Comparative efficacy of two next-generation Rift Valley fever vaccines

Rift Valley fever virus (RVFV) is a re-emerging zoonotic bunyavirus of the genus Phlebovirus. A natural isolate containing a large attenuating deletion in the small (S) genome segment previously yielded a highly effective vaccine virus, named Clone 13. The deletion in the S segment abrogates expression of the NSs protein, which is the major virulence factor of the virus. To develop a vaccine of even higher safety, a virus named R566 was created by natural laboratory reassortment. The R566 virus combines the S segment of the Clone 13 virus with additional attenuating mutations on the other two genome segments M and L, derived from the previously created MP-12 vaccine virus. To achieve the same objective, a nonspreading RVFV (NSR-Gn) was created by reverse-genetics, which not only lacks the NSs gene but also the complete M genome segment. We have now compared the vaccine efficacies of these two next-generation vaccines and included the Clone 13 vaccine as a control for optimal efficacy. Groups of eight lambs were vaccinated once and challenged three weeks later. All mock-vaccinated lambs developed high fever and viremia and three lambs did not survive the infection. As expected, lambs vaccinated with Clone 13 were protected from viremia and clinical signs. Two lambs vaccinated with R566 developed mild fever after challenge infection, which was associated with low levels of viral RNA in the blood, whereas vaccination with the NSR-Gn vaccine completely prevented viremia and clinical signs.     

汉滩型与汉城型汉坦病毒基因重排的初步研究

目的：探讨汉坦病毒汉滩型与汉城型之间能否发生基因重排以及发生重排的频率和特点。方法：用汉坦病毒汉滩型76－118株与汉城型SR－11株混合感染VeroE6细胞，空斑形成试验挑取子代病毒克隆株，分型聚合酶链反应方法鉴定子代病毒基因型。结果：大部分（68．19％）子代病毒的基因组来自7－118株或SR－11株；2株（4．55％）两型引物扩增均为阳性；2株（4．45％）两型引物扩增均为阴性；5株（11．36％）发生了M片段重排，3株（6．82％）发生了L片段重排，未发现S片段重排；1株M片段来自双亲株，1株S片段为双倍体。结论：证实汉坦病毒I型与II型之间可以发生重排。     

Mutations to A/Puerto Rico/8/34 PB1 gene improves seasonal reassortant influenza A virus growth kinetics

It is desirable for influenza vaccine virus strains to have phenotypes that include good growth and hemagglutinin (HA) protein yield. The quality of these characteristics varies among the vaccine viruses and is usually due to multigenic effects. Many influenza A virus vaccine viruses are made as reassortants of the high yield virus A/Puerto Rico/8/34 (PR/8) and a circulating seasonal virus. Co-infection of eggs with the two viruses, and selection of reassortants with the HA and neuraminidase (NA) segments from the seasonal virus, can result in viruses that contain a mixture of internal genes derived from both the high yield virus and the circulating virus. Segment 2 (PB1), which encodes the RNA-dependent RNA polymerase, frequently cosegregates with the seasonal HA and NA segments. We asked whether mutations based on the seasonal PB1 genes could improve vaccine virus strains. Here we report that mutations to the PR/8 PB1 gene, based on differences observed between seasonal and PR/8 PB1 genes, accelerate egg and cell culture based replication for a reassortant virus containing HA and NA segments from the low yield A/Wyoming/03/2003 (H3N2) vaccine virus.     

汉坦病毒76—118株与R22株基因重排的实验研究

目的；研究汉坦病毒汉滩型与汉城型之间能否发生基因重排，以及发生重排的频率和特点。方法：用汉坦病毒汉滩型（HTNV）76－118株与汉城型（SEOV）R22株混合感染Vero-E6细胞，空斑形成实验挑取子代克隆株24株，传供培养后用PCR方法鉴定。结果：发现24株子代病毒（70.83%)的基因组来自76－118株或R22株；1株（4.17%)HTNV型与SEOV型引物扩增均为阳性；1株（4.17%)两型病毒引物扩增均为阴性；4株（16.67%)发生了基因片段重排。结论：证实了汉坦病毒HTNV与SEOV之间可以发生重排。     

Characterization of the M protein and nucleoprotein genes of an avian influenza A virus which are involved in host range restriction in monkeys

