#Genesis and #dissemination of highly pathogenic #H5N6 #avian #influenza viruses (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Genesis and dissemination of highly pathogenic H5N6 avian influenza viruses

Lei Yang, Wenfei Zhu, Xiaodan Li, Hong Bo, Ye Zhang, Shumei Zou, Rongbao Gao, Jie Dong, Xiang Zhao, Wenbing Chen, Libo Dong, Xiaohui Zou, Yongcai Xing, Dayan Wang* and Yuelong Shu*

Author Affiliations: National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China



Clade highly pathogenic avian influenza viruses (H5Nx) have spread from Asia to other parts of the world. Since 2014, human infections with clade highly pathogenic avian influenza H5N6 viruses have been continuously reported in China. To investigate the genesis of the virus, we analyzed 123 H5 or N6 environmental viruses sampled from live poultry markets or farms during 2012–2015 in Mainland China. Our results indicated that clade H5N2/N6/N8 viruses shared the same hemaglutinin gene that originated in early 2009. During 2012–2015, the genesis of highly pathogenic avian influenza H5N6 viruses occurred via two independent pathways. Three major reassortants H5N6 viruses (Reassortant A, B, and C) were generated. Internal genes of Reassortant A/B and C viruses derived from clade H5N1 and H9N2 viruses, respectively. Many mammalian adaption mutations and antigenic variations were detected among the three reassortant viruses. Considering their wide circulation and dynamic reassortment in poultry, we highly recommend close monitoring of the viruses in poultry and humans.



Since 2014, clade highly pathogenic avian influenza virus (H5Nx) virus have caused many outbreaks both in wild and domestic birds globally. Severe human cases with novel H5N6 viruses in this group were also reported in China in 2014–2015. To investigate the genesis of the genetic diversity of these H5N6 viruses, we sequenced 123 H5 or N6 environmental viruses sampled from 2012–2015 in China. Sequence analysis indicated that three major reassortants of these H5N6 viruses had been generated by two independent evolutionary pathways. The H5N6 reassortants viruses had been detected in most provinces of southern China and neighboring countries. Considering the mammalian adaption mutations and antigenic variation detected, the spread of these viruses should be monitored carefully due to their pandemic potential.



*Corresponding author:Dr. Yuelong Shu, Phone: +86-010-58900850. Fax: +86-010-58900850. E-mail: yshu@cnic.org.cn.

*Dr. Dayan Wang, E-mail: dayanwang@cnic.org.cn

Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Keywords: Avian Influenza; H5N1; H5N6; H5N8; H5N9; Poultry; Human; China; Reassortant Strain; H9N2.


Shifting #clade #distribution, #reassortment, and emergence of new #subtypes of highly pathogenic #avian #influenza A(#H5) viruses collected in #Vietnamese #poultry from 2012 to 2015 (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Shifting clade distribution, reassortment, and emergence of new subtypes of highly pathogenic avian influenza A(H5) viruses collected in Vietnamese poultry from 2012 to 2015

Diep T. Nguyen1,2,3,4#, Yunho Jang5, Tho D. Nguyen1, Joyce Jones5, Samuel S. Shepard5, Hua Yang5, Nancy Gerloff5, Thomas Fabrizio6, Long V. Nguyen2, Ken Inui7, Genyan Yang5, Adrian Creanga5, Li Wang5, Duong T. Mai1, Sharmi Thor5, James Stevens5, Thanh L. To1, David E. Wentworth5, Tung Nguyen2, Dong V. Pham2, Juliet E. Bryant3,4 and C. Todd Davis5#

Author Affiliations: 1 National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam; 2 Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam; 3 Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam; 4 Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; 5 Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA; 6 St Jude’s Center for Excellence in Influenza Research and Surveillance, Memphis, TN, USA; 7 Food and Agriculture Organization of the United Nations, Hanoi, Vietnam



Whole genome sequences of representative highly pathogenic avian influenza A(H5) viruses from Vietnam were generated, comprising samples from poultry outbreaks and active market surveillance collected from January 2012 to August 2015. Six hemagglutinin gene clades were characterized. Clade 1.1.2 was predominant in southern Mekong provinces throughout 2012 and 2013, but gradually disappeared and was not detected after April 2014. Clade viruses spread rapidly during 2012 and were detected in the south and center of the country. A number of clade 1.1.2 and inter-clade reassortant viruses were detected with different combinations of internal genes derived from and viruses indicating extensive co-circulation. Although reassortment generated genetic diversity at the genotype level, there was relatively little genetic drift within the individual gene segments suggesting genetic stasis over recent years. Antigenically, clade 1.1.2,,, viruses remained related to earlier viruses and WHO recommended pre-pandemic vaccine strains representing these clades. Clade 7.2 viruses, although only detected in small numbers, were the exception as indicated by introduction of a genetically and antigenically diverse strain in 2013. Clade viruses (H5N1 and H5N6) were likely introduced in April 2014 and appeared to gain dominance across northern and central regions. Antigenic analyses of clade viruses compared to existing clade 2.3.4 candidate vaccine viruses (CVV) indicated the need for an updated vaccine virus. A/Sichuan/26221/2014 (H5N6), was developed and ferret antisera generated against this virus was demonstrated to inhibit some but not all clade viruses suggesting consideration of alternative clade CVVs.



Highly pathogenic avian influenza (HPAI) A(H5) viruses have circulated continuously in Vietnam since 2003 resulting in hundreds of poultry outbreaks and sporadic human infections. Despite significant reduction in the number of human infections in recent years, poultry outbreaks continue to occur and the virus continues to diversify. Vaccination of poultry has been used as a means to control spread and impact of the virus but due to the diversity and changing distribution of antigenically distinct viruses, the utility of vaccines in the face of mismatched circulating strains remains questionable. This study assesses the putative amino acid changes in viruses leading to antigenic variability, underscoring the complexity of vaccine selection for both veterinary and public health purposes. Given the overlapping geographic distribution of multiple, antigenically distinct clades of HPAI A(H5) viruses in Vietnam, the vaccine efficacy of bivalent poultry vaccine formulations should be tested in the future.



#Address correspondence to: Diep T Nguyen, diep.dahvn@gmail.com, C. Todd Davis, ctdavis@cdc.gov

Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Keywords: Avian Influenza; H5N1; H5N6; Poultry; Vietnam; Vaccines.


#Human #antibody 3E1 targets the #HA #stem region of #H1N1 and #H5N6 #influenza A viruses (Nat Commun., abstract)

[Source: Nature Communications, full page: (LINK). Abstract, edited.]

Article | OPEN

Human antibody 3E1 targets the HA stem region of H1N1 and H5N6 influenza A viruses

Wenshuai Wang, Xiaoyu Sun, Yanbing Li, Jinpeng Su, Zhiyang Ling, Tianlong Zhang, Fang Wang, Hong Zhang, Hualan Chen, Jianping Ding & Bing Sun

Nature Communications 7, Article number: 13577 (2016) / doi:10.1038/ncomms13577

Received: 05 August 2016 – Accepted: 17 October 2016 – Published online: 02 December 2016



As influenza A viruses remain a major threat to human health worldwide, the discovery of broadly neutralizing monoclonal antibodies that recognize conserved epitopes would facilitate the development of antibody-based therapeutic strategies. Here we report that a VH4-4-encoded human mAb named 3E1 could neutralize H1 and H5 subtype viruses in vitro and protect mice against the H1N1 and H5N6 viruses by inhibiting the low pH-induced conformational rearrangement of haemagglutinin (HA), hence blocking membrane fusion. The crystal structures of 3E1 Fab in complex with HA of two H1N1 strains reveal that 3E1, with both heavy and light chains, binds to a conserved epitope of the HA stem region, comprising parts of the fusion peptide, the F subdomain and the outermost β-strand preceding helix A. Altogether, these data suggest the potential of 3E1 as a therapeutic drug against H1 and H5 subtype viruses.

Keywords: Seasonal Influenza, Avian Influenza; H1N1; H5N6; Monoclonal Antibodies.


Novel #H7N2 and #H5N6 #Avian #Influenza A Viruses in Sentinel #Chickens: A Sentinel Chicken Surveillance Study (Front Microbiol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Front Microbiol. 2016 Nov 16;7:1766. eCollection 2016.

Novel H7N2 and H5N6 Avian Influenza A Viruses in Sentinel Chickens: A Sentinel Chicken Surveillance Study.

Zhao T1, Qian YH2, Chen SH2, Wang GL1, Wu MN1, Huang Y1, Ma GY2, Fang LQ1, Gray GC3, Lu B2, Tong YG1, Ma MJ1, Cao WC1.

Author information: 1State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China. 2Wuxi Center for Disease Control and Prevention Wuxi, China. 3Division of Infectious Diseases, Global Health Institute, Nicholas School of the Environment, