WO2013087727A1 - New efficient interferon-based treating methods - Google Patents

Abstract

The present invention is drawn to novel efficient interferon-based treating methods intended to be applied to patients suffering from cancer or viral infection. These treating methods can require prior identification of define mutations in protein or gene sequence of some endogenous interferon in said patients. The present invention is also drawn to a method of identifying efficient anti-cancer or anti-viral agents, comprising the steps of: a) contacting said agents with IFN receptor IFNGR1 and/or IL28RA, and b) detecting if said agent is an agonist of said IFN receptor.

Description

NEW EFFICIENT INTERFERON-BASED TREATING METHODS

DESCRIPTION OF THE PRIOR ART

Interferons (I FNs) are cytokines that play a key role in innate and adaptive immune responses. Despite the large number of immunological studies of these molecules, the relative contributions of the numerous I FNs to human survival remain largely unknown. Here, we evaluated the extent to which natural selection has targeted the human IFNs and their receptors, to provide insight into the mechanisms that govern host defense in the natural setting. We found that some IFN- a subtypes, such as IFN- a6, IFN-a8, IFN-a13, and IFN-a14, as well as the type I I I FN-γ , have evolved under strong purifying selection, attesting to their essential and nonredundant function in immunity to infection. Conversely, selective constraints have been relaxed for other type I IFNs, particularly for IFN-a10 and IFN- ε, which have accumulated missense or nonsense mutations at high frequencies within the population, suggesting redundancy in host defense. Finally, type III IFNs display geographically restricted signatures of positive selection in European and Asian populations, indicating that genetic variation at these genes has conferred a selective advantage to the host, most likely by increasing resistance to viral infection. Our population genetic analyses show that IFNs differ widely in their biological relevance, and highlight evolutionarily important determinants of host immune responsiveness.

IFNs are helicoidal cytokines released by host cells in response to the presence of pathogens or tumor cells. Human IFNs have been classified into three major types on the basis of the cognate receptors through which they signal, gene sequence similarity, and chromosomal location (Pestka et al., 2004 ). Type I IFNs include 17 subtypes (13 subtypes of IFN- a and IFNs β/ε/κ/ω), all of which bind to a receptor composed of two chains, IFNAR1 and IFNAR2 (Uze et al., 2007). The genes encoding type I IFNs are intronless and are located in a region spanning ~ 400 kb on chromosome 9, with the exception of IFNK , which is located ~6 Mb away from the other type I IFN genes (Trent et al., 1982 ; Henco et al., 1985 ; Diaz et al., 1994). There is only one type II IFN, IFN-γ, which signals via a receptor composed of the IFN- γ R1 and IFN- γ R2 subunits ( Wheelock and Sibley, 1965 ; Pestka et al., 2004 ). The more recently described type III IFNs constitute a group of three cytokines, IL-28A, IL-28B and IL-29 (also known as IFN- λ 2, IFN- A3, and IFN- A1 , respectively), the genes for which are clustered in a~50-kb region of chromosome 19 (Kotenko et al . , 2003 ; Sheppard et al., 2003). These IFNs activate a signaling pathway similar to that of type I IFNs, but act via a different receptor composed of the type III IFN specific IL-28RA and the IL-10RB, the latter subunit being also used by the IL-10 and IL-22 receptor (Kotenko et al., 1997 ; Xie et al., 2000). There is increasing evidence to suggest that type I and III IFNs have a different role from the type II IFN: IFN- α /β and IFN- λ appear to have potent antiviral activities, whereas IFN-γ has antibacterial, antiparisitic, and antifungal properties (Pestka et al., 2004 ; Zhang et al., 2008).

I n recent years, human genetics studies of both Mendelian and complex diseases have identified several variants affecting the production of, or the response to, IFNs, shedding light on the genuine functions of IFNs in the natural setting (Zhang et al., 2008). Disorders or specific mutations in genes involved in the IFN- γ circuit, such as in IFNGR1 and IFNGR2, confer a Mendelian predisposition to mycobacterial disease (Filipe-Santos et al., 2006), whereas the disorders or specific mutations in patients with impaired type I or type III responses are associated with a stronger predisposition to viral infections (Dupuis et al., 2003; Chapgier et al., 2006; Minegishi et al., 2006). Likewise, mutations affecting type I or type I I I I FN responses have been associated with various autoimmune pathologies (Crow et al., 2006a, b ; Glocker et al., 2009 ; Rice et al., 2009). Several epidemiological genetics studies have recently shown that genetic variants in the region encompassing the type III IFN IL28B gene are associated with the spontaneous clearance of hepatitis C virus (H CV) and the response to HCV therapeutic treatment (Ge et al., 2009 ; Suppiah et al., 2009 ; Tanaka et al., 2009 ; Thomas et al., 2009).

Ou r understand i ng of the mechan isms control li ng I F N production , the downstream signal ing pathways associated with these molecu les , and their involvement in physiology and pathology is starting to be fully appreciated, but several biological questions remain unanswered. Given that multiple I FN molecules signal through the same receptor (e.g., IFN- α /β and IFN- λ), are all IFNs equally relevant to host survival? Are some IFN genes more essential for immunity to infection whereas others display immunological redundancy? Does IFN-γ, which is not a prototypic antiviral cytokine, have a distinctive evolutionary signature? Has genetic variation at specific IFN gene loci conferred a selective advantage to the host, associated with an increase in resistance to infectious disease? Here, we tackled these questions using an evolutionary genetics approach, which investigates the way in which infections have shaped the variability of host defense genes by natural selection (Sabeti et al., 2006 ; Nielsen et al., 2007 ; Barreiro and Quintana-Murci, 2010). This approach, which has been shown to be an indispensable complement to clinical and epidemiological genetics, and to immunological studies (Casanova and Abel, 2007; Casanova et al., 201 1 ; Quintana-Murci et al., 2007 ), should help to determine the biological relevance of IFNs in the setting of a natural ecosystem governed by natural selection.

FIGURE LEGENDS Figure 1 : Patterns of nucleotide diversity for the three families of IFN genes and for the genes encoding their receptors in human populations. (A) Nucleotide diversity levels for the individual genes in populations representing major ethnic groups. The expected diversity (dotted lines) corresponds to the mean diversity levels observed for 20 autosomal noncoding regions in each geographic area (Laval et al. , 2010). (B) Comparison of nucleotide diversity between IFN families and receptors.

Figure 2: Proportion of chromosomes carrying at least one nonsynonymous or nonsense variant in the general human population. The red portion of the pie charts corresponds to the proportion of chromosomes carrying at least one nonsynonymous polymorphism, the black portion to the proportion of chromosomes carrying at least one nonsense polymorphism, and the blue portion to the proportion of chromosomes carrying neither nonsynonymous nor nonsense polymorphisms. Genes shaded in gray correspond to those encoding the receptor subunits of each IFN family. Figure 3: Estimation of the intensity of natural selection acting on the various

IFN families and their receptors. The strength of natural selection was assessed by estimating ω values. Under neutrality, ω is not significantly different from 1 . Values below 1 are consistent with selection against nonsynonymous variants, whereas values greater than 1 indicate an excess of amino acid changes. Bars indicate 95% Bayesian confidence intervals, and red circles indicate genes with ω estimates significantly above or below 1 . Genes shaded in gray correspond to those encoding the receptor subunits of each IFN family.

Figure 4: Detection of positive selection in Asia using the DIND test. We plotted

values against derived allele frequencies (DAFs). P-values were obtained by comparing the values for the three type III IFN genes against the expected

values obtained in 10 ⁴ simulations, taking into account the most conservative demographic model (Laval et al., 2010). The top dashed line on the graph corresponds to the 99th percentile, and the bottom to the 95th percentile. Dots above the 95th percentile dashed line correspond to mutations that have increased in frequency faster than expected under neutrality in the Asian population. These mutations have been most likely targeted by positive selection, and thus conferred an advantage to the host. Red and black dots correspond to nonsynonymous and silent polymorphisms, respectively. For DIND analyses concerning all genes encoding the 27 IFNs and their receptors in all populations, see Fig. 9.

Figure 5: Detection of positive selection on the basis of levels of population differentiation. Population pairwise F ST values are plotted against expected heterozygosity for all the SNPs identifi ed in our study for Africans versus Europeans (A), Africans versus Asians (B), and Europeans versus Asians (C). The dashed lines represent the 99th and 95th percentiles of the HGDP-CEPH genotyping dataset for the same individuals (represented by the density area in blue; Li et al., 2008). Black dots correspond to silent polymorphisms and red dots correspond to nonsynonymous polymorphisms.

Figure 6: Spatial distribution of positively selected variants across type I II IFN genes. Genomic organization of the three members of the type III IFN family, IL28B , IL28A , and IL29 . Filled boxes correspond to exonic regions, and arrows above exons indicate the direction of the open reading frame. Genetic variants displaying signatures of population-specific positive selection are shown; noncoding SNPs are indicated in black and amino acid changes in red. At the gene level, IL28A and IL28B displayed signatures of positive selection in Asia, and IL29 in both Europe and Asia (Table 2). At the SNP level, the action of positive selection targeting the fi ve SNPs at IL28B and the two at IL28A was supported by the DIND test ( Fig. 4 ), whereas that at the IL29 D188N variant was supported by the DIND test and iHS, as well as by the levels of population differentiation ( Fig. 5 ).

Figure 7: Detection of gene conversion events and influence of their removal on the estimation of purifying selection. To evaluate the power (i.e., the true discovery rate) of our method for gene conversion (GC) detection , we simulated two linked paralogous genes in the human and chimpanzee l ineages that d id or d id not experience gene conversion (Materials and methods). We estimated the parameter ω for the acceptor gene, under different scenarios: (left) neutral simulations in the absence/presence of gene conversion and after the removal of gene conversion events; (middle) simulations mimicking the effects of pu rifying selection in the absence/presence of gene conversion and after the removal of gene conversion events; and (right) neutral simulations in the complete absence of gene conversion and after the removal of gene conversion events. Our analyses showed that the removal of gene conversion events corrected the effect of gene conversion on the estimation of ω (left and middle). Mean ω values turned out to be almost identical in the absence of gene conversion and after the removal of the detected gene conversion events, highlighting the high power and the low false discovery rate (FDR) of the detection method used. Interestingly, our analyses showed that even in the absence of gene conversion (right), the removal of putative spurious signals of gene conversion had virtually no impact on the estimation of ω (low FDR).

Figure 8: Linkage disequilibrium maps for the three type III IFNs. Linkage disequilibrium (LD) maps for the African (top), European (middle), and Asian (bottom) populations. LD was estimated for SNPs with a minor allele frequency (MAF) > 0.01 . Numbers represent r 2 values, whereas colors indicate D' levels (white, no LD; lavender, low/intermediate LD; red, high LD). Red squares with no value correspond to r ² = 1 . Figure 9: Detection of positive selection by the DI ND test on the 27 genes encoding the IFNs and their receptors. Details of these analyses are given in the Materials and methods section and in Fig. 4. The results presented here correspond to those obtained using the most conservative demographic model (Laval et al., 2010). DETAILED DESCRIPTION OF THE INVENTION

In this study, we demonstrate that the different IFN families, and their individual members, have followed different evolutionary trajectories in humans. First, we found that type I IFN subtypes differ in their levels of evolutionary constraint.

Amino acid-altering variation has been constrained for some type I I FNs, with IFNA6, IFNA8, IFNA13, and IFNA14 found to have been subject to the strongest purifying selection Fig. 3). Low levels of amino acid-altering variation were also observed at IFNA2, IFNA5, IFNA21, IFNB1, IFNK, and IFNW1 ( Fig. 2 and Table 1 ). Conversely, selective constraints have been relaxed for other type I IFNs, which harbor nonsynonymous variants at high population frequencies (IFNA 1, IFNA4, IFNA7, IFNA 10, IFNA 16, and IFNA17). Furthermore, some IFNs present nonsense mutations in the homozygous state (IFNA 10 and IFNE), suggesting that they might be currently undergoing pseudogenization.