A reassortant virus possessing RNA segment 7, which codes for the M1 and M2 proteins, of the avian influenza A/Mallard/New York/6750/78 (H2N2) virus and the other seven RNA segments of the human influenza A/Udorn/307/72 (H3N2) virus had been shown previously to be markedly restricted in replication in the respiratory tract of squirrel monkeys. In contrast, a reassortant possessing segment 7 of another avian influenza virus, A/Pintail/Alberta/119/79 (H4N6), and the seven other RNA segments from the A/Udorn/72 virus was not restricted. The nucleotide and deduced amino acid sequence of the RNA segment 7 of each virus was determined to identify the structural basis for the attenuation phenotype specified by RNA segment 7 of the A/Mallard/78 virus. Analysis of the deduced amino acid sequences revealed only two amino acid differences in the M1 protein and one difference in the M2 protein, suggesting that the attenuation phenotype of a reassortant virus possessing segment 7 of the A/Mallard/78 virus may be specified by one to three amino acids. Reassortant viruses possessing RNA segment 6, which codes for the nucleoprotein, of either avian influenza virus and the other seven RNA segments of a human influenza virus were also restricted in replication in squirrel monkeys. A comparison of the deduced amino acid sequences of the two avian nucleopeoteins demonstrated only three amino acid differences indicating that these two avian viruses possess NP genes that are highly related. The high degree of relatedness of both the NP and M proteins of these two avian viruses contrasts with their divergent surface antigens. The structural basis for the attenuation phenotype of the NP gene of the A/Mallard/78 virus is being investigated.     

Generation of a reassortant avian influenza virus H5N2 vaccine strain capable of protecting chickens against infection with Egyptian H5N1 and H9N2 viruses

BackgroundAvian influenza H5N1 viruses have been enzootic in Egyptian poultry since 2006. Avian influenza H9N2 viruses which have been circulating in Egyptian poultry since 2011 showed high replication rates in embryonated chicken eggs and mammalian cells.MethodsTo investigate which gene segment was responsible for increasing replication, we constructed reassortant influenza viruses using the low pathogenic H1N1 PR8 virus as backbone and included individual genes from A/chicken/Egypt/S4456B/2011(H9N2) virus. Then, we invested this finding to improve a PR8-derived H5N1 influenza vaccine strain by incorporation of the NA segment of H9N2 virus instead of the NA of H5N1. The growth properties of this virus and several other forms of reassortant H5 viruses were compared. Finally, we tested the efficacy of this reassortant vaccine strain in chickens.ResultsWe observed an increase in replication for a reassortant virus expressing the neuraminidase gene (N2) of H9N2 virus relative to that of either parental viruses or reassortant PR8 viruses expressing other genes. Then, we generated an H5N2 vaccine strain based on the H5 from an Egyptian H5N1 virus and the N2 from an Egyptian H9N2 virus on a PR8 backbone. This strain had better replication rates than an H5N2 reassortant strain on an H9N2 backbone and an H5N1 reassortant on a PR8 backbone. This virus was then used to develop a killed, oil-emulsion vaccine and tested for efficacy against H5N1 and H9N2 viruses in chickens. Results showed that this vaccine was immunogenic and reduced mortality and shedding.DiscussionOur findings suggest that an inactivated PR8-derived H5N2 influenza vaccine is efficacious in poultry against H5N1 and H9N2 viruses and the vaccine seed replicates at a high rate thus improving vaccine production.     

The development and characterization of H5 influenza virus vaccines derived from a 2003 human isolate

The pandemic threat posed by highly pathogenic H5N1 influenza A viruses has created an urgent need for vaccines to protect against H5 virus infection. Because pathogenic viruses grow poorly in chicken eggs and their virulence poses a biohazard to vaccine producers, avirulent viruses produced by reverse genetics have become the preferred basis for vaccine production. Here, we investigated two key characteristics of potential H5 vaccine candidates: the hemaggutinin (HA) cleavage site sequence and its modification to attenuate virulence and the choice of background virus to provide a high-growth rate. We produced recombinant (6:2 reassortant) viruses that possessed a series of modified avirulent-type HA and neuraminidase genes, both of which were derived from an H5N1 human isolate. The other genes of these recombinant viruses were derived from donor virus strains known to grow well in eggs: the human strain A/Puerto Rico/8/34 (PR8) or an avian strain. All of the recombinant viruses grew well in eggs, were avirulent in chicks, and protected animals against infection with a wild-type virus. However, one of the recombinant viruses with an avian virus background acquired a mutation in the HA cleavage site sequence that conferred virulence potential to this virus. Moreover, vaccine candidates with the avian virus background were more virulent than those with the human virus background. We conclude that 6:2 recombinant viruses with a PR8 background are more suitable than those with an avian virus background for vaccine development and that the HA cleavage site sequence must be modified to minimize the potential for a vaccine virus to convert to a virulent form.     

A point mutation in the polymerase protein PB2 allows a reassortant H9N2 influenza isolate of wild-bird origin to replicate in human cells

H9N2 influenza A viruses are on the list of potentially pandemic subtypes. Therefore, it is important to understand how genomic reassortment and genetic polymorphisms affect phenotypes of H9N2 viruses circulating in the wild bird reservoir. A comparative genetic analysis of North American H9N2 isolates of wild bird origin identified a naturally occurring reassortant virus containing gene segments derived from both North American and Eurasian lineage ancestors. The PB2 segment of this virus encodes 10 amino acid changes that distinguish it from other H9 strains circulating in North America. G590S, one of the 10 amino acid substitutions observed, was present in ~ 12% of H9 viruses worldwide. This mutation combined with R591 has been reported as a marker of pathogenicity for human pandemic 2009 H1N1 viruses. Screening by polymerase reporter assay of all the natural polymorphisms at these two positions identified G590/K591 and S590/K591 as the most active, with the highest polymerase activity recorded for the SK polymorphism. Rescued viruses containing these two polymorphic combinations replicated more efficiently in MDCK cells and they were the only ones tested that were capable of establishing productive infection in NHBE cells. A global analysis of all PB2 sequences identified the K591 signature in six viral HA/NA subtypes isolated from several hosts in seven geographic locations. Interestingly, introducing the K591 mutation into the PB2 of a human-adapted H3N2 virus did not affect its polymerase activity. Our findings demonstrate that a single point mutation in the PB2 of a low pathogenic H9N2 isolate could have a significant effect on viral phenotype and increase its propensity to infect mammals. However, this effect is not universal, warranting caution in interpreting point mutations without considering protein sequence context.     

Characterization of the attenuating M and NP gene segments of the avian influenza A/Mallard/78 virus during in vitro production of avian-human reassortant vaccine viruses and after replication in humans and primates

A unique requirement for live attenuated reassortant influenza vaccines is the need to generate new reassortant vaccine viruses with the appearance of each new antigenic variant. Thus, the attenuation phenotype conferred by the attenuated donor influenza virus must remain genetically stable during the generation of each new reassortant vaccine virus. In this study we used nucleotide sequence analysis to evaluate the genetic stability of the attenuating M and NP genes of the avian influenza A/Mallard/NY/6750/78 attenuated donor virus during the in vitro generation and subsequent in vivo replication of avian-human (AH) influenza A reassortant vaccine viruses in monkeys and humans. Nucleotide sequence changes in the M and NP genes occurred at a rate of approximately 0.61 substitutions/1000 nt/reassortant during in vitro generation of four AH reassortant viruses. Only two nucleotide sequence changes occurred in the M and NP gene segments of four isolates of H1N1 or H3N2 AH vaccine viruses following 6-8 days of replication in seronegative children, and neither change affected amino acids previously identified as playing a potential role in attenuation. In addition, there were no changes in the nucleotide sequence of the M and NP genes of single gene AH reassortant viruses following five serial passages in squirrel monkeys. Finally, there was no change in the level or duration of replication of the single gene reassortant viruses in the upper or lower respiratory tract of monkeys following serial passage.(ABSTRACT TRUNCATED AT 250 WORDS)     

Improvement of H5N1 influenza vaccine viruses: influence of internal gene segments of avian and human origin on production and hemagglutinin content

The H5N1-clade 1 influenza vaccine strain NIBRG-14 produces exceptionally low amounts of antigen, a problem recently encountered also for initial pandemic H1N1-2009 vaccine seeds. Here, we report on a strategy that may contribute to overcome this obstacle. Influenza vaccine viruses usually consist of two segments coding for the antigenic HA and NA proteins of a wild-type strain and the six residual internal gene segments of the vaccine donor strain A/PR/8/34 (PR8). To enhance the antigen yield from H5N1 vaccine virus we generated by reverse genetics a set of PR8-based reassortant viruses expressing the HA and NA segments of the prototypic strain A/Vietnam/1203/2004 and additional replacements of the internal M or PB1 genes of PR8. The reassortants were compared to the parental PR8 and H5N1 viruses in terms of growth in embryonated chicken eggs and the amount of incorporated antigenic HA protein. Compared to NIBRG-14, three out of six viruses displayed an increased replication in embryonated chicken eggs and higher HA content that was also maintained after ether/detergent extraction of virions. Electron microscopic analysis showed that the reassortment hardly affected particle shape and size. Two selected H5N1 reassortant viruses were investigated concerning their pathogenicity in ferrets and found to behave as low pathogenic as the PR8 donor strain. In conclusion, this study shows that replication and antigen content of PR8-derived H5N1 influenza vaccine viruses can be improved by incorporation of heterologous internal gene segments without compromising their attenuated character.     

Genetic characterization and molecular clock analyses of the Crimean-Congo hemorrhagic fever virus from human and ticks in India, 2010–2011

A nosocomial outbreak of Crimean Congo hemorrhagic fever (CCHF) was reported among humans in Ahmadabad district, Gujarat, India during January, 2011. In the present study we provide the complete genomic sequences of four CCHFV isolates derived from two human patients and two pools of Hyalomma anatolicum ticks during the period of this outbreak and the complete S segment sequence of two retrospective human serum samples, positive for CCHFV in 2010. Sequence-based molecular characterization of the Indian CCHFV showed that they possessed the functional motifs known to occur in the S, M and L gene segment products as in other CCHF viruses. The S segment of the six Indian CCHF viruses showed 99.8% nucleotide identity. Notably both tick isolates shared 100% nucleotide identity with one of the Indian human isolates of 2011. Phylogenetic analysis based on the S segment demonstrated that the Indian CCHFV isolates formed a distinct cluster in the Asian-Middle East group IV of CCHF viruses. The S segment was closest to a Tajikistan strain TADJ/HU8966 of 1990 (98.5% nucleotide identity) and was of South-Asia 2 type while the M segment was of type M2. Both M and L segments were closest to an Afghanistan strain Afg09-2990 of 2009 (93% and 98% nucleotide identity, respectively). The Indian isolates were thus identified as a South-Asia 2/M2 far-east virus combination and the differing parental origin in the S and L/M segments is suggestive that it may be an intra-genotypic reassortant. Molecular clock studies further revealed that the ancestry of the viruses was not very recent and dated back to about 33 years on the basis of the S segment while it was about 15 years based on the M segment. Thus though the 2011 outbreak may not have resulted from a very recent introduction, considering that so far there is no evidence of multiple circulating strains in the country, the possibility of a recent re-introduction of the virus from any of the neighboring countries cannot be ruled out. The study thus warrants the need for continued surveillance and increased sampling of CCHFV in different parts of the country.     

Development of high yield reassortants for influenza type B viruses and analysis of their gene compositions

A critical step in producing the annual inactivated influenza vaccine is the development of high yield (hy) seed viruses by reassortment for improved growth in ovo. Although hy reassortants for type A influenza viruses have been developed for many years, hy B influenza reassortant virus development for vaccine production has proven difficult. In this study, we have developed fourteen hy influenza type B reassortants as vaccine candidate strains with B/Lee/40 as the donor virus. Upon characterization by the Influenza Division at the Centers for Disease Control and Prevention (CDC) and the verification of HA by sequencing, all B reassortants were found to be antigenically indistinguishable from the wild type (wt) parents and suitable for vaccine production. However, only one hy reassortant seed virus from this group was used by a manufacturer for vaccine production. In general, hy reassortants showed an increase in hemagglutination (HA) titers over their wt parents by approximately 8 fold (range 1–32 fold). Gene compositions of the hy B reassortants were analyzed by restriction fragment length polymorphism (RFLP) and the wt origin of the HA and neuraminidase (NA) were confirmed. However, in contrast to hy A reassortants which require the M gene (hy donor A/PR/8/34) for high yield, all fourteen hy B reassortants obtained the NP gene from the hy donor strain (B/Lee/40). The parental source for the remaining genes varied among the hy B reassortants. The results indicate that the B/Lee/40 NP and PB1 gene segments are important contributors to high yield growth in influenza B reassortant viruses for both Yamagata and Victoria lineages. The B/Lee/40 PB2 gene along with wt NS gene also contributed to the improved growth for hy reassortants of Yamagata lineage.     

