDG FDSRVTALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKS AVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (589 amino acids)

American MKTMKLLPLKIAVTSAMMVGLGMASTANAQQQKSPKTEI FLPNLFDNDNTELTDPLYHNMI

LGNTALLTQENQYKFYADDGNGVPDSLLFNKILHDQLLHGFKEGDTI IPLDENGKPVYKLD

012E

SIVEQGKTKTVYSVTTKTATADDVNSAYSRGIQGDIDDLYEANKENVNRLIEHGDKIFANE ESVQYLNREVQNNIENIHELAQQQDQHSSDIKTLKKNVEKDLLDLSGRLIAQKEDIAQNQT DIQDLATYNELQDQYAQKQTEAI DALNKASSENTQNIAKNSNHIKTLENNIEEGLLELSGH

(SEQ ID

LIDQKADLTKDIKALESNVEEGLLDLSGRLI DQKADIAQNQANIQDLAAYNELQDAYAKQQ NO : 44)

TEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNE LQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKA SAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAI DANKASADTKFAAT ADAITKNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNALDTKVNAFDGRITALDSKVE NGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGN KKGSYNIGVNYEF (684 amino acids)

Greek MKTMKLLPLKIAVTSALIVGLGAASTANAQQQQKTKTEVFLPNLFYNDYIEETDLLYHNMI

LGDTAALVDRQNYSNSQLKFYSNDEESVPDSLLFSKMLNNQQLNGFKAGDI I IPVDANGQV

MC317

IYQKDTRVEGGKTRTVLSVTTKIATQQDVDSAYSRGIQGKVNDLDDEMNFLNHDITSLYDV

(SEQ ID TANQQDDIKGLKKGVKDLKKGVKGLNKELKELDKEVGVLSRDIGSLNDDVAQNNESIEDLY NO : 45) DFSQEVADSIGEIHAHNKAQNETLQDLITNSVENTNNITKNKADIQALENNVVEELFNLSG

RLI DQKADLTKDIKTLESNVEEGLLELSGHLIDQKADIAKNQADIAQNQANIQDLAAYNEL QDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAI DALNKASSENTQNI AKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTKNQN TLIEKDKEHDKLITANKTAIDENKASADTKFAATADAITKNGNAITKNAKSITDLGTKVDG FDGRVTALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKS AVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (650 amino acids)

American MKTMKLLPLKIAVTSALIVGLGAVSTTNAQAQSRSLDQIQTKLADLAGKIAAGKNGGGQNN

QNNQNDINKYLFLSQYANILTMEELNNNWKNSSSIETLETDFGWLENDVADLEDGVEELT

V1122

KNQNTLIEKDEEHDRLIAQNQADIQTLENNVVEELFNLSDRLI DQKADIAKNQADIAQNNE

(SEQ ID SIEELYDFDNEVAEKIGEIHAYTEEVNKTLQDLITNSVKNTDNIDKNKADI DNNINHIYEL NO : 46) AQQQDQHSSDIKTLKNNVEEGLLELSGHLIDQKADLTKDIKTLENNVEEGLLDLSGRLIDQ

KADIAKNQADIAQNQTDIQDLAAYNELQDQYAQKQTEAI DALNKASSENTQNIEDLAAYNE LQDAYAKQQTEAI DALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKA SAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAI DENKASADTKFAAT ADAITKNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNAFDGRITALDSKVENGMAAQA ALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNI GVNYEF (616 amino acids)

American MKTMKLLPLKIAVTSALIVGLGTASTANAQVASPANQKIQQKIKKVRKELRQDIKSLRNDI

DSNTADIGSLNDDVADNQDDILDNQADIAKNQDDIEKNQADIKELDKEVGVLSREIGSLND

P44

DIADNYTDI IDNYTDI IDNQANIAKNQDDIEKNQADIKELDKEVGVLSREIGSLNDDVADN QDDIAKNQADIQTLENNVEEGLLELSGHLLDQKADIDNNINNIYELAQQQDQHSSDIKTLK

(SEQ ID

KNVEEGLLELSGHLI DQKTDIAQNQANIQDLATYNELQDQYAQEQTEAIDALNKASSENTQ NO : 47)

NIAKNSNRIKALESNVEEGLLELSGHLIDQKADLTKDIKALESNVEEGLLELSGHLIDQKA DIAQNQANIQDLAAYNELQDQYAQKQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQ TEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIA KNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAIDANKVSADTKFAATADAITKNGN AITKNAKSITDLGTKVDAFDSRVTALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPY SVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF

(668 amino acids)