We also found that some nonsynonymous polymorphisms at several I FNA genes, for the most part observed at low population frequencies, appear to have been introduced by gene conversion from their paralogs (Table S5). This observation supports the notion that, besides gene duplication, gene conversion has contributed to the evolution of type I IFNs in mammals (Hughes, 1995 ; Woelk et al., 2007 ; Genin et al., 2009b). Together, the strong constraints characterizing some type I IFNs suggest that they fulfill an essential, nonredundant function in host defense. In contrast, the high population frequencies of missense or nonsense mutations, occurring through mutation or gene conversion, found in other type I IFN subtypes, suggest that these molecules are highly redundant.

Our findings provide evolutionary evidence of the complexity of the biological actions of type I IFNs. Indeed, in the mouse model, they play a key role in protective antiviral immunity to multiple experimental infections (Jouanguy et al., 2007 ; Vilcek, 2006 ). In humans, primary immunodeficiencies of the type I I FN pathway, including STAT-1 and TYK-2 deficiencies, have also shown that type I IFNs are critical for antiviral immunity (Dupuis et al., 2003 ; Chapgier et al., 2006, 2009 ; Minegishi et al., 2006 ; Zhang et al., 2008). The integration of our population genetics data into a clinical framework thus indicates that at least one subgroup of type I I FNs plays a critical, nonredundant role in antiviral immunity in natural conditions. A greater tolerance for the increase in frequency of missense or nonsense mutations in the general population is observed in another set of type I IFNs, suggesting that the functions they fulfill are largely overlapping with other IFN subtypes. The existence of multiple type I IFNs and differences in their degrees of diversity and redundancy may attest to the great capacity of this host defense system to evolve, to develop efficient antiviral responses.

However, there is a growing body of work showing that type I I FN activity can also be detrimental to the host (Decker et al., 2005 ; Vilcek, 2006 ; Trinchieri, 2010 ). Experimental data from mice and clinical observations in human patients have shown that IFN production can be harmful in the context of infection and can increase morbidity (Gresser et al. 1975 ; Riviere et al., 1977 ; Vilcek, 1984). Such adverse effects of increased IFN production have also been observed in the context of autoimmune diseases (Banchereau and Pascual, 2006 ; Crow et al., 2003), such as systemic lupus erythematosus (Banchereau et al., 2004 ; Crow, 2007 ; Le Bon et al., 2006a ; Le Bon et al., 2006b). In addition, there is increasing evidence to suggest that type I IFNs have opposing roles in viral and bacterial infection (Decker et al., 2005 ; Vilcek, 2006 ; Trinchieri, 2010). Such a multifaceted mechanism of host defense is illustrated by IFN- a 8 and IFN- a 13, which are both under strong selective constraint yet display high and low antiviral potency, respectively (Foster and Finter, 1998; Foster et al., 1996 ; Jaks et al., 2007 ; Koyama et al., 2006 ; Lavoie et al., 201 1 ). However, differences in bioactivity between IFN subtypes will depend not only on their respective potencies and distinct receptor-binding chemistries, as recently shown for a subset of type I IFNs (Thomas et al., 201 1 ), but also on their individual production. Few studies have systematically assessed the levels of expression of the multiple type I I FNs (Coccia et al., 2004 ; Genin et al., 2009a) and, because of the differences in experimental conditions used, there is as yet no clear consensus as to which subtypes are the most expressed in different cell types. In light of this, we hypothesize that type I IFNs presenting various antiviral potencies and/or production could have been maintained, and selected for, to regulate global type I IFN activity. To test this hypothesis, further analyses are needed to (a) characterize the expression and potency of the individual type I IFN subtypes under different conditions of infection and in different cell types, in particular for those exhibiting the strongest signatures of purifying selection; (b) define how the variation in both production and potency of the various subtypes is under genetic control (i.e., host genetic variation in both protein coding regions and regulatory regions); and (c) evaluate how the combination of the whole set of type I IFN subtypes, with their varying functional diversity, affects downstream of purifying selection; (b) define how the variation in both production and potency of the various subtypes is under genetic control (i.e., host genetic variation in both protein coding regions and regulatory regions); and (c) evaluate how the combination of the whole set of type I IFN subtypes, with their varying functional diversity, affects downstream transcriptional programs and host responses at the organism level.

Second, we found that the type II IFNG was the only gene, across all three families of human IFNs and their receptors, to display a complete absence of amino acid-altering mutations. This gene was subject to the strongest purifying selection of all IFNs, and we previously showed that IFNG is among the -10% of immune-related genes subject to the most intense selective constraints on amino acid variation in humans (Manry et al., 201 1 ). Clinical genetic studies have demonstrated that six genes involved in the IFN- γ circuit (IL-12/23— IFN- γ) play a critical role in protective immunity (Filipe-Santos et al., 2006). Specifically, disorders of IFNy production caused by mutations affecting IL-12B, IL-12RB1 , or specific NEMO mutations, and impaired IFN- Y responses caused by IFNGR1, IFNGR2, or specific STAT1 mutations, are associated with Mendelian susceptibility to mycobacterial disease in patients resistant to most viruses (Zhang et al., 2008). Population and clinical data show that no variation with a significant impact on protein function is tolerated at loci involved in IFN- γ-mediated immunity, indicating that the IFN-γ pathway is essential and nonredundant in host survival, including host defense against mycobacteria.

Finally, our data showed that type I I I I FNs are the only group of I FNs where selective pressures have involved processes of geographically restricted adaptation, revealing that genetic variation at these genes has conferred a selective advantage to specific human populations (Fig. 6). There is increasing evidence from clinical genetic studies to support a major role of these molecules in antiviral immunity (Zhang et al., 2008), so the selection pressure acting on type III IFN genes may be of viral origin. Strong support for this notion has been provided by recent genome-wide association studies. Indeed, the five IL28B polymorphisms we identified as being under positive selection in Asia have been associated with the spontaneous clearance of HCV and a better response to pegylated IFN oribavirin treatment for chronic HCV infection in populations of African, European, and Asian ancestry (Ge et al., 2009 ; Suppiah et al., 2009 ; Tanaka et al., 2009 ; Thomas et al., 2009 ; Rauch et al., 2010). These SNPs include two located in the regulatory region of IL28B (SNP - 3180A>G, rs12979860; and SNP -370G, rs28416813), one in an intron (SNP 6850T rs1 1881222), one in the 3 _ region (SNP 1388T>G, rs4803217), and one nonsynonymous SNP of IL28B (SNP 502G>A, R70K, rs8103142). Interestingly, based on the odds ratios for protective alleles, it has been suggested that variation of the IL28B gene may confer a stronger protective effect in Asians than in individuals of European or African ancestry (O'Brien, 2009). However, the environmental, genetic, and evolutionary factors underlying this difference remain unknown. Our data provide new insight into the relationship between type III I FN variation and ethnic background, by showing that Asian populations have evolved the most adaptively and protective alleles have increased in frequency among Asians as a result of positive selection, rather than simple genetic drift. Given the chronic and insidious nature of HCV pathogenesis, it is unlikely that HCV, at least in its modern form, is really responsible for the selection pressure exerted on IL28B. In light of this, we hypothesize that other ancestral and more virulent flaviviruses are responsible for the selective footprints observed. To this end, it will be instructive to determine whether IL28B polymorphisms are associated with natural immunity to related viruses (e.g., hemorrhagic flaviviruses and/or encephalogenic alphaviruses).

The overlap between the IL28B variants found here to be under positive selection and those associated with the spontaneous clearance of HCV infection provides an important proof-of-concept for the value of the evolutionary approach, as a complement to epidemiological and medical genetics studies. This is particularly important for positively selected IL28A and IL29 variants, whose function is not yet fully appreciated. The strongest signature of positive selection we observed concerned a nonsynonymous SNP in IL29 (SNP 2054G>A, D188N, rs30461 ) in European and Asian populations. However, the way in which this variant confers a selective advantage to the host and the pathogens responsible for exerting a selective pressure on IL29 remains to be identified. Because the th ree type I I I I F Ns operate as independent genetic entities, we propose that the signatures of positive selection, which appear to be independent, displayed by each type III IFN reflect their different relative contributions to human fitness and survival. Additional studies are required to unravel the immunological role and phenotypic expression of type III IFN subtypes, particularly polymorphisms shown to be under positive selection , in relation to susceptibility to, or the pathogenesis of infectious diseases or autoimmune disorders.

In conclusion, our population genetics data indicate that the various members of the human IFN families differ in biological relevance, ranging from highly constrained to redundant and expendable. The identification of individual IFN genes subject to strong constraints or to adaptive evolution, attesting to their important role in immunity to infection, paves the way for additional studies to evaluate the potential of these molecules for use in vaccination, diagnosis, and treatment. More generally, our study provides a paradigm of the use of population genetics in the context of infection, with a view to improving our understanding of the biological importance of immunity-related genes in host defense in the natural setting.

Accordingly, in a first aspect, the present invention is drawn to a method for treating cancer or viral infection in a patient in need thereof, comprising the administration of a combination of at least two interferons (IFNs) chosen in the group consisting of: I FNA2, I FNA5, I FNA6, I FNA8, IFNA13, IFNA14, I FNA21 , I FNB1 , IFNK and IFNW1.

Preferably, said combination contains at least IFNA8 or IFNA 6, more preferably at least IFNA6 and IFNA8. In a rather preferred embodiment, at least three interferons are administered.

In a preferred embodiment, said viral infection is Hepatitis C.

The present invention is also drawn to a combination of at least two interferons (IFNs) chosen in the group consisting of: IFNA2, IFNA5, I FNA6, I FNA8, I FNA1 3, IFNA14, IFNA21 , IFNB1 , IFNK and I FNW1 , preferably containing I FNA6 and/or I FNA8, for use for treating cancer or viral infection in a patient in need thereof.

The present invention also concerns the use of a combination of at least two interferons (I FNs) chosen in the group consisting of: I FNA2, I FNA5, I FNA6, I FNA8, I FNA13, I FNA14, I FNA21 , I FN B 1 , I FN K and I FNW1 , preferably containing I FNA6 and/or I FNA8, for the preparation of a medicament intended to be used for treating cancer or viral infection in a patient in need thereof. In a second aspect, the present invention is drawn to an in vitro method for identifying efficient anti-cancer or anti-viral agents, comprising the steps of:

- contacting said agents with IFN receptor IFNGR1 and/or IL28RA,

- detecting if said agent is an agonist of said IFN receptor. Preferably, in this aspect, said agent is an agonist of IFNGR1 and IL28RA.

In a third aspect, the present invention is drawn to a method for treating cancer or viral infection in a patient in need thereof, comprising the steps of:

- testing if the protein sequence of the endogenous I L28A interferon of said patient contains an Alanine in position 1 12 and/or an Histidine in position 160, and - administering IL28A interferon of SEQ ID NO:2 if said endogenous I L28A protein contains an Alanine in position 1 12 and/or an Histidine in position 160.

The present invention is also drawn to IL28A interferon of SEQ ID NO:2 for use for treating cancer or viral infection in a patient whose endogenous I L28A interferon protein contains an Alanine in position 1 12 and/or an Histidine in position 160. The present invention also concerns the use of I L28A interferon of SEQ I D

NO:2 for the preparation of a medicament intended to be used for treating cancer or viral infection in a patient in which the endogenous IL28A interferon protein contains an Alanine in position 1 12 and/or an Histidine in position 160.

In a fourth aspect, the present invention is drawn to a method for treating cancer or viral infection in a patient in need thereof, comprising the steps of:

- testing if the protein sequence of the endogenous I L28B interferon of said patient contains an Arginine in position 70, or

- testing if the IL28B gene of said patient contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and

- administering I L28B interferon of SEQ I D NO:4 if said endogenous I L28B protein contains an Arginine in position 70 or if said IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ I D NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3).

The present invention is also drawn to IL28B interferon of SEQ ID NO:4 for use for treating cancer or viral infection in a patient in which the protein sequence of the endogenous IL28B interferon contains an Arginine in position 70, or in which the IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ I D NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3). The present invention is also drawn to the use of IL28B interferon of SEQ I D

NO:4 for the preparation of a medicament intended to be used for treating cancer or viral infection in a patient whose endogenous IL28B interferon protein contains an Arginine in position 70, or in which the IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3).

In a fifth aspect, the present invention is drawn to a method for treating cancer or viral infection in a patient in need thereof, comprising the steps of:

- testing if the protein sequence of the endogenous I L29 interferon of said patient contains an Aspartic acid in position 188, and - administering IL29 interferon of SEQ ID NO:6 if said endogenous IL29 protein contains an Aspartic acid in position 188.