Generation of an attenuated H5N1 avian influenza virus vaccine with all eight genes from avian viruses

In the face of disease outbreaks in poultry and the potential pandemic threat to humans caused by the highly pathogenic avian influenza viruses (HPAIVs) of H5N1 subtype, improvement in biosecurity and the use of inactivated vaccines are two main options for the control of this disease. Vaccine candidates of influenza A viruses of H5N1 subtype have been generated in several laboratories by plasmid-based reverse genetics with hemagglutinin (HA) and neuraminidase (NA) genes from the epidemic strains of avian viruses in a background of internal genes from the vaccine donor strain of human strains, A/Puerto Rico/8/34 (PR8). These reassortant viruses containing genes from both avian and human viruses might impose biosafety concerns, also may be do if C4/F AIV would be a live attenuated vaccine or cold-adaptive strain vaccine. In order to generate better and safer vaccine candidate viruses, we genetically constructed attenuated reassortant H5N1 influenza A virus, designated as C4/F AIV, by plasmid-based reverse genetics with all eight genes from the avian strains. The C4/F AIV virus contained HA and NA genes from an epidemic strain A/Chicken/Huadong/04 (H5N1) (C4/H5N1) in a background of internal genes derived from a low pathogenic strain of A/Chicken/F/98(H9N2). The reassortant virus was attenuated by removal of the multibasic amino acid motif in the HA gene by mutation and deletion (from PQRERRRKKR (downward arrow) G to PQIETR (downward arrow) G). The intravenous pathogenicity index (IVPI) of C4/F AIV virus was 0, whereas that of the donor virus C4/H5N1 was 3.0. The virus HA titer of C4/H5N1 in the allantoic fluid from infected embryonated eggs was as high as 1:2048. The inactivated vaccine prepared from the reassortant virus C4/F AIV-induced high HI titer in vaccinated chickens and gave 100% protection when challenged with highly pathogenic avian influenza virus of H5N1 subtype.     

Genetic stability of live, cold-adapted influenza virus components of the FluMist/CAIV-T vaccine throughout the manufacturing process

FluMist is a live-attenuated, trivalent influenza vaccine (LAIV) recently approved for intranasal administration. To demonstrate genetic stability during manufacture of the vaccine viruses in LAIV and a similar vaccine in development (CAIV-T), full genome consensus sequences were determined at multiple manufacturing stages for four influenza type A and five type B strains. The critical cold-adapted (ca), temperature-sensitive (ts) and attenuated (att) mutations were preserved in the virus manufacturing intermediates. Moreover, sequence identity was observed for all vaccine intermediates of the same strain. Minor sequence differences were noted in the shared gene segments of the vaccine viruses and their common progenitor master donor virus (MDV) and several of the hemagglutinin (HA) and neuraminidase (NA) genes contained nucleotide differences when compared to the wild-type parent. Nonetheless, all vaccine viruses retained the ca, ts, and att phenotypes. Thus, genetic and phenotypic stability of the vaccine viruses is maintained during the manufacture of LAIV/CAIV-T vaccines.     

贵阳市2012-2015年B型流行性感冒病毒血凝素基因特性分析

目的 了解2012-2015年贵阳市B型流行性感冒（以下简称流感）病毒的变异和流行特点,分析其与WHO推荐的疫苗株和我国的代表株匹配情况。方法 将21份标本进行血凝素基因片段1（haemagglutinin 1,HA1）基因序列测定,通过DNA Star version 7.1等软件对测序产物进行分析。结果 贵阳市B型流感病毒存在BY和BV两种谱系;核苷酸同源性显示,BV系与疫苗株B/Brisbane/60/2008的同源性为97.8%~99.3%;2013-2014年BY系与疫苗株B/Massachusetts/02/2012的同源性为96.2%~96.5%,与既往的疫苗株B/Wisconsin/01/2010同源性为99.0%~99.3%;2015年BY系与疫苗株B/PHUKET/3073/2013同源性为99.2%~99.5%;2012-2015年BV系与我国代表株B/Chongqing-Yuzhong/1384/2010同源性为96.8%~99.0%,BY系与种子疫苗株B/Hubei-Wujiagang/158/2009为98.2%~99.2%。与当年度疫苗株相比,2013-2014年BY系毒株有9个氨基酸位点发生变异,其中A134P位点涉及到抗原决定簇A区,N142K涉及到B区;2015年BY系毒株发生新的L198Q变异,且涉及到D区;BV系氨基酸位点替换多样,但很少涉及到抗原决定簇。结论 2012-2015年贵阳市人群中B型流感病毒在不断地发生改变,除2013-2014年疫苗株与流行株匹配性不佳以外,其余年度的匹配性均较好,能起到保护作用。     

Possible outcomes of reassortment in vivo between wild type and live attenuated influenza vaccine strains