American MKTMKLLPLKIAVTSAMIVGLGATSTVNAQVVEQFFPNI FFNENHDELDDAYHNMILGDTA

IVSNSQDNSTQLKFYSNDEDSVPDSLLFSKLLHEQQLNGFKAGDTI I PLDKDGKPVYTKDT

V1171

RTKDGKVETVYSVTTKIATQDDVEQSAYSRGIQGDIDDLYDINREVNEYLKATHDYNERQT

(SEQ ID EAI DALNKASSANTDRIDTAEERIDKNEYDIKALESNVEEGLLELSGHLIDQKADLTKDIK NO : 48) ALESNVEEGLLELSGHLI DQKADLTKDIKALESNVEEGLLDLSGRLIDQKADIAQNQANIQ

DLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAI DALNKA SSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQT EAI DALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAK NKADADASFETLTKNQNTLIEKDKEHDKLITANKTAI DANKASADTKFAATADAITKNGNA ITKNAKSITDLGTKVDGFDGRVTALDTKVNALDTKVNAFDGRITALDSKVENGMAAQAALS GLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVN YEF (674 amino acids)

American MKTMKLLPLKIAVTSAMI IGLGAASTANAQSRDRSLEDIQDSI SKLVQDDI DTLKQDQQKM TTA24 NKYLLLNQLANTLITDELNNNVIKNTNSIEALGDEIGWLENDIADLEEGVEELTKNQNTLI

EKDEEHDRLIAQNQADIQTLENNWEELFNLSGRLIDQEADIAKNNASIEELYDFDNEVAE

(SEQ ID

RIGEIHAYTEEVNKTLENLITNSVKNTDNIDKNKADIDNNINHIYELAQQQDQHSSDIKTL NO : 49)

KNNVEEGLLELSGHLIDQKADLTKDIKALESNVEEGLLDLSGRLLDQKADLTKDIKALESN VEEGLLDLSGRLLDQKADIAQNQTDIQDLAAYNELQDQYAQKQTEAI DALNKASSENTQNI EDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSS DIKTLAKASAANTNRIATAELGIAENKKDAQIAKAQANANKTAIDENKASADTKFAATADA ITKNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNAFDGRITALDSKVENGMAAQAALS GLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVN YEF (613 amino acids) American MKTMKLLPLKIAVTSAMIVGLGATSTVNAQVVEQFFPNI FFNENHDELDDAYHNMILGDTA IVSNSQDNSTQLKFYSNDEDSVPDSLLFSKLLHEQQLNGFKAGDTI I PLDKDGKPVYTKDT

035E

RTKDGKVETVYSVTTKIATQDDVEQSAYSRGIQGDIDDLYDINREVNEYLKATHDYNERQT

(SEQ ID EAI DALNKASSANTDRIDTAEERIDKNEYDIKALESNVEEGLLELSGHLIDQKADLTKDIK NO: 50) ALESNVEEGLLELSGHLIDQKADLTKDIKALESNVEEGLLDLSGRLLDQKADIAKNQADIA

QNQTDIQDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQ QDQHSSDIKTLAKASAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAI DANKASADTKFAATADAITKNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNALDTKVN AFDGRITALDSKVENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPN LAFKAGAAINTSGNKKGSYNIGVNYEF (576 amino acids)

American MKTMKLLPLKIAVTSAMMVGLGMASTANAQQQKSPKTEI FLPNLFDNDNTELTDPLYHNMI

LGNTALLTQENQYKFYADDGNGVPDSLLFNKILHDQLLHGFKEGDTI I PLDENGKPVYKLD

SP12-6

SIVEQGKTKTVYSVTTKTATADDVNSAYSRGIQGDIDDLYEANKENVNRLIEHGDKIFANE

(SEQ ID ESVQYLNREVQNNIENIHELAQQQDQHSSDIKTLKKNVEKDLLDLSGRLIAQKEDIAQNQT NO: 51) DIQDLATYNELQDQYAQKQTEAI DALNKASSENTQNIAKNSNHIKTLENNIEEGLLELSGH

LIDQKADLTKDIKALESNVEEGLLDLSGRLI DQKADIAQNQANIQDLAAYNELQDAYAKQQ TEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAI DALNKASSENTQNIEDLAAYNE LQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKA SAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAIDANKASADTKFAAT ADAITKNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNALDTKVNAFDGRITALDSKVE NGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGN KKGSYNIGVNYEF (684 amino acids)

American MKTMKLLPLKIAVTSAMI IGLGAASTANAQATETFLPNLFDNDYTETTDPLYHGMILGNTA

ITQDTQYKFYAENGNEVPDSLFFNKILHDQQLNGFKEGDTI IPLDENGKPVYKLDEITENG

SP12-5

VKRKVYSVTTKTATREDVEQSAYSRGIQGDI DDLYEANKENVNRLIEHGDKIFANEESVQY

(SEQ ID LNKEVQNNIENIHELAQQQDQHSSDIKTLKKNVEEGLLELSGRLIAQKEDIAQNQTDIQDL NO: 52) ATYNELQDQYAQKQTEAIDALNKASSENTQNIAKNSNHIKTLENNIEEGLLELSGHLIDQK