The present invention is also drawn to the I L29 interferon of SEQ ID NO:6 for use for treating cancer or viral infection in a patient whose endogenous IL29 interferon protein contains an Aspartic acid in position 188. The present invention is also drawn to the use of I L29 interferon of SEQ I D

NO:6 for the preparation of a medicament intended to be used for treating cancer or viral infection in a patient in which the endogenous IL29 interferon protein contains an Aspartic acid in position 188.

The present invention also relates to a method for treating cancer or viral infection in a patient in need thereof, comprising the steps of: a) testing if the protein sequence of the endogenous I L28A interferon of said patient contains an Alanine in position 1 12 and/or an Histidine in position 160, and b1 ) testing if the protein sequence of the endogenous IL28B interferon of said patient contains an Arginine in position 70, or b2) testing if the IL28B gene of said patient contains the nucleotides: -37C

(position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and c) administering a pharmaceutical composition containing IL28A interferon of SEQ ID NO:2 and I L28B interferon of SEQ ID NO:4 if said endogenous IL28A protein contains an Alanine in position 1 12 and/or an Histidine in position 160 and if said endogenous IL28B protein contains an Arginine in position 70 or if said IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3). In other terms, the invention relates to a pharmaceutical composition containing

IL28A interferon of SEQ ID NO:2 and I L28B interferon of SEQ I D NO:4, for use for treating cancer or viral infection in a patient in need thereof. Preferably, said patient is characterized as follows: the protein sequence of its endogenous IL28A interferon contains an Alanine in position 1 12 and/or an Histidine in position 160, and the protein sequence of its endogenous IL28B interferon contains an Arginine in position 70, or its IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3). Once a patient carrying these at least two mutations in IL28A and IL28B has been identified by classical in vitro tests, the said patient will be efficiently treated with a pharmaceutical composition containing I L28A interferon of SEQ ID NO:2 and IL28B interferon of SEQ ID NO:4.

The present invention also relates to the use of I L28A interferon of SEQ I D NO:2, IL28B interferon of SEQ ID NO:4 for preparing a pharmaceutical composition intended to be used for treating patients suffering from a cancer or a viral infection, preferably patients exhibiting i) an endogenous IL28B protein containing an Arginine in position 70 or an IL28B gene containing the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ I D NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and ii) an endogenous I L28A protein containing an Alanine in position 1 12 and/or an Histidine in position 160.

The present invention also relates to a method for treating cancer or viral infection in a patient in need thereof, comprising the steps of: a) testing if the protein sequence of the endogenous I L28A interferon of said patient contains an Alanine in position 1 12 and/or an Histidine in position 160, and b) testing if the protein sequence of the endogenous I L29 interferon of said patient contains an Aspartic acid in position 188, and c) administering a pharmaceutical composition containing I L28A interferon of

SEQ ID NO:2 and IL29 interferon of SEQ I D NO:6 if said endogenous I L28A protein contains an Alanine in position 1 12 and/or an Histidine in position 160 and if said endogenous IL29 protein contains an Aspartic acid in position 188.

In other terms, the invention relates to a pharmaceutical composition containing IL28A interferon of SEQ ID NO:2 and IL29 interferon of SEQ ID NO:6, for use for treating cancer or viral infection in a patient in need thereof. Preferably, said patient is characterized as follows: the protein sequence of its endogenous I L28A interferon contains an Alanine in position 1 12 and/or an Histidine in position 160, and the protein sequence of its endogenous IL29 interferon contains an Aspartic acid in position 188. Once a patient carrying these at least two mutations in I L28A and I L29 has been identified by classical in vitro tests, the said patient will be efficiently treated with a pharmaceutical composition containing IL28A interferon of SEQ ID NO:2 and I L29 interferon of SEQ ID NO:6.

The present invention also relates to the use of I L28A interferon of SEQ I D NO:2 and IL29 interferon of SEQ ID NO:6 for preparing a pharmaceutical composition intended to be used for treating patients suffering from a cancer or a viral infection, preferably patients exhibiting i) an endogenous IL29 protein containing an Aspartic acid in position 188, and ii) an endogenous IL28A protein containing an Alanine in position 1 12 and/or an Histidine in position 160. The present invention also relates to a method for treating cancer or viral infection in a patient in need thereof, comprising the steps of: a) testing if the protein sequence of the endogenous I L29 interferon of said patient contains an Aspartic acid in position 188, and b1 ) testing if the protein sequence of the endogenous I L28B interferon of said patient contains an Arginine in position 70, or b2) testing if the IL28B gene of said patient contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and c) administering a pharmaceutical composition containing I L29 interferon of

SEQ ID NO:6 and IL28B interferon of SEQ ID NO:4 if said endogenous IL29 protein contains an Aspartic acid in position 1 88 and if said endogenous I L28B protein contains an Arginine in position 70 or if said IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3).

In other terms, the invention relates to a pharmaceutical composition containing IL29 interferon of SEQ ID NO:6 and I L28B interferon of SEQ I D NO:4, for use for treating cancer or viral infection in a patient in need thereof. Preferably, said patient is characterized as follows: its endogenous I L29 protein contains an Aspartic acid in position 188 and its endogenous IL28B protein contains an Arginine in position 70 or its IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3). Once a patient carrying these at least two mutations in IL29 and IL28B has been identified by classical in vitro tests, the said patient will be efficiently treated with a pharmaceutical composition containing IL29 interferon of SEQ ID NO:6 and IL28B interferon of SEQ ID NO:4.

The present invention also relates to the use of IL29 interferon of SEQ ID NO:6 and I L28B interferon of SEQ I D NO:4 for preparing a pharmaceutical composition intended to be used for treating patients suffering from a cancer or a viral infection, preferably patients exhibiting i) an endogenous IL29 protein containing an Aspartic acid in position 188, and ii) an endogenous IL28B protein containing an Arginine in position 70 or an IL28B gene containing the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3).

In another aspect, the present invention relates to a method for treating cancer or viral infection in a patient in need thereof, comprising the steps of: a) testing if the protein sequence of the endogenous I L29 interferon of said patient contains an Aspartic acid in position 188, and b1 ) testing if the protein sequence of the endogenous IL28B interferon of said patient contains an Arginine in position 70, or b2) testing if the IL28B gene of said patient contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and c) testing if the protein sequence of the endogenous IL28A interferon of said patient contains an Alanine in position 1 12 and/or an Histidine in position 160, d) administering a pharmaceutical composition containing I L28A interferon of SEQ ID NO:2, IL29 interferon of SEQ ID NO:6 and IL28B interferon of SEQ ID NO:4, if said endogenous I L29 protein contains an Aspartic acid in position 188, if said endogenous IL28B protein contains an Arginine in position 70 or if said IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and if said endogenous IL28A protein contains an Alanine in position 1 12 and/or an Histidine in position 160.

In other terms, the invention relates to a pharmaceutical composition containing IL28A interferon of SEQ ID NO:2, IL29 interferon of SEQ ID NO:6 and IL28B interferon of SEQ I D NO:4, for use for treating cancer or viral infection in a patient in need thereof. Preferably, said patient is characterized as follows: its endogenous I L29 protein contains an Aspartic acid in position 1 88, its endogenous I L28B protein contains an Arginine in position 70 or its IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and its endogenous I L28A protein contains an Alanine in position 1 12 and/or an Histidine in position 160. Once a patient carrying these at least three mutations in IL29, IL28A and IL28B has been identified by classical in vitro tests, the said patient will be efficiently treated with a pharmaceutical composition containing IL28A interferon of SEQ ID NO:2, IL29 interferon of SEQ ID NO:6 and IL28B interferon of SEQ ID NO:4.

In this aspect, the present invention therefore relates to a pharmaceutical composition containing I L28A interferon of SEQ I D NO:2, I L29 interferon of SEQ I D NO:6 and IL28B interferon of SEQ ID NO:4. This pharmaceutical composition is preferably used for treating a cancer or a viral infection in a patient in need thereof. This pharmaceutical composition is more preferably used for treating patients exhibiting i) an endogenous IL29 protein containing an Aspartic acid in position 188, ii) an endogenous IL28B protein containing an Arginine in position 70 or an IL28B gene containing the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ I D NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and iii) an endogenous I L28A protein containing an Alanine in position 1 12 and/or an Histidine in position 160.

The present invention also relates to the use of I L28A interferon of SEQ I D NO:2, IL29 interferon of SEQ ID NO:6 and I L28B interferon of SEQ I D NO:4 for preparing a pharmaceutical composition intended to be used for treating patients suffering from a cancer or a viral infection , preferably patients exhibiting i) an endogenous IL29 protein containing an Aspartic acid in position 188, ii) an endogenous IL28B protein containing an Arginine in position 70 or an IL28B gene containing the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and iii) an endogenous I L28A protein containing an Alanine in position 1 12 and/or an Histidine in position 160.

All the pharmaceutical compositions of the invention may contain an acceptable pharmaceutical carrier. I n the present description, "pharmaceutically acceptable carrier" means a com pou nd , or a com bi nation of com pou nds , contai ned i n a pharmaceutical composition, that does not cause secondary reactions and that, for example, facilitates administration of the active compounds, increases its lifespan and/or effectiveness in the organ ism , increases its solubility in solution or improves its storage. Such pharmaceutical carriers are well-known and will be adapted by a person skilled in the art according to the nature and the administration route of the active compounds selected. A typical pharmaceutical composition for intravenous infusion could be made up to contain 250 ml of sterile Ringer's solution, and 100 mg of the combination. Actual methods for preparing parenterally administrable compounds will be known or apparent to those skilled in the art and are described in more detail in for example, Remington's Pharmaceutical Science, 17th ed., Mack Publishing Company, Easton, Pa. (1985), and the 18th and 19th editions thereof, which are incorporated herein by reference.

In a sixth aspect, the present invention is drawn to a method for treating cancer or viral infection in a patient in need thereof, comprising the steps of: i) sequencing the endogenous sequence of at least one interferon gene chosen in the group consisting of: IFNA2, IFNA5, IFNA6, IFNA8, IFNA 13, IFNA 14, IFNA21, IFNB1,

IFNK and IFNW1; ii) identifying if said at least one sequence contains a nonsense mutation or a stop mutation, iii) administering to the patient the wild type form of the corresponding IFN protein in case said at least one sequence contains a nonsense mutation or a stop mutation.

The present invention is also drawn to a wild-type form of I FNA2, I FNA5, IFNA6, IFNA8, IFNA13, IFNA14, IFNA21 , IFNB1 , IFNK or IFNW1 protein for its use for treating cancer or viral infection in a patient having a nonsense mutation or a stop mutation in said endogenous interferon protein. In particular, if the patient has a nonsense mutation or a stop mutation in its endogenous IFNA2, the present invention is drawn to a wild-type form of IFNA2 for its use for treating cancer or viral infection in said patient.

In particular, if a patient has a nonsense mutation or a stop mutation in its endogenous IFNA5, the present invention is drawn to a wild-type form of IFNA5 for its use for treating cancer or viral infection in said patient. In particular, if a patient has a nonsense mutation or a stop mutation in its endogenous IFNA6, the present invention is drawn to a wild-type form of IFNA6 for its use for treating cancer or viral infection in said patient.

In particular, if a patient has a nonsense mutation or a stop mutation in its endogenous IFNA8, the present invention is drawn to a wild-type form of IFNA8 for its use for treating cancer or viral infection in said patient.

In particular, if a patient has a nonsense mutation or a stop mutation in its endogenous IFNA13, the present invention is drawn to a wild-type form of IFNA13 for its use for treating cancer or viral infection in said patient. In particular, if a patient has a nonsense mutation or a stop mutation in its endogenous IFNA14, the present invention is drawn to a wild-type form of IFNA14 for its use for treating cancer or viral infection in said patient.

In particular, if a patient has a nonsense mutation or a stop mutation in its endogenous IFNA21 , the present invention is drawn to a wild-type form of IFNA21 for its use for treating cancer or viral infection in said patient.

In particular, if a patient has a nonsense mutation or a stop mutation in its endogenous IFNB1 , the present invention is drawn to a wild-type form of IFNB1 for its use for treating cancer or viral infection in said patient.

In particular, if a patient has a nonsense mutation or a stop mutation in its endogenous IFNK, the present invention is drawn to a wild-type form of IFNK for its use for treating cancer or viral infection in said patient.

