Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments

Lam, Tommy Tsan-Yuk; Chong, Yee Ling; Shī, Mǎng; Hon, Chung-Chau; Li, Jun; Martin, Darren P.; Tang, Julian W.; Mok, Chee Keng; Shih, Shin‐Ru; Yip, Chi-Wai; Jiang, Jingwei; Hui, Raymond; Pybus, Oliver G.; Holmes, Edward C.; Leung, Frederick Chi-Ching

doi:10.1016/j.meegid.2013.03.015

Cited by 22 publications

(23 citation statements)

References 55 publications

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“…Interestingly, we found that 91.0% (10/11) mosaics identified here were isolated from terrestrial birds (Table 1), which was consistent with a previous report [50]. To investigate four previously unreported mosaic sequences, the selected datasets of manually concatenated full genomes of H5N1 viruses were analyzed (Figure 2).…”

Section: Resultssupporting

confidence: 87%

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Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China

et al. 2014

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The direct precursors of the A/Goose/Guangdong/1/1996 (GS/GD) virus lineage and its reassortants have been established geographically and ecologically. To investigate the variation and evolutionary dynamics of H5N1 viruses, whole-genome viral sequences (n = 164) were retrieved from the NCBI Influenza Virus Resource. Here, we present phylogenetic evidence for intrasubtype reassortments among H5N1 viruses isolated from China during 1996–2012. On the basis of phylogenetic analysis, we identified four major groups and further classified the reassortant viruses into three subgroups. Putative mosaic structures were mostly found in the viral ribonucleoprotein (vRNP) complexes and 91.0% (10/11) mosaics were obtained from terrestrial birds. Sequence variability and selection pressure analyses revealed that both surface glycoproteins (HA and NA) and nonstructural protein 1 (NS1) have higher dN/dS ratio and variability than other internal proteins. Furthermore, we detected 47 positively selected sites in genomic segments with the exception of PB2 and M1 genes. Hemagglutinin (HA) and neuraminidase (NA) are considered highly variable due to host immune pressure, however, it is not known what drives NS1 variability. Therefore, we performed a thorough analysis of the genetic variation and selective pressure of NS1 protein (462 available NS1 sequences). We found that most of positively selected sites and variable amino acids were located in the C-terminal effector domain (ED) of NS1. In addition, we focused on the NS1–RNA and NS1–protein interactions that were involved in viral replication mechanisms and host immune response. Transcriptomic analysis of H5N1-infected monkey lungs showed that certain PI3K-related genes were up-regulated.

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Section: Resultssupporting

confidence: 87%

“…Lam et al . has previously found that most of the mosaic sequences that belonged to subtype H5N1 were sampled from Mainland China [50]. One noticeable feature was that the majority of mosaic sequences identified here were sampled between 1997 and 2004.…”

Section: Resultsmentioning

confidence: 53%

Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China

et al. 2014

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“…Alignments were constructed with MUSCLE v3.5 (21) with manual adjustment. All data sets were screened and filtered for mosaic sequences prior to subsequent analyses, as previously described (22).…”

Section: Methodsmentioning

confidence: 99%

Expansion of Genotypic Diversity and Establishment of 2009 H1N1 Pandemic-Origin Internal Genes in Pigs in China

Liang

Lam

Fan

et al. 2014

J Virol

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IMPORTANCEShortly after the emergence of the 2009 pandemic H1N1 (pdm/09) influenza virus, it was transmitted from humans to pigs and this continues to occur around the world. Many reassortants between pdm/09-origin viruses and enzootic swine influenza viruses (SIVs) have been detected. However, the long-term impact of pdm/09-origin viruses on the SIV gene pool, which could lead to the generation of influenza viruses with the potential to infect humans, has not been systematically examined. From extensive surveillance of SIVs over a 38-month period in southern China, it was found that although neither complete pdm/09 viruses nor their surface genes could persist in pigs, their internal genes did persist. Over the survey period, these internal genes became predominant, potentially replacing those of the enzootic SIV lineages. The altered diversity of the SIV gene pool needs to be closely monitored for changes in the potential for SIV transmission to humans.

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“…Nucleotide sequences generated in this study were combined with all publicly available sequences of avian influenza A viruses in GenBank (http://www.ncbi.nlm.nih.gov/GenBank) and H10N8 and H7N9 human virus sequences from GISAID (http: //gisaid.org/). Sequences with Ͼ5 ambiguous nucleotides, or Ͻ70% of the length of the coding region, or that were mosaic (18) were excluded. Sequences were aligned by using MUSCLE v3.5 (19), with manual adjustments.…”

Section: Methodsmentioning

confidence: 99%

Emergence and Evolution of H10 Subtype Influenza Viruses in Poultry in China

Lam

Chai

et al. 2015

J Virol

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The cases of human infections with H10N8 viruses identified in late 2013 and early 2014 in Jiangxi, China, have raised concerns over the origin, prevalence, and development of these viruses in this region. Our long-term influenza surveillance of poultry and migratory birds in southern China in the past 12 years showed that H10 influenza viruses have been introduced from migratory to domestic ducks over several winter seasons at sentinel duck farms at Poyang Lake, where domestic ducks share their water body with overwintering migratory birds. H10 viruses were never detected in terrestrial poultry in our survey areas until August 2013, when they were identified at live-poultry markets in Jiangxi. Since then, we have isolated 124 H10N8 or H10N6 viruses from chickens at local markets, revealing an ongoing outbreak. Phylogenetic analysis of H10 and related viruses showed that the chicken H10N8 viruses were generated through multiple reassortments between H10 and N8 viruses from domestic ducks and the enzootic chicken H9N2 viruses. These chicken reassortant viruses were highly similar to the human isolate, indicating that market chickens were the source of human infection. Recently, the H10 viruses further reassorted, apparently with H5N6 viruses, and generated an H10N6 variant. The emergence and prevalence of H10 viruses in chickens and the occurrence of human infections provide direct evidence of the threat from the current influenza ecosystem in China. IMPORTANCEAfter the outbreak of avian-origin H7N9 influenza viruses in China, fatal human infections with a novel H10N8 virus were reported. Utilizing data from 12 years of influenza surveillance in southern China, we showed that H10 viruses were regularly introduced by migratory ducks to domestic ducks on Poyang Lake, a major aggregative site of migratory birds in Asia. The H10 viruses were maintained and amplified in domestic ducks and then transmitted to chickens and reassorted with enzootic H9N2 viruses, leading to an outbreak and human infections at live-poultry markets. The emergence of the H10N8 virus, following a pathway similar to that of the recent H7N9 virus, highlights the role of domestic ducks and the current influenza ecosystem in China that facilitates influenza viruses moving from their reservoir hosts through the live-poultry system to cause severe consequences for public health.

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Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments

Cited by 22 publications

References 55 publications

Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China

Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China

Expansion of Genotypic Diversity and Establishment of 2009 H1N1 Pandemic-Origin Internal Genes in Pigs in China

Emergence and Evolution of H10 Subtype Influenza Viruses in Poultry in China

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