ADLTKDIKALESNVEEGLLDLSGRLLDQKADIAKNQADIAQNQTDIQDLAAYNELQDQYAQ KQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAY NELQDAYAKQQTEAI DALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLA KASAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAIDANKASADTKFA ATADAITKNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNALDTKVNAFDGRITALDSK VENGMAAQAALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTS GNKKGSYNIGVNYEF (686 amino acids)

Swedish MKTMKLLPLKIAV SAMI IGLGAASTANAQAKNDI LEDLPYLIKKIDQNELEADIGDI ALEK

YLALSQYGNILALEELNKALEELDEDVGWNQNDIANLEDDVETLTKNQNALAEQGEAIKEDLQG

BC5 LADFVEGQEGKILQNETSIKKNTQRNLVNGFEIEKNKDAIAKNNESIEDLYDFGHEVAESIGEI

HAHNEAQNETLKGLITNSIENTNNITKNKADIQALENNWEELFNLSGRLIDQKADIDNNINNI

(SEQ ID

YELAQQQDQHSSDIKTLKKNVEEGLLELSGHLIDQKTDIAQNQANIQDLATYNELQDQYAQKQT NO: 53)

EAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDA YAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDR IAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAIDANKASADTKFAATADAITKNGNA I KNAKSI DLGTKVDGFDSRVTALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGK FNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (630 amino acids)

American MKTMKLLPLKIAVTSALIVGLGAASTANAQAQDRSLEQIQDKLANLVEKIEQAKSQNGQSQ

KDINQYLLLSQYANVLTMEELNNNVVKNSSSIETLDNDIAWLNDDLIDLDKEVGVLSRDIG

7169

SLHDDVAQNQADIKTLKNNWEELFNLSDRLIDQEADIAQNNESIEDLYDFGREVAESIGE

(SEQ ID IHAHNEAQNETLKDLITNSVKNTDNITKNKADIQALENDVGKELLNLSGRLIDQKADIDNN NO: 54) INHIYELAQQQDQHSSDIKTLKNNVEEGLLELSGHLIDQKADLTKDIKALESNVEEGLLDL

SGRLLDQKADIAQNQANIQDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNE LQDAYAKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKA SAANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAI DANKASADTKFAAT ADAITKNGNAITKNAKSITDLGTKVDGFDSRVTALDTKVNAFDGRITALDSKVENGMAAQA ALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNI GVNYEF (616 amino acids)

Finnish MKTMKLLPLKIAVTSAMI IGLGATSTVNAQVVEQFFPNI FFNENHDELDDAYHNMILGDTA

IVSNSQDNSTQLKFYSNDEDSVPDSLLFSKLLHEQQLNGFKAGDTI I PLDKDGKPVYTKDT

FIN2344

RTKDGKVETVYSVTTKIATQDDVEQSAYSRGIQGDIDDLYDINREVNEYLKATHDYNERQT

(SEQ ID EAI DALNKASSANTDRIDTAEERIDKNEYDIKALESNVGKDLLDLSGRLIAQKEDIDNNIN NO: 55) HIYELAQQQDQHSSDIKTLKNNVEEGLLELSGHLIDQKADLTKDIKTLESNVEEGLLDLSG

RLI DQKADIAQNQANIQDLAAYNELQDQYAQKQTEAIDALNKASSENTQNIEDLAAYNELQ DAYAKQQTEAI DALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKVSA ANTDRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAIDANKASADTKFAATAD AITKNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNAFDGRITALDSKVENGMAAQAAL SGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGV NYEF (614 amino acids)

American MKTMKLPPLKIAVTSAMI IGLGAASTANAQTTETFLPNLFDNDYTETTDPLYHGMILGDTA

ITQDTQYKFYAENGNEVPDSLFFNKILHDQLLNGFKAGDTI IPLDENGKPVYKLDERTENG

V1118

VKRKVYSVTTKTATQADVEQSAYSRGIQGDI DDLYEANKENVNRLIEHGDKIFANEESVQY

(SEQ ID LNREVQNNIENIHELAQQQDQHSSDIKTLKKNVEKDLLDLSGRLIAQKEDIAQNQTDIQDL NO: 56) ATYNELQDQYAQKQTEAI DALNKASSENTQNIAKNSNHIKTLENNIEECLLELSGHLI DQK

ADLTKDIKALESNVEEGLLDLSGRLIDQKADIAQNQANIQDLAAYNELQDAYAKQQTEAID ALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAY AKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANT DRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAIDANKASADTKFAATADAIT KNGNAITKNAKSITDLGTKVDGFDGRVTALDTKVNALDTKVNAFDGRITALDSKVENGMAA QAALSGLFQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSY NIGVNYEF (679 amino acids)