In particular, if the patient has a nonsense mutation or a stop mutation in its endogenous IFNW1 , the present invention is drawn to a wild-type form of IFNW1 for its use for treating cancer or viral infection in said patient. The present invention is also drawn to the use of a wild-type form of IFNA2,

IFNA5, IFNA6, IFNA8, IFNA13, IFNA14, IFNA21 , IFNB1 , IFNK or IFNW1 protein for the preparation of a medicament intended to be used for treating cancer or viral infection in patients having a nonsense mutation or a stop mutation in said endogenous interferon protein. As used herein, the term "cancer" encompasses any type of cancer. Preferably, it is an epithelial cancer, a non-epithelial cancer, a solid or a non-solid cancer. Cancers consisting of epithelial cancer cells include, for example, lung cancer, breast cancer, gastric cancer, colorectal cancer, uterine cervical cancer, uterine cancer, oral cancers, i.e. cancer of the oral cavity (e.g., laryngeal cancer, pharyngeal cancer, lingual cancer, etc.), cancer of the oropharynx, oropharyngeal squamous cell carcinoma (OSCC), or head and neck squamous cell carcinoma, prostate cancer, colon cancer, squamous cell carcinoma, including oral squamous cell carcinoma (OSCC), adenocarcinoma and the like; cancers consisting of aforementioned non-epithelial cancer cells (sarcoma) i n c l u d e , fo r exa m p l e , l i p o s a rco m a , o ste o s a rco m a , c h o n d ros a rco m a , rhabdomyosarcoma, leiomyosarcoma, fibrosarcoma, angiosarcoma, and the like. Other cancers also can be treated by the present invention , including, for example, basalioma, Merkel cell carcinoma, myxoma, non-small cell tumor, oat cell tumor, papilloma, bronchiolar tumor, bronchial tumor; leukemia such as chronic myeloid leukemia, B cell tumor, mixed cell tumor, null cell tumor, T cell tumor; HTLV-II related tumors such as lymphocytic acute leukemia, lymphocytic chronic tumor, mastocytoma, and myeloma; histiocytic malignant tumors such as Hodgkin's tumor, non-Hodgkin's lymphoma, malignant melanoma, mesothelioma, Ewing sarcoma, Kaposi sarcoma, periosteoma, adenofibroma, adenolymphoma, craniopharyngioma, dysgerminoma, mesenchymoma, mesonephroma, ameloblastoma, cementoma, odontoma, thymoma, adenocarcinoma, cholangioma, cholesteatoma, cylindroma, cystic adenoma, cystic tumor, granulosa cell tumor, ovarian tumor, hepatic cancer, syringocarcinoma, islet cell tumor, Leydig cell tumor, Sertoli cell tumor, theca cell tumor, leiomyoma, myoblastoma, ependymoma, neural myoma, glioma, medulloblastoma, periosteoma, neurilemma, neu roblastoma , neu roepithelioma , n eu rofibroma , neu roma , paragangl ioma , nonchromaffin paraganglioma, angiokeratoma, hematolymphangioma, sclerosing hemangioma, glomus tumor, angioendothelioma, lymphangioma, lymphangiomyoma, lymphagiosarcoma, pineocytoma, carcinosarcoma, colorectal sarcoma, neurofibroma and the like.

In a preferred embodiment, the methods of the invention enable to treat IFN- involving cancers such as chronic myeloid leukemia, Kaposi sarcoma and infantile hemangioma. As used herein, the term "viral infection" encompasses an infection involving any identified virus. Preferably, said virus is selected in the group consisting of: the influenza virus, the hepatitis A virus, the Hepatitis B virus, the Hepatitis C virus, the Hepatitis E virus, the Hepatitis G virus, the HIV virus, the yellow fever virus, the dengue virus, the Japanese encephalitis virus, the tick-borne encephalitis virus, the Usutu or West Nile viruses, the Rift Valley fever or Toscana viruses, the chikungunya virus, the respiratory synticial virus, the Rocio virus, the morbillivirus, the Murray encephalitis virus, the Wesselbron virus, the Zika virus, the lymphocytic choreomeningitis virus, the Ebola virus, the Marburg virus, the Crimean-Congo hemorrhagic fever virus, the Lassa virus, the Junin virus, the Machupo virus, the Sabia virus, the Guanarito virus, the mumps virus, the rabies virus, the rubella virus, the varicella zoster virus, the herpes simplex types 1 and 2, more generally an alphavirus, an adenovirus, an echovirus, a rotavirus, a flavivirus, a rhinovirus, an orthobunyavirus, a poliovirus, a human parvovirus, an enterovirus, a coronavirus, a human papillomavirus, the hu man cytomegalovirus, the Epstein-Barr virus, the parainfluenzae viruses from types 1 , 2 and 3, or any identified virus.

In a preferred embodiment, the methods of the invention enable to treat viral infections caused by viruses of the Flaviviridae family, more particularly viruses of the Flavivirus and the Hepacivirus genera. In a more preferred embodiment, the said viral infections are caused by viruses selected in the group consisting of: the Hepatitis C virus, the Hepatitis B virus, the yellow fever virus, the dengue virus, the Japanese encephalitis virus, the tick-borne encephalitis virus, the West Nile virus, the Murray encephalitis, the Saint-Louis encephalitis and the Kyasanur forest disease. In an even more preferred embodiment, the said viral infection is caused by the

Hepatitis C virus. SEQUENCES

SEQ ID NO : 1 (natural) DNA of human IL28A (promoter + gene)

TGGTGGCACAAATCTGTAATCTCAGCTACTTGGGAGGCTAAGGCAAGAGAATCGCTTGAACCCA GGAGGTGGAGGTTGCAGTTAGTCAAGATTTTGCACTGCACTCCAGCCTGGGTGACCGAACAAGA CCCTGTCTCAAAATATATATATATATATATGCCAGGAGGGGTGGCTCAGGCCTGTAATCTCAGC ACTTTAATAGGCTGGGTGAGGAGGATGGCTTGAGCCCAGGAGTTTGAGGCTGCAGTGAGCTGTG ATCATGCCATTGCACTCCAGTGACAGAGTGAGACCCTGTCTTAAACAACAACAAAACCAGAGCA GGTGGAATCCTCCTGGGAACATACCTTCCTGTAGGTTACCCCTGAGTCTCCATCAGTTTCTCTT TCCCTCCAGCTGCTCATCTGGCTCACTAGCCCTGCCCTGCTCTGGGCTTTCCCAGCCTGGGGCT CCCCTGGTGGCCGGTGTCTTACCTGAGGCTGTGTTTTCACTTTTCCTACATCAGCTGGGACTGC CCTTCTGTCAGGGATAAAAGCTGCCCCATGGAGCTCAGGCAGGAATTACATCCCAGACAGAGCT CAAAACTGACAGAAAGAGTCAAAGCCAGGACACAGTCTGAGATCCAGAAGAGGGGACTGAAAAG AACAGAGACTCCAGACAAGACCCAAACAGACCCTGGGTGACAGCCTCAGAGTGTTTCTTCTGCT GACAAAGACCAGAGATCAGGAATGAAACTAGGTGAGTCCCACATCTCTGTCCGTGCTCAGCTCC TGCAGCCCCTGCCCTCAGTGGGCAGCCTCTCCATCCCCTCAGCTCCCTTTCTCTCTGTGACACA GACATGACTGGGGACTGCACGCCAGTGCTGGTGCTGATGGCCGCAGTGCTGACCGTGACTGGAG CAGTTCCTGTCGCCAGGCTCCACGGGGCTCTCCCGGATGCAAGGGGCTGCCACATAGCCCAGTT CAAGTCCCTGTCTCCACAGGAGCTGCAGGCCTTTAAGAGGGCCAAAGATGCCTTAGTGAGTCTC CCCCTGCCCTCCTGCCATGGACTAGCCTCCACCCCCACTCCAAGCGTCACCATGCTTTCCCACT CCCAGCTTCCTTCACTGGGCTAGCCTCCACCCTCCCTGCAGTGGGCTATCTCATGCTCCTACTG TAGGGACTGACTCATGTTTTCCTGTAGAAGAGGGTCCTCTACCATCCTCCCAGCAGTTAACCTC CCCTATCCTGTTGTCAGCCATCCTCCAATCCCACCAGGATGGTCTAACCTCCACCCCTCCTGCT GGGGCTAACCTGTGCCTTTGCTGTCTAGGAAGAGTCGCTTCTGCTGAAGGACTGCAGGTGCCAC TCCCGCCTCTTCCCCAGGACCTGGGACCTGAGGCAGCTGCAGGTGAGAGGGGGAGTCAGGCCCA CCCCTGCTCTCCCAGCCCCACTCACCTGGCTCTGTAGTGGCCCCTTCACCGTCTCTTTCTCCCT TGTCTCTCTCTCTTCTCCTCACACCTGCTCTCCCTTCCCTCCGCTCCCACCTGACCACACTGGC TGTGCCCTCTCCCCTGTGCCTGTCACCTTCACTTGTTCCTCTCTATCCTGCTCCCCAACCTGTT CCCCTCACCTCCCCCCTCACCTGCTCTTTCTCACCTCTCCTCAGGTGAGGGAGCGCCCCATGGC TTTGGAGGCTGAGCTGGCCCTGACGCTGAAGGTTCTGGAGGCCACCGCTGACACTGACCCAGCC CTGGTGGACGTCTTGGACCAGCCCCTTCACACCCTGCACCATATCCTCTCCCAGTTCCGGGCCT GTGTGAGTCGTTGGGGCCTGGGCACCCAGGTCTGTGAGCTCTGAGCAGCGTCCTTCCCCTTGCC AAGGCCCCGGCTCACACACCGCCCTCCTCTGCCCACAGATCCAGCCTCAGCCCACGGCAGGGCC CAGGACCCGGGGCCGCCTCCACCATTGGCTGTACCGGCTCCAGGAGGCCCCAAAAAAGGTGAGT GACCCGGGAAGAGAGGGACTGAGGTCTGGGGAGCCACTGGGAGCCCAGAACCCAGACAGCCCCT GACCCATCCCCTCCTCCCTACAGGAGTCCCCTGGCTGCCTCGAGGCCTCTGTCACCTTCAACCT CTTCCGCCTCCTCACGCGAGACCTGAATTGTGTTGCCAGTGGGGACCTGTGTGTCTGACCCTCC CACCAGTCATGCAACCTGAGATTTTATTTATAAATTAGCCACTTGTCTTAATTTATTGCCACCC AGTCGCTATTTATGTATTTGTGTGTGTAAATCCAACTCACCTCCAGGAAAATGTTTATTTTTCT ACTTTTTATAACCCTTGTTGAAATAAACAAAGGAAAAGACACTCATGACGTTGGACTGTGTGTC TGTTGGTGTGTATTTCCTTTGTGTTGCTGCCATAACAACGCTAAAAGTAGCATCTTCCAAAGAC ACACTTGATGAGCTGGGAGTCTGCAGGTCAGAGGCTCGCTGGCCCTGGCTGGTTTCTCTCCTGT GGGACTCACAGGCTAGAATCCAAGCATTGCTGCTGGGCTCTTACTGGGAGCTCTGAAGAGAAAC TCTTTCCAGGGTCAGTCACATTGTTGGCAGATCACTGTTCCTTGCTGCTGTAGGACTAAGGTTC CTGCCCCCTCCTGGCTATGGGTCCATCCTGAGCTGACTCTGCTGAAGGGTTCTCCACTCCTCTC ACTAAGCTAACCTCTACCCTCCCTGCAGTGGGCTATCTCATGCTCCTACTATAGGGGCTGATTC ATGTCCTCCTGCAGTGGAGGGTCCTGTAACATCCTCCCGGGAGTTAACCTC

Initiating codon (ATG) and stop codon (TGA) are underlined.

SEQ ID NO : 2 (natural) amino acid sequence of IL28A containing 112T and 160Y

MKLDMTGDCTPVLVLMAAVLTVTGAVPVARLHGALPDARGCHIAQFKSLSPQELQAFKRAKDAL EESLLLKDCRCHSRLFPRTWDLRQLQVRERPMALEAELALTLKVLEATADTDPALVDVLDQPLH TLHHILSQFRACIQPQPTAGPRTRGRLHHWLYRLQEAPKKESPGCLEASVTFNLFRLLTRDLNC VASGDLCV

SEQ ID NO: 3 (natural) DNA of human IL28B (promoter + gene)

AGGCCCCCCGGCGCTGCCTGCTCTCGCACTACCGCTCGCTGGAGCCCCGGACGCTGGCGGCTGC CAAGGCGCTGAGGGACCGCTACGTAAGTCACCGCCCAGCCCCTGTGCCCCCTGGGACCCTGGCC CCACCGGGTTCCCATACACCCGTTCCTGTCCCAAGGGGTCCTGCGTCCTAGCGCCCAGCAGGCG CCTCTCCTATGTCAGCGCCCACAATTCCCACCACGAGACCCCCGCAGTCCCCGTCGTCAGCGCG AACGCAGGCTCAGGGTCAATCACAGAAGGGAGCCCTGCCGGGAGGACTCGGCTCCAGGTCGGGG CGAGGGGCTTTGCTGGGGGAGCGCGGAGTGCAATTCAACCCTGGTTCGCGCCTTCGGGGAGCTC CCTGGTTCAGTACACGACAGGCACGACCGTGCGCTGCCAGTACCCATCCACGTCCAGGAATCCC AGACTGTGCAGAGGTTAGGGGCCCTGGCGAGGGGGCCTAGCCGTATGCGATAAGCGCCGCTTGT CCCGCAGGAGGAAGAGGCGCTGAGCTGGGGGCAGCGCAACTGCTCCTTCCGCCCCAGGAGGGAT CCTCCGCGGCCATCGGTGAGGCCCGGGAGTGGGCGGGAGAGGCATGGCCCGGGCGCGGCCCGCT CTAACGCCCTCTCGTCCCCGCAGTCCTGCGCTCGGCTCCGCCACGTGGCCCGGGGCATCGCGGA CGCCCAGGCAGTGCTCAGCGGCCTGCACCGCTCGGAGCTGCTCCCCGGCGCCGGCCCGATCCTG GAGCTGCTGGCGGCCGCGGGGAGGGATGTGGCGGCCTGCGTGAGTGACGGCCGCGCCCCGCCGC CCCTCTCCCCCGCCAGCTTCTCTGCATCCTCAGGCCCACGGCGAGCCCCAGCGCTTTGCCAATC TGTCCTGCTTAGCGGAAAAACCCATCCAGACCGGAGTCGGGTCCTCTGGGTGTCCTGAAATCCG GGCTCGAGTCTGCGGCTGGGAGGGCCACGGGCAGATGCAGAGAGGGGCTTCGTCCTTCGCCTTT TCCATTTGCCTCATGTCCCACCTCCAGCTTGAGCTGGCACGGCCAGGCTCCTCCAGGAAGGTCC CCGGGGCCCAGAAGAGGCGTCACAAACCCCGGAGAGCGGTGAGTGCAACAGGCAATACAGGGTT AGCCCGCAGGGAGGACCAGGCGAGGCTGACAAGGACGGGACTGAGGCTGCGAGCAGCGGGACTG GAGGGGGATTCCGGGGGCGGGGGGAAGAGCCTGGCTTAGCCCCGCTGCCCTCCCTCCCTGGCTC CAGGACTCGCCTCGGTGCCGCAAAGCCAGCGTGGTCTTCAACCTCCTGCGCCTGCTCACGTGGG AGCTCCGGCTGGCTGCACACTCTGGGCCTTGCCTCTGACCCCGCCCCCTCTGGCAGCACGGAAA CCTCCACGCCATTGGCTGCCGAAAGCAGCTCCTGTCGTCCATTGGGCTGGCCGGGCGAGGCTCT CAGTCAATGGGTGCTGAGGCACGAAAACTTCTTCGCAGCCTTGGGCCTGACTTGGATCCACTGT CTCAGATATAAGAGGAGCGGGTCCTTCTACAGGGAAGAGACCACAGTTCTCCAGGAAGCCACGA TATTTCCTCGGGGTGCATTGTACGACCCTCCAACGGTTGCTGTGGCAGGAAAAAACTTGAGCTC TGGAAACCGTGGCTGACCCCAGGCAACAGGGACCAGTTCCTCCTTGTGTGGTTACCAGGACACC CCCAACACCAGGTCCTAACCCCGGATTTGTAGCCCCACAGCCAGCTTTGAGATTCTGTGAATCC GTGACTCTTGGATCCGGCATCTAAGGGACACCAATCCATGAGGGATTTGGTAGTGAAAGGCCCA AGGGTCCTTAACCGACTGTGGTTCTTTGGATTCCCTTACGTGTGTTTGTATTTGTGAAGTTCCT GTGCATTTGCTATTCTGTCTCCCGGTTTAAATTTATTGCCAGTTATCAAAGAGTGTTTTGATCG CATTGGTTGTTTTCCGTATGATGATTGTGAGGTGCACCTTACAGCAAAAAAAGAGGCCGAGCCA GGGACTCAGGTGGCCTGAGTTTCAGTTCTGACCCTGCCAGTTAATTACAGTGGAATTCAGGGCA AATTACTTTTCTGAGCCTCTGTTTCCTCACCTATAGGATGGGTTAGCATACTTGCCTTGTGGAG GAGTAGTGTCCGTTGAGATCACGTTTTAAACTCTCCAGCTGAGGTCCTAGTATGGTCTTAATGA GTGGATTCTATTAAATAATCACTCACATAAATACACAAACAATTGTGTTATTAATTTTTTCTCC AAATCTGTGCATTAGCAATCTGCGTTGCTGAATGCACCCCTCCTTGCCAAGGTCACACGGCTAG TGAGGGTCAGAACCAGGTTTGAACCCCAGACCCTTCATCTCCAAGACCCATGCTCTTCACCACT GCCTGAACTTCCCTAAGAAAGACGGCACCCACGTGGTGTCCTTCAAGTCCTTCGTCACACCTCA ATTCTTGAGCAGAGCCTCATATTCCTGAGTCCTTCCTTGCCTGGGCAATTAAGAAATATTGGCC TCTGGGCATGGTGGCTCACACTGAAATCCCAGCAATTTGGGAGGCCTAGACAGAGAGATGACTT GACATCAGGAATTTGAGACCAGCCTTGCCAACATGGTGAAACGCCATCTCTACTAAAAATATAA AAATTAGCTGGGAATGGTGGCACAAATCTGTAATCTCAGCTACTTGGGAGGCTAAGGCAAGAGA ATTGCTTGAACCCAGGAGGCGGAGGTTGCAGTTAGCCAAGATTTTGCACTGCACTCCAGCCTGG GTGACCGAACAAGACCCTGTCTCAAAATATATATATATATATATATATATATATGCCAGGAGTG GTGGCTCAGGCCTGTAATCTCAGCACTTTAATAGGCTGGGTGAGGAGGATGGCTTGAGCCCAGG AGTTTGAGGCTGCAGTGAGCTGTGATCATGCCATTGCACTGCAGTGACAGAGTGAGACCCTGTC TTAAACAACAACAAAACCAGAGCAGGTGGAATCCTCTTGGGAACATACCTTCCTGTAGGTTACC CCTGAGTCTCCATCAGTTTCTCTTTCCCTCCAGCTGCTCATCTGGCTCACTAGCCCTGCCCTGC TCTGGGCTTTCCCAGCCTGGGGCTCCCCTGGTGGCCGGTGTCTTACCTGAGGCTGTGTTTTCAC TTTTCCTACATCAGCTGGGACTGCCCTTCTGTCAGGGATAAAAGCTGCCCCATGGAGCTCAGGC AGGAATTACATCCCAGACAGAGCTCAAAACTGACAGAAAGAGTCAAAGCCAGGACACAGTCTGA GATCCAGAAGAGGGGACTGAAAAGAACAGAGACTCCAGACAAGACCCAAACAGACCCTGGGTGA CAGCCTCAGAGTGTTTCTTCTGCTGACAAAGACCAGAGATCAGGAATGAAACTAGGTGAGTCCC ACATCTCTGTCCGTGCTCAGCTCCTGCAGCCCCTGCCCTCAGTGGGCAGCCTCTGCATTCCCTC AGCTCCCTTTCTCTCTGTGACACAGACATGACCGGGGACTGCATGCCAGTGCTGGTGCTGATGG CCGCAGTGCTGACCGTGACTGGAGCAGTTCCTGTCGCCAGGCTCCGCGGGGCTCTCCCGGATGC AAGGGGCTGCCACATAGCCCAGTTCAAGTCCCTGTCTCCACAGGAGCTGCAGGCCTTTAAGAGG GCCAAAGATGCCTTAGTGAGTCTCCCCCTGCCCTCCTGCCATGGACTAGCCTCCACCCGCACTC CAAGGGTCACCATGCTTTCCCACTCCCAGCTTCCTTCACTGGGCTAGCCTCCACCCTCCCTGCA GTGGGCTATCTCATGCTCCTACTGCAGGGACTGACTCATGTTTTCCTGAAGAAGAGGGTCCTCT ACCATCCTCCCAGCAGTTAACCTCCCCTATCCTGTTGTCAGCCATCCTCCAATCCCATCAGAGT GGTCTAACCTCCACCCCTCCTGCTGGGGCTAACCTGTGCCTTTGCTGTCTAGGAAGAGTCGCTT CTGCTGAAGGACTGCAAGTGCCGCTCCCGCCTCTTCCCCAGGACCTGGGACCTGAGGCAGCTGC AGGTGAGAGGGGGAGTCAGGCCCACCCCTGCCCTCCCAGCCCTGCTCACCTGGCTCTGTAGTGG CCCCTTCACCTTCTCCTTCTCCATTGTCCCTCTCTCCTCTCCCCACACCTGCTACCCCTTCCCT CTGCTCCTACCTGACCACACTGGCTGTGCCCTCTCCCCTGTGCCTGTCACCTTCACTTGTTCCT CTCTATCCTCCTCCCCCAACCTGTTCCCCTCACCTCCCCCCTCACCTGCTCTTTCTCACCTCTC CTCAGGTGAGGGAGCGCCCCGTGGCTTTGGAGGCTGAGCTGGCCCTGACGCTGAAGGTTCTGGA GGCCACCGCTGACACTGACCCAGCCCTGGGGGATGTCTTGGACCAGCCCCTTCACACCCTGCAC CATATCCTCTCCCAGCTCCGGGCCTGTGTGAGTCGTCAGGGCCCGGGCACCCAGGTCTGTGAGC TCTGAGCAGCGTCCTTCCCCTGGCCAAGGCCCCGGCTCACACACCGCCCTCCTCTGCCCACAGA TCCAGCCTCAGCCCACGGCAGGGCCCAGGACCCGGGGCCGCCTCCACCATTGGCTGCACCGGCT CCAGGAGGCCCCAAAAAAGGTGAGTGACCCGGGAAGAGAGGGACTGAGGTCTGGGGAGCCACTG GGAGCCCAGAACCCAGACAGCCCCTGACCCATCCCCTCCTCCCTACAGGAGTCCCCTGGCTGCC TCGAGGCCTCTGTCACCTTCAACCTCTTCCGCCTCCTCACGCGAGACCTGAATTGTGTTGCCAG CGGGGACCTGTGTGTCTGACCCTTCCGCCAGTCATGCAACCTGAGATTTTATTTATAAATTAGC CACTTGGCTTAATTTATTGTCACCCAGTCGCTATTTATGTATTTGTGTATGTAAATCCAACTCA CCTCCAGGAAAATGTTTATTTTTCTACTTTTTGAAATCCTTGTTGAAATAAACAATGAGGAAAA GACACCCATGACGTGGGACTGTGTGTGCGTTGGTGTGTATTTCCTTTGCATTGCTGCCATAACA AATTACCCTAAA

Initiating codon (ATG) and stop codon (TGA) are underlined.