Reassortment of influenza viruses in nature has been well documented. Genetic reassortment plays a key role in emergence of new influenza A strains, including pandemic viruses. Permissive host can be simultaneously coinfected with multiple influenza viruses. During genetic reassortment gene segments are exchanged between parental viruses that may lead to some enhancement of virulence of reassortant progeny. At present, vaccination with live attenuated cold-adapted (ca) reassortant vaccine (LAIV) is used as an effective public health measure for influenza prophylaxis. However, there are concerns about a potential of simultaneous infection of human host with ca and wild type (wt) influenza viruses which might produce progeny that contain novel, more virulent genotypes. The aim of this study was to investigate potential consequences of reassortment of wt with LAIV strains in vivo.     

Efficacy of a recombinant Rift Valley fever virus MP-12 with NSm deletion as a vaccine candidate in sheep

Rift Valley fever virus (RVFV), a mosquito-borne virus in the Bunyaviridae family and Phlebovirus genus, causes RVF, a disease of ruminants and man, endemic in Sub-Saharan African countries. However, outbreaks in Yemen and Saudi Arabia demonstrate the ability for RVFV to spread into virgin territory and thus the need exists to develop safe and efficacious vaccines that can be used outside the endemic zones. Commercial RVFV vaccines are available but have limitations that prevent their use in disease-free countries. Consequently, there are ongoing efforts to develop and/or improve RVFV vaccines with global acceptability. In this study a previously developed MP-12-derived vaccine candidate with a large deletion of the NSm gene in the pre Gn region of the M segment (arMP-12-ΔNSm21/384) developed by T. Ikegami, that was already shown to be safe in pregnant sheep causing neither abortion nor fetal malformation was further evaluated. This vaccine was tested for protection of sheep from viremia and fever following challenge with virulent RVFV ZH501 strain. A single vaccination with arMP-12-ΔNSm21/384 fully protected sheep when challenged four weeks post vaccination, thereby demonstrating that this vaccine is efficacious in protecting these animals from RVFV infection.     

The phosphoprotein of attenuated measles AIK-C vaccine strain contributes to its temperature-sensitive phenotype

Measles AIK-C vaccine strain exhibits temperature-sensitivity (ts). To identify the structural proteins, which contribute to the ts property of AIK-C virus, reverse genetics was used. MV-minigenome RNA was replicated at 32.5, 37, and 39 degrees C when the plasmids expressing N, P, and L proteins of the Edmonston strain (the parental strain of AIK-C) were used, whereas the minigenome RNA replicated only at 32.5 degrees C but did not at 37 degrees C and higher temperature when N, P, and L protein expression plasmids of the AIK-C strain were used. A series of minigenome experiments revealed that the amino acid substitution of leucine at position 439 of the P protein by proline (P439-Pro) contributes to the ts phenotype of AIK-C. Four recombinant viruses having various P genes were rescued from the modified AIK-C genome cDNA and ts-characteristics were compared in Vero cells by plaque formation assay. The results showed that the P439-Pro of AIK-C virus played a key role in the ts phenotype, but the other substitutions in the P gene might have an accessory function in the expression of the phenotype.     

Whole-genome,deep pyrosequencing analysis of a duck influenza A virus evolution in swine cells

We studied the sub-population level evolution of a duck influenza A virus isolate during passage in swine tracheal cells. The complete genomes of the A/mallard/Netherlands/10-Nmkt/1999 strain and its swine cell-passaged descendent were analysed by 454 pyrosequencing with coverage depth ranging from several hundred to several thousand reads at any point. This allowed characterization of defined minority sub-populations of gene segments 2, 3, 4, 5, 7, and 8 present in the original isolate. These minority sub-populations ranged between 9.5% (for segment 2) and 46% (for segment 4) of their respective gene segments in the parental stock. They were likely contributed by one or more viruses circulating within the same area, at the same period and in the same or a sympatric host species. The minority sub-populations of segments 3, 4, and 5 became extinct upon viral passage in swine cells, whereas the minority sub-populations of segments 2, 7 and 8 completely replaced their majority counterparts. The swine cell-passaged virus was therefore a three-segment reassortant and also harboured point mutations in segments 3 and 4. The passaged virus was more homogenous than the parental stock, with only 17 minority single nucleotide polymorphisms present above 5% frequency across the whole genome. Though limited here to one sample, this deep sequencing approach highlights the evolutionary versatility of influenza viruses whereby they exploit their genetic diversity, predilection for mixed infection and reassortment to adapt to a new host environmental niche.