American MKTMKLLPLKIAVTSALIVGLGAASTANAQETLEEVLESIKQINEQDLQDDIGYNSALDRY

LVLSQYGNLLIAKELNENVEKNSNSIAKNSNSIADLEADVGYLAENQNTLIEQNETINQEL

V1145

EGITHELESFIAYAHAQDQKNLVNEFEIEKNKDAIAKNNESIEDLYDFGHEVAESIGEIHA

(SEQ ID YTEEVNKTLENLITNSVKNTDNITKNKADIQALESNVEKELLNLSGRLIDQKADI DNNINH NO: 57) IYELAQQQDQHSSDIKTLKKNVEEGLLELSGHLIDQKSDIAQNQTDIQDLATYNELQDQYA

QKQTEAI DALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAA YNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAI DALNKASSEN TQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAYAKQQTEAID ALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKASAANTDRIAKNKAD ADASFETLTKNQNTLIEKDKEHDKLITANKTAIDANKASADTKFAATADAITKNGNAITKN AKSITDLGTKVDGFDSRVTALDTKVNAFDGRITALDSKVENGMAAQAALSGLFQPYSVGKF NATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYEF (724 amino acids)

American MKTMKLLPLKIAVTSALIVGLGAASTANAQAQARDRSLEDIQALIGNIDVDKIRSQKQKNP

EIFQYLLLNQLSNTLITDELNNNVIKNTNSIETLDNDIAWLNDDLIDLDKEVGVLSRDIGS

V1156

LHDDVAQNQADIKTLENNVVEELFNLSDRLI DQEAEIAQNNESIEDLYDFGREVAESIGEI

(SEQ ID HAHNEAQNETLKDLITNSVKNTDNIDKNKADIQALENNVEEGLLELSGHLI DQKADLTKDI NO: 58) KALESNVEEGLLDLSGRLLDQKADIAKNQADIAQNQTDIQDLAAYNELQDQYAQKQTEAID

ALNKASSENTQNIEDLAAYNELQDAYAKQQTEAIDALNKASSENTQNIEDLAAYNELQDAY AKQQTEAIDALNKASSENTQNIAKNQADIANNINNIYELAQQQDQHSSDIKTLAKVSAANT DRIAKNKADADASFETLTKNQNTLIEKDKEHDKLITANKTAIDANKASADTKFAATADAIT KNGNAITKNAKSITDLGTKVDGFDSRVTALDTKVNAFDGRITALDSKVENGMAAQAALSGL FQPYSVGKFNATAALGGYGSKSAVAIGAGYRVNPNLAFKAGAAINTSGNKKGSYNIGVNYE

F (611 amino acids)

UspA2 may be UspA2 from M. catarrhalis strain ATCC(a US registered trademark) 25238™, American 2933. American 2912, American 2908, Finnish 307, Finnish 353, Finnish 358, Finnish 216, Dutch H2, Dutch F10, Norwegian 1, Norwegian 13, Norwegian 20, Norwegian 25, Norwegian 27, Norwegian 36, BC5SV, Norwegian 14, Norwegian 3, Finish 414, Japanese Z7476, Belgium Z7530, German Z8063, American 012E, Greek MC317, American V1122, American P44, American VI 171, American TTA24, American 035E, American SP12-6, American SP12-5, Swedish BC5, American 7169, Finnish FIN2344, American V1118, American V1145 or American V1156. UspA2 may be UspA2 as set forth in any of SEQ ID NO: 10 or SEQ ID NO: 22 - SEQ ID NO: 38. UspA2 may be UspA2 from another source which corresponds to the sequence of UspA2 in any one of SEQ ID NO: 10 or SEQ ID NO: 22 - SEQ ID NO: 58. Corresponding UspA2 sequences may be determined by one skilled in the art using various algorithms. For example, the Gap program or the Needle program may be used to determine UspA2 sequences corresponding to any one of SEQ ID NO: 10 or SEQ ID NO: 22 - SEQ ID NO: 58.

UspA2 may be a sequence with at least 95% identity, over the entire length, to any of SEQ ID NO: 10 or SEQ ID NO: 22 - SEQ ID NO: 58. In one embodiment, UspA2 may be a sequence as set forth in an amino acid sequence selected from the group consisting of SEQ ID NO: 10, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57 and SEQ ID NO: 58 or any subset of SEQ ID NO: 1 or SEQ ID N0.22 through SEQ ID NO:58.

Immunogenic fragments of UspA2 comprise immunogenic fragments of at least 450 contiguous amino acids of SEQ ID NO: 1, 490 contiguous amino acids of SEQ ID NO: 10 (for example, the UspA2 fragment of MC-004 or MC-005), 511 contiguous amino acids of SEQ ID NO: 10 (for example, the UspA2 fragment of construct MC-001, MC-002, MC-003 or MC-004), 534 contiguous amino acids of SEQ ID NO: 10 (for example, the UspA2 fragment of MC-009 or MC- 011) or 535 contiguous amino acids of SEQ ID NO: 10 (for example, the UspA2 fragment of MC- 007, MC-008 or MC-010). The immunogenic fragments may elicit antibodies which can bind SEQ ID NO: 10. Immunogenic fragments of UspA2 may comprise immunogenic fragments of at least 450, 490, 511, 534 or 535 contiguous amino acids of SEQ ID NO: 10. Immunogenic fragments of UspA2 may comprise immunogenic fragments of UspA2, for example any of the UspA2 constructs MC-001 (SEQ ID NO. 11), MC-002 (SEQ ID NO. 12), MC-003 (SEQ ID NO. 13), MC-004 (SEQ ID NO. 14), MC-005 (SEQ ID NO. 15), MC-006 (SEQ ID NO. 16), MC-007 (SEQ ID NO. 17), MC-008 (SEQ ID NO.18), MC-009 (SEQ ID NO. 19), MC-010 (SEQ ID NO. 20) or MC-011 (SEQ ID NO. 21). The immunogenic fragments may elicit antibodies which can bind the full length sequence from which the fragment is derived. In another aspect of the invention, the immunogenic composition comprises an immunogenic fragment of UspA2, suitably an isolated immunogenic polypeptide with at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% to a polypeptide selected from the group consisting of MC-001 (SEQ ID NO. 11), MC-002 (SEQ ID NO. 12), MC-003 (SEQ ID NO. 13), MC-004 (SEQ ID NO. 14), MC-005 (SEQ ID NO. 15), MC-006 (SEQ ID NO. 16), MC-007 (SEQ ID NO. 17), MC-008 (SEQ ID NO.18), MC-009 (SEQ ID NO. 19), MC-010 (SEQ ID NO. 20) or MC-011 (SEQ ID NO. 21) e.g. MC009 SEQ ID NO. 19 (corresponding to Seq ID No. 69 of WO2015/125118A1).

Immunogenicity of UspA2 polypeptides may be measured as described in WO2015/125118A1; the contents of which are incorporated herein by reference.

The immunogenic compositions of the present invention may comprise protein D, PE-PilA and UspA2 for example:

- PD 10 μg/ PE-PilA (LVL735 construct, as described in WO2012/139225) 10 μς/ UspA2 (MC009 construct, as described in WO2015125118) 10 μς/ ASOIE

- PD 10 μg/ PE-PilA (LVL735 construct, as described in WO2012/139225) 10 μς/ UspA2 (MC009 construct, as described in WO2015125118) 3.3 μς/ ASOIE

The above two specific immunogenic compositions were evaluated in a mouse Moraxella catarrhalis lung inflammation model in WO2015125118 (Example 14).

Dosage

The amount of the immunogenic composition which is required to achieve the desired therapeutic or biological effect will depend on a number of factors such as means of administration, the recipient and the type and severity of the condition being treated, and will be ultimately at the discretion of the attendant physician or veterinarian. The present invention provides an immunogenic composition comprising an immunogenic polypeptide from Haemophilus influenzae or an immunogenic fragment thereof and/or an immunogenic polypeptide from Moraxella catarrhalis or an immunogenic fragment thereof for use in the treatment or prevention of a recurrence of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD) associated with a bacterial infection in a subject. In one embodiment, one or more previous exacerbations in the same subject were caused wholly or in part by M. catarrhalis. In a further embodiment, one or more previous exacerbations in the same subject were caused wholly or in part by H. influenzae. In general, a typical dose of the immunogenic polypeptide from Moraxella catarrhalis or an immunogenic fragment thereof may be expected to lie in the range of from about 0.001 mg - 0.120 mg. More specifically, a typical dose in a human may lie in the range of from about 0.003 mg to about 0.03 mg of protein. In general, a typical dose of the immunogenic polypeptide from H. influenzae or an immunogenic fragment thereof may be expected to lie in the range of from about 0.005 mg to about 0.05 mg. This dose may be administered as a single unit dose. Several separate unit doses may also be administered. For example, separate unit doses may be administered as separate priming doses within the first year of life or as separate booster doses given at regular intervals (for example, every 1, 5 or 10 years).

In a further embodiment, two doses of an immunogenic composition according to the present invention are administered, optionally according to a 0, 2 month vaccination schedule, wherein the second dose is administered about two-months after the first dose (e.g. at the end of the second month or at the beginning or the third month, for example, the first dose on Day 1 and the second dose on Day 61).

Formulations and Adjuvants

Formulations comprising the immunogenic compositions of the invention may be adapted for administration by an appropriate route, for example, by the intramuscular, sublingual, transcutaneous, intradermal or intranasal route. In one embodiment, the immunogenic compositions of the present invention are administered intramuscularly. Such formulations may be prepared by any method known in the art.

The immunogenic compositions of the present invention may additionally comprise an adjuvant. When the term "adjuvant" is used in this specification, it refers to a substance that is administered in conjunction with the immunogenic composition to boost the patient's immune response to the immunogenic component of the composition.

Suitable adjuvants include an aluminum salt such as aluminum hydroxide gel or aluminum phosphate or alum, but may also be a salt of calcium, magnesium, iron or zinc, or may be an insoluble suspension of acylated tyrosine, or acylated sugars, cationically or anionically derivatized saccharides, or polyphosphazenes. In one embodiment, the protein may be adsorbed onto aluminium phosphate. In another embodiment, the protein may be adsorbed onto aluminium hydroxide. In a third embodiment, alum may be used as an adjuvant.

Suitable adjuvant systems which promote a predominantly Thl response include: non-toxic derivatives of lipid A, Monophosphoryl lipid A (MPL) or a derivative thereof, particularly 3-de-O- acylated monophosphoryl lipid A (3D-MPL) (for its preparation see GB 2220211 A); and a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl lipid A, together with either an aluminum salt (for instance aluminum phosphate or aluminum hydroxide) or an oil-in-water emulsion. In such combinations, antigen and 3D-MPL are contained in the same particulate structures, allowing for more efficient delivery of antigenic and immunostimulatory signals. Studies have shown that 3D-MPL is able to further enhance the immunogenicity of an alum-adsorbed antigen (Thoelen et al. Vaccine (1998) 16:708-14; EP 689454-B1).

AS01 is an Adjuvant System containing MPL (3-0-desacyl-4'- monophosphoryl lipid A),

QS21 ((Quillaja saponaria Molina, fraction 21) Antigenics, New York, NY, USA) and liposomes. AS01B is an Adjuvant System containing MPL, QS21 and liposomes (50 μg MPL and 50 μg QS21). AS01E is an Adjuvant System containing MPL, QS21 and liposomes (25 μg MPL and 25 μg QS21). In one embodiment, the immunogenic composition or vaccine comprises AS01. In another embodiment, the immunogenic composition or vaccine comprises AS01B or AS01E. In a particular embodiment, the immunogenic composition or vaccine comprises AS01E.

AS02 is an Adjuvant Aystem containing MPL and QS21 in an oil/water emulsion. AS02V is an Adjuvant System containing MPL and QS21 in an oil/water emulsion (50 μg MPL and 50 μg QS21).

AS03 is an Adjuvant System containing a-Tocopherol and squalene in an oil/water (o/w) emulsion. AS03A is an Adjuvant System containing α-Tocopherol and squalene in an o/w emulsion (11.86 mg tocopherol). AS03B is an Adjuvant System containing α-Tocopherol and squalene in an o/w emulsion (5.93 mg tocopherol). AS03c is an Adjuvant System containing α-Tocopherol and squalene in an o/w emulsion (2.97 mg tocopherol). In one embodiment, the immunogenic composition or vaccine comprises AS03.

AS04 is an Adjuvant System containing MPL (50 μg MPL) adsorbed on an aluminum salt

(500 μg Al3+ ). In one embodiment, the immunogenic composition or vaccine comprises AS04.

A system involving the use of QS21 and 3D-MPL is disclosed in WO 94/00153. A composition wherein the QS21 is quenched with cholesterol is disclosed in WO 96/33739. An additional adjuvant formulation involving QS21, 3D-MPL and tocopherol in an oil in water emulsion is described in WO 95/17210. In one embodiment the immunogenic composition additionally comprises a saponin, which may be QS21. The formulation may also comprise an oil in water emulsion and tocopherol (WO 95/17210). Unmethylated CpG containing oligonucleotides (WO 96/02555) and other immunomodulatory oligonucleotides (WO 0226757 and WO 03507822) are also preferential inducers of a TH1 response and are suitable for use in the present invention.

Additional adjuvants are those selected from the group of metal salts, oil in water emulsions, Toll like receptor agonists, (in particular Toll like receptor 2 agonist, Toll like receptor 3 agonist, Toll like receptor 4 agonist, Toll like receptor 7 agonist, Toll like receptor 8 agonist and Toll like receptor 9 agonist), saponins or combinations thereof.

Possible excipients include arginine, pluronic acid and/or polysorbate. In a preferred embodiment, polysorbate 80 (for example, TWEEN (a US registered trademark) 80) is used. In a further embodiment, a final concentration of about 0.03% to about 0.06% is used. Specifically, a final concentration of about 0.03%, 0.04%, 0.05% or 0.06% polysorbate 80 (w/v) may be used.

Thus, in one aspect of the invention, the immunogenic composition comprises a pharmaceutically acceptable excipient or carrier.

In another aspect of the invention, the immunogenic composition comprises an adjuvant, e.g. ASOIE.

The present invention provides a method for the treatment or prevention of exacerbations in chronic obstructive pulmonary disease. The exacerbation of COPD may be an acute exacerbation. The method comprises administering to a subject in need thereof a therapeutically effective amount of the immunogenic composition of the invention. In an additional aspect, the present invention provides a method for the treatment or prevention of a condition or disease caused wholly or in part by Moraxella catarrhalis and/or Haemophilus influenzae.

Examples

Example 1: Lung Microbiome Analysis and Stochastic Modeling of COPD Exacerbations in the AERIS Study

Chronic Obstructive Pulmonary Disease (COPD) is a chronic inflammatory disorder resulting in irreversible decline in lung function as a consequence of inhalation of tobacco smoke or other irritants (1). One of the difficulties in treating and managing COPD is the heterogeneity of this complex disease in terms of severity, progression, exercise tolerance, and nature of symptoms (2, 3). This complexity is also evident in acute exacerbations of COPD (AECOPD), which are transient and apparently stochastic periods of increased COPD symptoms requiring additional medical treatment and often hospitalization (4). Known subtypes of exacerbations are defined by the nature of key triggers including bacterial or viral infections, and/or high eosinophil levels, and these events are typically treated with a combination of antibiotics and steroids in a non-specific manner (5).

The lung microbiome represents an emerging opportunity to understand COPD heterogeneity and exacerbations. The healthy human lung contains a variety of commensal microbiota throughout the respiratory tract, and these bacteria can show substantial heterogeneity between individuals, across regions within the lung, and over time within an individual (6-8). Alterations in the taxonomic composition of the lung microbiome, known as dysbiosis, have been associated with multiple lung diseases and in particular may play a functional role in disease severity and exacerbations in COPD (6, 9).

Multiple studies have reported differences in the microbiome between healthy and disease states, differences correlated with COPD severity and associated with exacerbation states within an individual, and interactions between the microbiome and host immune response (7, 9-12). Notably, however, many lung microbiome studies have adopted a cross-sectional design which prevents a longitudinal examination of the microbiome to assess the stability of taxa and correlations with clinical traits monitored over long periods of time and covering multiple exacerbations.

The Acute Exacerbation and Respiratory Infections in COPD (AERIS) observational cohort study allows for a unique examination of the lung microbiome with a rich set of microbiology and clinical measurements longitudinally observed in stable time points and exacerbation events in 104 patients with COPD (a subset of the full cohort of 127 patients) (13).

Disclosed herein are data from the 16S rRNA sequencing analysis of the AERIS patient cohort. Through integrated analyses using the total AERIS dataset, the present inventors were able to explore the dynamics of the lung microbiome in COPD across multiple clinical visits and to determine the clinical associations of these changes in a deeply phenotyped cohort.

Methods

Study design The AERIS study (ClinicalTrials.gov: NCT01360398) was a prospective, observational cohort study based at University Hospital Southampton (UHS). The study protocol has been described in detail

(13).

Processing of sputum samples

All study procedures for sputum sampling, the detection of exacerbations, and pathogen detection have been described previously (13). Briefly, patients were followed monthly in the stable state and reviewed within 72 hours of onset of AECOPD symptoms. Sputum samples were obtained by spontaneous expectoration or induced and were processed according to standard methods. COPD exacerbation subtypes were determined using previously-defined criteria (5).

16S rRNA amplification and sequencing

The V4 hypervariable region of the 16S rRNA gene was amplified with specific primers (515F/806R), including Illumina sequencing adapters and sample-specific barcodes, and sequenced on an Illumina MiSeq desktop sequencer. Sequence data are deposited in NCBI's Sequence Read Archive (PRJNA377739).

16S rRNA sequence analysis

Paired-end sequence reads were filtered for quality, assembled using PEAR (14), and then processed using the QIIME pipeline (15).

Statistical analyses

Comparisons of bacterial taxonomic relative abundances and alpha diversities were performed with a linear mixed model controlling for gender, age, and repeated measures on the same subject within a group. Longitudinal comparisons of relative abundances between stable and exacerbations time points were performed with a paired t-test. Markov chain analysis was performed by counting transitions between adjacent exacerbations with the subtype of exacerbation classifying each state. Statistical analyses were performed using the 'R' language and environment (version 3.3.2).

Results

Population and sampling

Samples for 16S rRNA sequencing were analyzed from 104 subjects with available sputum samples in the first year of the study (Figure 1). Characteristics of the cohort used for microbiome analysis were similar to those of the full cohort (unpublished observations).

Table 2: Characteristics of the cohort for microbiome analysis

Characteristic N = 101

Age (years) at enrolment, mean ± SD 67.1 ± 8.4 Female sex, n (%) 42 (41.6%) BMI at enrolment, mean ± SD 27.6 ± 5.4 Current smokers, n (%) 40 (39.6%) Medication for COPD, n (%) 101 (100%)

Inhaled corticosteroids, n (%) 94 (93.1%) COPD status, GOLD stage, n (%)

Mild 0 (0%) Moderate

Severe

Very severe

Bronchiectasis status, n (%)

Number of exacerbations experienced by subject in 12 months,

(%)

One exacerbation

Two exacerbations

Three or more exacerbations

FEVi after bronchodilator use (% predicted), mean ± SD

Table abbreviations: N-number of subjects in the microbiome cohort, n-number of subjects corresponding to characteristic, SD-standard deviation, COPD-chronic obstructive pulmonary disease, GOLD-global initiative for chronic obstructive lung disease, FEV-forced expiratory volume in 1 second.

Lung microbiome composition in stable state

An analysis of the relative abundances of bacterial taxa identified in the set of 584 microbiome samples passing quality control revealed bacteria commonly observed in the lung microbiome with Firmicutes, Proteobacteria, and Bacteroidetes representing the three most abundant phyla and Veillonella, Haemophilus, Streptococcus, Prevotella, and Moraxella representing the five most abundant genera. The number of successfully sequenced microbiome sputum samples averaged 5.7 per subject with 2.1 collected during an exacerbation. The relative abundances of Firmicutes and Bacteroides correlated with higher alpha diversity, while the abundance Proteobacteria had a negative correlation with other taxa and alpha diversity.

We first compared the composition and diversity of the lung microbiome to trends observed in previous studies. As described in other studies describing the lung microbiome in COPD, we observed a shift towards increasing Proteobacteria with increasing disease severity (16,17). More specifically this shift included a significant increase in Haemophilus (Proteobacteria) and decreases in Prevotella (Bacteroidetes) and Veillonella (Firmicutes), as well as decreased Shannon's entropy (Pad] < 0.05 for each) with increasing disease severity (Figure 2A).

Changes in the lung microbiome in exacerbation states

When comparing stable and exacerbation samples across all individuals, the differences were less pronounced than differences between disease severities, with no significant changes in alpha diversity measures or main taxa relative abundances with the exception of the genus Moraxella (Proteobacteria) which showed a significant increase in relative abundance in exacerbations (P = 0.0134) (Figure 2B). To confirm these results within longitudinally-sampled individuals we also used a paired t-test to compare matched stable and exacerbation events within an individual. Again, Moraxella showed a significant increase in exacerbation (P = 0.0153) (Figure 2C).

Clinical and microbiology data have been used as biomarkers to stratify subtypes of COPD and AECOPD (5) and some of these have revealed distinct lung microbiome profiles (9). We compared the composition of previously defined exacerbation subtypes characterized by sputum potentially-pathogenic bacterial culture, viral-PCR, or eosinophil percentage. The two most dissimilar exacerbation signatures were bacterial and eosinophilic. Another classification of COPD with a unique microbiome profile is that of bronchiectasis, where we observed a substantial increase in Haemophilus (P = 1.2E-5) which was evident in both stable and exacerbation events. Longitudinal stability of the lung microbiome

Intensive longitudinal sampling within the AERIS study allowed us to assess the relative stability of the lung microbiome within an individual. To analyze temporal microbiome stability, we computed UniFrac distance (weighted and unweighted) between all pairs of microbiome profiles within a subject, and stratified results based on comparisons between stable-stable, stable- exacerbation, and exacerbation-exacerbation comparisons. In all groups, we found UniFrac distance to be significantly lower within an individual compared to distances between individuals (Figure 3A-B). This result suggests that individuals have somewhat distinct lung microbiomes from each other. Moreover, weighted UniFrac distances were significantly higher for stable-exacerbation and exacerbation-exacerbation comparisons relative to stable-stable comparisons (P < 1.0E-3) (comparisons using unweighted UniFrac distance not significant) (Figure 3B). This measure-specific result suggests that dysbiosis events in the lung may typically result from changes in the relative abundance of pre-existing bacteria (detected by weighted UniFrac) rather than complete removal or appearance of novel species (detected by unweighted UniFrac).

Moreover, given that weighted UniFrac distances involving exacerbations (stable- exacerbation and exacerbation-exacerbation) were higher than stable-stable, it appears exacerbation events are most likely to be associated with dysbiosis within an individual. While the lung microbiome may have a degree of within-subject stability, there remains a large degree o