SEQ ID NO:4 (natural) Amino acid of human IL28B (containing 70K)

MTGDCMPVLVLMAAVLTVTGAVPVARLRGALPDARGCHIAQFKSLSPQELQAFKRAKDALEESL LLKDCKCRSRLFPRTWDLRQLQVRERPVALEAELALTLKVLEATADTDPALGDVLDQPLHTLHH ILSQLRACIQPQPTAGPRTRGRLHHWLHRLQEAPKKESPGCLEASVTFNLFRLLTRDLNCVASG DLCV

SEQ ID NO:5 (natural) DNA of human IL29 (promoter + gene)

ACATAGTAAAACCCAGTCTCTACTAAAAATACAAAAACTAGCCAGGCGTGATGGCATGCACCTG TAATCCCAACTACTTAGGAGGCTGAGGCAGGAGAATCGCTTCAACTCGGGAGGCAGAAGTTGCA GTGAGCCAAGATTGCACCATTGCACTCCAGCCTGGGCAACAAGAGCAAAACTACGTCTCAAAAA ATAATAATAACAATAAAATAAAAAACAAGCTTTTTTTTTTTTGAAACAGGATCTCACTCCATCA CCCAGGCTGGAGTGCAGTGGCACGATCTTGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGTG ATTCTCATGCCTCGGCCTCCTGAGTAGCTGAGACCACAGGCGCATGCCACCACACCTGGCTAAT TTAGAATAAAAAAGAAGCTTCCTCTCTGCCACTCAGGTAGCCTTATCCCTAATCTCAGCCTCCG TCAGGGACTCCCTGAGGCCAGTTGGCTGAAAGCTGCCCAGGGAGTTCTAAGGATTTCAGTTTCT CTTTCCTTCTTGATGCAGCTCCCAGCTCACTTGGCCCTGCCCACACCTGTTCCCTCATCAGGCT CCCAGACGGGCCCCGCCCACTCATGCCTCTTAAGTCAAAGTGGAAATTCTCATTTCCAATTACC TTTTCACTTTACACACATCATCTTGGATTGCCCATTTTGCGTGGCTAAAAAGCAGAGCCATGCC GCTGGGGAAGCAGTTGCGATTTAGCCATGGCTGCAGCTTGGACCGTGGTGCTGGTGACTTTGGT GCTAGGCTTGGCCGTGGCAGGCCCTGTCCCCACTTCCAAGCCCACCACAACTGGGAAGGGCTGC CACATTGGCAGGTTCAAATCTCTGTCACCACAGGAGCTAGCGAGCTTCAAGAAGGCCAGGGACG CCTTGGTGAGTTCCTGTTGCTGTGGATGAACCACTTCTACGGGTGTCCCAATTACTGCCCTTCT ACTGTGGGCTAGCCTCTAGCCTTCCAACTATGGCAAACCTCTATCCTTTCTGCACTGGGTTAAA CCCATGCTGTCAGGCCAACTTCATCCTTGCTGCTATGAGCTAGCTTCCAGCCATCCTGCTGTGG GCTAACCCCTGCCCTTGCTCTCTAGGAAGAGTCACTCAAGCTGAAAAACTGGAGTTGCAGCTCT CCTGTCTTCCCCGGGAATTGGGACCTGAGGCTTCTCCAGGTGAGCTGAAAGTCAGGCCCCCTTC ACCCTTCCCTTGACCCTCTCCCCCCTCTTCTTAAGTGGCCCCTTAGCCTTCTTTGTTTCCCTTG TCCTTCACTCTCTTGGACCTCTCCTCACCTGTCCTGTGCCCCTGCCACTTCAAAACTGCTCTCT TGACTCTGTCCTTCCCCTGGGTCCCTTTTATCATCTCCCATCGGCCCCACTTCCCTAGCTCGCT CACCTGTCCCTGTCACTTCCACTCTCACTCTTCATTTCTCTCCCAAATGTCTCCAGTCTGTCGC CCACCTGTGCCTTTCGTCCTGCTCCACTTCTCCCTGTCTGTTCCCAACACTGACCCCCTCTCCC TCTCACCTGCCTCTGTCACCTGTCCCTCATTATCTCTCACTGACATTCATCCAGCTCATGCTCC CCCCTCATCCACCCTTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTGCTCTA TGGCCCAGGCTGGAGTGCAGTGGCATGATCTCGGTTCACTGCAACCTCTGCCTCCCGGGTTCAA GCAATTATCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCATGTGCCATGATGCCCAGCT AATTTTTGTATTTTTAGCAGAGACGGGGTTTCACTATGTTGGCCAGGCTTGGTCTCGAAATCCT GACCTCAGGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCAC ACCCAGCCCTACCCTTCTTCTCTGTGCATGCAACTGTCCCTCTCTTACTGTGCCCCCAACCTGC TTTCTCCTCACCCGTCCCCACCCCGCCCCAGAGAACTTCTGTGACCCCCGTAAGTCCCCTTTCA TTTGTCTCCATTTCACTTATCCCCTCACCTGCCTCCTTGACCATCCTGCCTCACCTGTATCCTT CCTCATGTCTTCCCCCTCCTGTCTCCTTCTCCCCAGACCCCTCACCTGTCCCCACCACATGCAC TGTGTCACCGACCTTCCCCAGGACTGCCTACCTGTCCCCACTAACTGGGTCTTCTTGCCTGTTC TCCCTCACCTGCTCTTTCTCACCTCTCCTCAGGTGAGGGAGCGCCCTGTGGCCTTGGAGGCTGA GCTGGCCCTGACGCTGAAGGTCCTGGAGGCCGCTGCTGGCCCAGCCCTGGAGGACGTCCTAGAC CAGCCCCTTCACACCCTGCACCACATCCTCTCCCAGCTCCAGGCCTGTGTGAGTCCTTGGGGCC CGGGCACCCAGGTCTGTGGGCTCTGAGCAGCATCCTTCCCCTGTGGTGGCCCAGGCTCCGCCTC ACACACCGCCCTCTTCTGCCCACAGATCCAGCCTCAGCCCACAGCAGGGCCCAGGCCCCGGGGC CGCCTCCACCACTGGCTGCACCGGCTCCAGGAGGCCCCCAAAAAGGTGAGTGACCCAGGAAGAG AAGGACCAGGGTCTGGGGAGCCAATAGGAGCCCAGACCCTGGACAGCCCCTGACCCATCCCCTC CTCCCCTACAGGAGTCCGCTGGCTGCCTGGAGGCATCTGTCACCTTCAACCTCTTCCGCCTCCT CACGCGAGACCTCAAATATGTGGCCGATGGGAACCTGTGTCTGAGAACGTCAACCCACCCTGAG TCCACCTGACACCCCACACCTTATTTATGCGCTGAGCCCTACTCCTTCCTTAATTTATTTCCTC TCACCCTTTATTTATGAAGCTGCAGCCCTGACTGAGACATAGGGCTGAGTTTATTGTTTTACTT TTATACATTATGCACAAATAAACAACAAGGAATTGGAACCTTCTGTGATAGGTGAATCCTTGAG TGTGTGTGTGATTGTGGGTCTGTGACTGGGTGTGGATGTCTGGGTGATGCAGGCAAAATTTGTG ACTCGTTGTGTATATTTGTGTG

Initiating codon (ATG) and stop codon (TGA) are underlined.

SEQ ID NO:6 (natural) Amino acid sequence of human IL29 (containing D188N)

MAAAWTVVLVTLVLGLAVAGPVPTSKPTTTGKGCHIGRFKSLSPQELASFKKARDALEESLKLK NWSCSSPVFPGNWDLRLLQVRERPVALEAELALTLKVLEAAAGPALEDVLDQPLHTLHHILSQL QACIQPQPTAGPRPRGRLHHWLHRLQEAPKKESAGCLEASVTFNLFRLLTRDLKYVADGNLCLR TSTHPEST

EXAMPLES

MATERIAL AND METHODS Population samples. Sequence variation for all hu man I FN s and their receptors was determined in 186 individuals from sub-Saharan Africa, Europe and Asia (62 individuals per geographic region) from the HGDP-CEPH panel (Cann et al., 2002). Sub-Saharan African popu lations were composed of 1 9 Bantu from Kenya , 21 Mandenka from Senegal and 22 Yoruba from Nigeria; European populations were composed of 20 French, 14 Italians, 6 Orcad ians and 22 Russians; the Asian populations were composed of 15 Han Chinese and 33 individuals from Chinese minorities, 10 Japanese and 4 Cambodians. Population structure within continental regions has been shown to be limited (Li et al., 2008) and to have a negligible influence on the inference of natural selection (Manry et al., 201 1 ). This study was approved by the Institut Pasteur Institutional Review Board (no. RBM 2008.06).

DNA sequencing. We sequenced the 27 genes encoding the I FNs and their receptors using Sanger sequencing. Given the extremely high sequence identity among I FN genes (i.e. , the type I I FNA genes, as well as type I I I I FN genes, are organized into two distinct clusters of paralogous genes), Sanger sequencing was the most appropriate choice to differentiate with confidence regions that are highly paralogous. Another advantage of Sanger sequencing is the reliable detection of low- frequency variants, which are the substrate used to detect and estimate the intensity of purifying selection. This contrasts with publicly available whole genome sequence datasets that, even if they include IFNs (e.g., 1 ,000 Genomes), are depleted for low- frequency variants, particularly non synonymous mutations (Durbin et al., 2010), due to the low coverage at which the genomes have been sequenced. For each gene, we sequenced all the exon regions and at least as much of the non-exon regions, including intron, 5' and 3' regions (Table S1 ). All sequences were obtained with the Big Dye Terminator kit and a 3730 XL automated sequencer from Applied Biosystems. Sequence files and chromatograms were inspected with GENALYS software (Takahashi et al., 2003). All singletons or am biguous polymorph isms were systematically reamplified and resequenced. We were unable to resequence the first exon of IFNGR2 and the first exon of IL10RB, for technical reasons, probably due to the very high GC content of the region (73% and 72%, respectively). The reference sequences used are given in Table S1.

Gene conversion analyses. Because interlocus gene conversion requires high levels of sequence identity between loci (Mansai and Innan, 2010), we sought to detect gene conversion events based on (i) the local homology observed between two paralogs and (ii) the ancestral/derived state of each base pair in humans determined using the correspond ing ch im panzee ortholog . For a pair of genes, X and Y, resequenced in two different individuals, each sequence was subdivided in fragments of 40 bp. Each fragment defined in gene X was compared to all the possible fragments in gene Y irrespective of their location. This procedure was performed for all pairs of individuals in our sample (N=186). We retained pairs of fragments with a sequence identity higher than 90%. Within these pairs, a mutation observed at a given position in gene X was declared as being a putative gene conversion event when its derived state (fixed or polymorphic) was equal to the ancestral or derived state observed at the same position in gene Y. However, situations that could be most parsimoniously explained by a single point mutation (i.e., a mutation fixed for the derived state in gene X and fixed for the ancestral allele at the same position in gene Y) were not considered as a conversion event. For each gene, this method provided a set of mutations probably resulting from gene conversion. We declared the putative acceptor and donor genes on the basis of the frequencies of converted mutations (i.e., the donor has the highest frequency of the conversion event). We evaluated the power of the method to detect gene conversion events and the influence of their removal on the detection of selection by means of coalescence simulations, using SIMCOAL v2 (Laval and Excoffier, 2004). We simu lated two duplicated genes in the human and chimpanzee lineages, with the gene duplication predating the divergence of the two species. Twenty human sequences (10 individuals) and 1 chimpanzee sequence were simulated , with the following parameters: the recombination rate expected in humans (I cM/Mb), a human/chimpanzee divergence time of 5 million years, constant population sizes (N = 1 ,000 individuals) and a mutation rate adjusted to the number of mutations observed in our dataset. The two duplicated genes, each 2,000 bp long, were simulated using a global sequence identity between paralogs set to be equal to 90%. I n add ition , 30% of sites were set to be non synonymous, with a sequence identity set to be equal to 95% in coding regions. When gene conversion was introduced, a fixed number of conversion events were simulated using a tract length set at 100 bp (consistent with empirical estimates of mean tract length (Mansai and Innan, 2010)). We allowed conversion when sequence identity between tracts was higher than 60%, specifying that 90% of the conversion events simulated involved a sequence identity higher than 90%. Then, all mutations present in the tract of the donor gene (both fixed and polymorphic within the human lineage) were copied in the acceptor gene. To evaluate the impact of gene conversion in a more realistic scenario, we also introduced purifying selection on non synonymous sites, by using a lower mutation rate at non synonymous sites with respect to silent sites. We then applied our method of gene conversion detection and calculated the power to detect the gene conversion events and the false discovery rate (Fig. S1 ).

All variants identified as resulting from gene conversion were not considered in the statistical analyses to detect selection. It should be noted that ignoring the events most parsimoniously explained by a point mutation (i.e., fixed mutations in humans) will have no effect on the detection of selection using analyses based on intra-species polymorphism, and cannot generate false positive signals of purifying selection using inter-species tests corrected for gene conversion (Fig. S1 ). In addition, we verified manually if some of the amino acid altering polymorphisms detected as resulting from gene conversion could be ambiguously explained by gene conversion or mutation, because the erroneous removal of such sites can create spurious signals of purifying selection. Two events were identified as false positives, in IFNA 10 and IFNA 17, and the corresponding mutations were thus not excluded from our analyses. Statistical analyses. We used Haploview software (Barrett et al., 2005) to obtain and visualize levels of linkage disequilibrium in the various genomic regions. Haplotype reconstruction was performed by the Bayesian method, implemented in Phase (v.2.1 .1 ) (Stephens and Donnelly, 2003). We applied the algorithm five times, using different randomly generated seeds, and checked the consistency of the results across runs. The entire dataset was used for the calculation of sequence-based neutrality statistics, including Tajima's D, Fu & Li's D^*, Fu & Li's P, Fay & Wu's H, in DnaSP v5.1 (Rozas et al., 2003). P-values for the various neutrality tests were estimated from 10⁴ coalescent simulations, performed with SIMCOAL 2.0 (Laval and Excoffier, 2004), under a finite-site model and using the recombination rate of the tested region reported in HapMap Phase II (Frazer et al., 2007) and the deCODE recombination rate given in the UCSC database (http://genome.ucsc.edu) (Kong et al., 2002). Each of the 10⁴ coalescent simulations was conditional on the observed sample size and the number of segregating sites observed for each gene. We corrected for the effects of demography on diversity patterns, by considering two demographic models based on resequencing data for noncoding regions in a set of populations similar to those studied here (Laval et al., 2010; Voight et al., 2005). The main difference between these two demographic models is that the Laval's model takes intercontinental population migration into account (Laval et al., 2010). We used the McDonald-Kreitman Poisson Random Field (MKPRF) method (Bustamante et al., 2005; Sawyer and Hartl, 1992) to search for the effects of natural selection, taking into account both inter-species divergence and within-species polymorphism. For the detection of recent positive selection events, we used the Derived Intra-allelic Nucleotide Diversity (DIND) test, based on the ίττ_Α/ίττ₀ ratio, where ίπ_Α and ίττ₀ are the levels of nucleotide diversity associated with the haplotypes carrying the ancestral and the derived alleles, respectively (Barreiro et al., 2009). This test is based on the rationale that a derived allele under positive selection present at high frequency in the population should display lower levels of nucleotide diversity at linked sites than expected and therefore a ίττ_Α/ίττ₀ ratio higher than expected . Singletons and doubletons were excluded from this analysis. To define statistical significance, the ίττ_Α/ίττ₀ values estimated for all I FNs and their receptors were compared against a background distribution obtained by means of 10⁴ simulations of the genomic regions concerned, conditional on the number of segregating sites and the recombination rate of the regions, and integrating the demographic models previously described (Laval et al., 2010; Voight et al., 2005). We also used tests based on levels of extended haplotype homozygosity, such as the integrated Haplotype Score (iHS) (Voight et al., 2006). These tests share a similar rationale: an allele that has a high population frequency and that is associated with an unusually long-range haplotype as compared to genome-wide expectations is likely to have been targeted by recent positive selection. This is explained by the rapid increase in allele frequency of the advantageous allele meaning that recombination will not have enough time to substantially break down the haplotype on which the selected mutation arose (reviewed in (Nielsen et al., 2007)). We assessed the levels of population differentiation for the entire SNP panel, using the F_ST statistics derived from the analysis of variance (ANOVA) (Excoffier et al., 1992). We identified SN Ps presenting extreme levels of population differentiation, a signature of positive selection (Barreiro et al., 2008; Nielsen et al., 2007; Sabeti et al., 2006), by comparing the observed F_ST values for individual SNPs in the genes studied here with a genome-wide F_ST distribution. This was calculated using -640,000 SNPs genotyped in the same subset of individuals from the HGDP-CEPH dataset (Li et al., 2008), with the exception of five individuals who were not genotyped. Because F_ST values depend on allele frequencies, F_ST comparisons were confined to SNPs presenting similar allele frequencies (i.e., similar expected heterozygosities). Empirical P-values for each SN P in the 27 genes were estimated as previously described (Barreiro et al., 2009). As the genome-wide F_ST distribution of the HGDP-CEPH dataset, used here to represent the neutral distribution, includes loci targeted by positive selection (Pickrell et al., 2009), the comparison of F_ST values of IFNs against this distribution represents a highly conservative approach to detecting selection. We defined genes under selection conservatively as those (i) for which significant results were obtained after both demographic corrections or for which results are significant at the genome-wide level, and (ii) for which significant results were obtained in at least two tests of selection based on different aspects of the data (e.g., allele frequency spectrum tests and F_ST) in the same population. To test the robustness of our results, and to prevent the detection of false positive signatures of positive selection, we measured the probability, within and between the genes in our dataset, of observing neutral simulations exhibiting "significant" results. Specifically, we calculated the number of simulations that exhibit at least two significant tests among Tajima's D, DIND test and F_ST, for each gene given the observed P-values, and corrected by the number of genes in our dataset (27 genes). The functional impact of all amino acid-altering mutations (benign, possibly damaging or probably damaging) was predicted with the Polyphen algorithm v2 HumDiv (Adzhubei et al., 2010). This method, which takes into account protein structure and/or sequence conservation information for each gene, has been shown to be the best predictor of the fitness effects of amino acid substitutions (Williamson et al., 2005).

RESULTS

To obtain insight into the selective forces that have driven the evolution of the three families of IFNs in humans, we characterized the levels of sequence-based diversity in the 21 genes encoding the IFNs and the 6 genes encoding their receptor chains, by full resequencing in a panel of 186 healthy individuals originating from sub- Saharan Africa, Europe, and Asia. We sequenced a total of 81.5 kb in each individual - 24% of which corresponded to protein-coding regions, the rest comprising noncoding exons, introns, and promoter regions (Table S1 ) - and identified 1 ,066 polymorphisms, including 988 single-nucleotide polymorphisms (SNPs) and 78 insertions/deletions (Table S2). This resequencing dataset was used to estimate several population genetic parameters and summary statistics that were, when relevant, compared with available genome-wide datasets based on genotyping or resequencing. These analyses allowed us to explore the effects of natural selection on I FN evolution since the divergence of the human and chimpanzee lineages and within different human populations. Naturally occurring genetic diversity varies between IFNs and populations

We observed remarkable differences in the levels of nucleotide diversity within the population between the genes encoding the various IFNs and their receptors and between IFN families (Fig. 1 and Table S3). The extremely low level of nucleotide diversity observed for the type II IFNG , which was uniform across populations, contrasted with several type I IFNA genes, such as IFNA4 , IFNA7 , IFNA 10 , IFNA16 , IFNA 17 , and IFNA21 , which displayed high levels of diversity (Fi g . 1 A ). I n accordance with the "Out of Africa" model (Lewin, 1987) and genome-wide datasets (i.e., HapMap and 1 ,000 Genomes Project; Altshuler et al., 2010 ; Durbin et al., 2010 ), African populations generally displayed the highest levels of diversity. However, one third of the IFN genes (mostly type I IFNA genes: IFNA4 , IFNA5 , IFNA6 , IFNA7 , IFNA 14 and IFNA 17 ) were most diverse in the Asian population , which in turn presented the lowest diversity for the three members of the type III IFN family (Fig. 1 and Table S3). Because the type I IFNA genes, as well as the three type III IFN genes, display high levels of sequence identity and are organized into two distinct clusters of paralogous genes (Pestka et al., 2004 ; Woelk et al., 2007), gene conversion is likely to have been an important mechanism for the evolution of these gene families. Indeed, in multigene families, gene conversion among paralogous loci has been shown to play an important role in the introduction of genetic variation to each gene ( I nnan and Kondrashov, 2010 ; Ohta, 2000, 2010 ). We thus evaluated the extent to which gene conversion has contributed to the levels of nucleotide diversity observed at these two groups of IFN genes. To do so, we screened highly homologous regions among paralogs for the presence of human-specific sites (polymorphic or fixed) that have been most likely introduced by gene conversion events rather than by point mutations (Materials and methods). This analysis allowed us to detect a substantial number of putative gene conversion events (Table S4), 30 of which corresponded to polymorphic amino acid-altering mutations (Table S5). As gene conversion is usually disregarded in population genetics tests, owing to the uncertainty associated with the underlying models of gene conversion, all variants identified as resulting from gene conversion were not considered in the statistical analyses to detect natural selection. Functional diversity is not evenly distributed between human IFNs

We identified 245 SNPs in coding regions, including 164 nonsynonymous and 8 nonsense mutations present in the general human population. The occurrence and frequency distribution of these variants differed markedly between the various IFNs and between populations (Fig.2, Table 1 , and Table S3). IFNs with very low levels of amino acid-altering variation are represented by IFNG, in which no nonsynonymous mutations were observed, and by a group of type I IFNs ( IFNA2 , IFNA5 , IFNA6 , IFNA8 , IFNA13 , IFNA14 , IFNA21 , IFNB1 , IFNK , and IFNW1 ) and the two receptor subunits IFNGR1 and IL28RA , which presented nonsynonymous mutations at a low frequency within the population. In contrast, we found that 13 genes accumulated nonsynonymous variants at very high frequency in the human population (-30-100%; Fig. 2 and Table 1 ). Most of these variants were predicted to be benign by the PolyPhen algorithm (Adzhubei et al., 2010), but some genes, such as IFNA10 , IFNA 16 , IFNA17 , IFNAR1 , IL28A , and IL29 , presented high frequencies of missense mutations predicted to alter protein function (i.e., damaging mutations; Table 1 and Table S3).

The most extreme cases were those of IFNA10 and IFNE, for which nonsense mutations were present in the homozygous state, at high frequency, in several populations. For example, one of the nonsense mutations of IFNA 10 (SNP 60T>A,

C20STOP, rs101 19910), which is located i n the signal peptide, abolishes the translation of the entire protein. Surprisingly, this stop mutation has attained a worldwide frequency of 34%, ranging from 18% in Europeans to 54% in Asians. The IFNE nonsense mutation (SNP 21 10T, Q71 STOP, rs2039381 ) decreases the length of the protein by two thirds and has attained a worldwide frequency of 7%, increasing to 15% in Asia. Such high frequencies of nonsynonymous or nonsense mutations in some IFN genes may reflect either a relaxation of selective constraints caused by the redundancy of the genes concerned, or a selective advantage accounted for by the higher frequency of functionally advantageous variants.

Purifying selection has operated differently among IFN family members

We investigated whether and how natural selection has driven the observed heterogeneous patterns of diversity of the various I FNs and their receptors, by first estimating the direction and strength of selection within the human species as a whole. To this end, we measured d_s and d_N, i.e., the number of silent and nonsynonymous fixed differences between humans and chimpanzees, together with p_s and p_N, i.e., the number of silent and nonsynonymous polymorphic sites observed within humans. We used the McDonald-Kreitman Poisson random field method (Sawyer and Hartl, 1992 ; Bustamante et al., 2005 ) to estimate ω (i.e., ω α Θ_Ν / 9_S , where Θ_Ν and 9_S are estimates of the rate of nonsynonymous and silent mutations) and to assess the selection pressure driving amino acid substitutions. Under neutrality, ω i s n ot significantly different from 1. Values <1 indicate a deficit of nonsynonymous variants, whereas values >1 reflect an excess of amino acid changes. We found that only IFNA6 , IFNA8 , IFNA13 and IFNA14 , and IFNG had ω value signifi cantly <1 , consistent with their evolution under the strongest purifying selection (Fig. 3). Among type I IFNs, we removed from our analyses a few low-frequency nonsynonymous mutations that were found to result from gene conversion at IFNA6 , IFNA 13 , and IFNA14 , whereas no gene conversion events were detected at IFNA8 (Table S5). Our simulation analyses showed that the removal of gene conversion-derived events cannot produce spurious signals of purifying selection (Fig. 7). However, because of the minimal, but nonnull, uncertainty in our procedure for gene conversion detection, IFNA8 represents the most robust target of purifying selection among type I IFNs. At the other extreme, IL28B was the only gene that had a ω value significantly greater than 1 , consistent with the action of positive selection. Positive selection has targeted type III IFNs in non-African populations

We next investigated the ways in which positive selection has affected I FN genes in a population-specific manner, as populations from different continents have clearly been historically exposed to different selection pressures (Novembre and Di Rienzo, 2009 ). We performed various intraspecies neutrality tests on various aspects of the data, including the allele frequency spectrum (i.e., Tajima's D , Fu and Li's D ^* and F ^*, and Fay and Wu's H tests), levels of population differentiation (i.e., F_ST ), and haplotype-based tests (i.e., derived allele nucleotide diversity [DIND] and integrated haplotype score [iHS] tests; Kreitman, 2000 ; Nielsen et al., 2007 ). As most of these tests are known to be sensitive to the effects of demography and selection, we used simulation-based or empirical procedures to correct for the influence of demography on the patterns of population genetic diversity. For the allele frequency spectrum and DIND tests, we incorporated into our neutral expectations two demographic models based on multiple, noncoding genomic regions sequenced in a set of populations similar to those used here (Laval et al., 2010 ; Voight et al., 2005). For the population differentiation tests, we obtained a background expectation of genome-wide F_ST by analyzing the publicly available HGDP-CEPH dataset (Li et al., 2008) from the same set of individuals we sequenced in this study. I n addition , we complemented our analyses of recent positive selection by obtaining the iHS values for each SNP in the populations of the HapMap Phase-ll dataset (Frazer et al., 2007).

We defined genes under selection conservatively as those (a) for which significant results were obtained after both demographic corrections or for which results were significant at the genome-wide level, and (b) for which significant results were obtained in at least two tests of selection based on different aspects of the data (e.g., allele frequency spectrum tests and F_ST) in the same population. With these stringent criteria, most type I IFNs and the type I I IFN did not show compelling signatures of selection in any of the continental populations here studied. In contrast, we found that positive selection had strongly affected the members of the type III IFN family in European and Asian populations (Fig. 4, Fig. 5 , and Table 2). In addition, the results of the neutrality tests for type III IFNs remained significant after correction for multiple testing, emphasizing the intensity of the events of positive selection detected. The three type III IFN genes are adjacent to each other on an ~ 50-kb region of chromosome 19 (Fig. 6), but they nonetheless displayed low levels of linkage disequilibrium in all populations (Fig 8). This suggests that independent positive selection events have targeted IL28A, IL28B , and IL29 .

IL28A and IL28B deviated significantly from neutral expectations in the Asian population, in allele frequency spectrum tests (Table 2). Furthermore, the derived alleles of two SNPs in IL28A and five in IL28B were found to be associated with significantly lower levels of surrounding nucleotide diversity, given their high population frequency (>90%), in Asia (see the DIND test in Fig. 4 and Fig. 8). Interestingly, the two SNPs in IL28A and one in IL28B correspond to amino acid-altering variants (IL28A SNP 983G>A, A1 12T, rs8103362; IL28A SNP 12270T, H160Y, rs61735713; IL28B SNP 502G>A, R70K, rs8103142). These amino acid changes therefore appear to have increased in frequency more rapidly than would be expected under neutrality, in the Asian population, consistent with the action of population-specific positive selection. We also detected strong signals of positive selection at the IL29 locus. First, allele frequency spectrum tests detected a significant excess of rare variants in both Europeans and Asians (Table 2). Second, very high levels of population differentiation were observed at the IL29 locus between African and Eurasian populations (mean F_ST = 0.42). In particular, the nonsynonymous variant 2054G>A (D188N, rs30461 , predicted to be probably damaging by PolyPhen), presented extreme levels of differentiation between Africans and Eurasians (F_ST Africa/Asia = 0.71 , P = 0.014; F_ST Africa/Europe = 0.66, P = 0.025, using the HGDP-CEPH dataset; Fig. 5 ). Remarkably, this SNP not only presented the highest degree of population differentiation of all SNPs in our dataset but was also among the most highly differentiated SNPs at the level of the entire human genome. Indeed, the D188N variant falls into the group of 1 39 nonsynonymous SNPs presenting the largest allele frequency differences among populations in the 1 ,000 Genomes project (Durbin et al. 2010). In addition, this nonsynonymous variant gave a significant result for the DIND test in Asian populations (ίπΑ/ίπϋ = 3.71 , P < 0.01 ; Fig. 4) and gave a significant iHS value of 2.285 in Europeans from the HapMap Phase II dataset (his was not calculated for Asian HapMap populations, because this SNP has a frequency >95%). These results suggest that IL29 variation, and the D188N variant in particular, has conferred a selective advantage to Eurasian populations.

Chromosomal position (Chr. position) of each SNP is given according to the hgl9 (GRCh37) human assembly. "ATG" denotes the nucleotide position of each SNP; +1 corresponding to the "A" of the "ATG". The position of each SNP was determined using the reference sequence listed in Table SI. "AA change" denotes the amino acid change. For both the ATG nucleotide position and the amino acid change, the first variant corresponds to the ancestral form and the second to the derived form. PolyPhen v2 HumDiv predictions are as follows: BEN, benign; PSD, possibly damaging; and PRD, probably damaging. The frequencies of both derived allele frequencies and genotypes are given in %. Genotype frequencies: A/A = homozygous for the ancestral allele; A/D = heterozygous; D/D = homozygous for the derived allele.

Acceptor sites in acceptor genes are polymorphic SNPs whose derived allele has probably been brought about by gene conversion from a donor gene. The 40 bp around the acceptor site must be >90% identical with the 40 bp fragment around the donor site. The donor site can be either polymorphic or fixed (see Methods).

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Claims

1 . Method for treating cancer or viral infection in a patient in need thereof, comprising the administration of a combination of at least two interferons (I FNs) chosen in the group consisting of: I FNA2, IFNA5, IFNA6, I FNA8, I FNA13, IFNA14, I FNA21 , IFNB1 , IFNK and IFNW1 .

2. Method according to claim 1 , wherein said combination contains at least IFNA8 or IFNA 6.

3. Method according to claim 1 , wherein said combination contains at least IFNA6 and IFNA8.

4. Method according to any one of claim 1 to 3, wherein three interferons are administered.

5. Method according to any one of claim 1 to 4, wherein said viral infection is Hepatitis C.

6. Method for identifying efficient anti-cancer or anti-viral agents, comprising the steps of:

- contacting said agents with IFN receptor IFNGR1 and/or IL28RA,

- detecting if said agent is an agonist of said IFN receptor.

7. Method according to claim 6, wherein said agent is an agonist of I FNGR1 and IL28RA.

8. Method for treating cancer or viral infection in a patient in need thereof, comprising the steps of:

- testing if the protein sequence of the endogenous IL28A interferon of said patient contains an Alanine in position 1 12 and/or an Histidine in position 160, and - administering IL28A interferon of SEQ ID NO:2 if said endogenous I L28A protein contains an Alanine in position 1 12 and/or an Histidine in position 160.

9. Method for treating cancer or viral infection in a patient in need thereof, comprising the steps of:

- testing if the protein sequence of the endogenous I L28B interferon of said patient contains an Arginine in position 70, or - testing if the IL28B gene of said patient contains the nucleotides: -37C

(position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and

- administering IL28B interferon of SEQ ID NO:4 if said endogenous IL28B protein contains an Arginine in position 70 or if said IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ I D NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3).

10. Method for treating cancer or viral infection in a patient in need thereof, comprising the steps of: - testing if the protein sequence of the endogenous I L29 interferon of said patient contains an Aspartic acid in position 188, and

- administering IL29 interferon of SEQ ID NO:6 if said endogenous IL29 protein contains an Aspartic acid in position 188.

1 1 . Method for treating cancer or viral infection in a patient in need thereof, comprising the steps of: i) sequencing the endogenous sequence of at least one interferon gene chosen in the group consisting of: IFNA2, IFNA5, IFNA6, IFNA8, IFNA 13, IFNA 14, IFNA21, IFNB1, IFNK and IFNW1; ii) identifying if said at least one sequence contains a nonsense mutation or a stop mutation, iii) administering to the patient the wild type form of the corresponding IFN protein in case said at least one sequence contains a nonsense mutation or a stop mutation.

12. Method for treating cancer or viral infection in a patient in need thereof, comprising the steps of: a) testing if the protein sequence of the endogenous I L28A interferon of said patient contains an Alanine in position 1 12 and/or an Histidine in position 160, and b1 ) testing if the protein sequence of the endogenous IL28B interferon of said patient contains an Arginine in position 70, or b2) testing if the IL28B gene of said patient contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), c) administering a pharmaceutical composition containing IL28A interferon of

SEQ ID NO:2 and I L28B interferon of SEQ ID NO:4 if said endogenous IL28A protein contains an Alanine in position 1 12 and/or an Histidine in position 160 and if said endogenous IL28B protein contains an Arginine in position 70 or if said IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3).

13. Method for treating cancer or viral infection in a patient in need thereof, comprising the steps of: a) testing if the protein sequence of the endogenous I L28A interferon of said patient contains an Alanine in position 1 12 and/or an Histidine in position 160, and b) testing if the protein sequence of the endogenous I L29 interferon of said patient contains an Aspartic acid in position 188, c) administering a pharmaceutical composition containing IL28A interferon of SEQ ID NO:2 and IL29 interferon of SEQ ID NO:6 if said endogenous IL28A protein contains an Alanine in position 1 12 and/or an Histidine in position 160 and if said endogenous IL29 protein contains an Aspartic acid in position 188.

14. Method for treating cancer or viral infection in a patient in need thereof, comprising the steps of: a) testing if the protein sequence of the endogenous I L29 interferon of said patient contains an Aspartic acid in position 188, and b1 ) testing if the protein sequence of the endogenous IL28B interferon of said patient contains an Arginine in position 70, or b2) testing if the IL28B gene of said patient contains the nucleotides: -37C

(position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and c) administering a pharmaceutical composition containing I L29 interferon of SEQ ID NO:6 and IL28B interferon of SEQ ID NO:4 if said endogenous IL29 protein contains an Aspartic acid in position 188 and if said endogenous IL28B protein contains an Arginine in position 70 or if said IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3).

15. Method for treating cancer or viral infection in a patient in need thereof, comprising the steps of: a) testing if the protein sequence of the endogenous I L29 interferon of said patient contains an Aspartic acid in position 188, and b1 ) testing if the protein sequence of the endogenous IL28B interferon of said patient contains an Arginine in position 70, or b2) testing if the IL28B gene of said patient contains the nucleotides: -37C

(position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), c) testing if the protein sequence of the endogenous I L28A interferon of said patient contains an Alanine in position 1 12 and/or an Histidine in position 160, d) administering a pharmaceutical composition containing I L28A interferon of

SEQ ID NO:2, IL29 interferon of SEQ ID NO:6 and IL28B interferon of SEQ ID NO:4, if said endogenous I L29 protein contains an Aspartic acid in position 188, if said endogenous IL28B protein contains an Arginine in position 70 or if said IL28B gene contains the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ ID NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and if said endogenous I L28A protein contains an Alanine in position 1 12 and/or an Histidine in position 160.

16. A pharmaceutical composition containing I L28A interferon of SEQ I D NO:2, IL29 interferon of SEQ ID NO:6 and IL28B interferon of SEQ ID NO:4.

17. A pharmaceutical composition containing IL28A interferon of SEQ I D NO:2, I L29 interferon of SEQ ID NO:6 and IL28B interferon of SEQ ID NO:4, for use for treating cancer or a viral infection in a patient in need thereof.

18. The pharmaceutical composition for use according to claim 17, wherein said patient exhibits an endogenous IL29 protein containing an Aspartic acid in position 188, an endogenous IL28B protein containing an Arginine in position 70 or an IL28B gene containing the nucleotides: -37C (position 351 1 in SEQ ID NO:3), -3180A (position 368 in SEQ ID NO:3), 685C (position 4232 in SEQ I D NO:3) and / or 1388T (position 4935 in SEQ ID NO:3), and an endogenous IL28A protein containing an Alanine in position 1 12 and/or an Histidine in position 160.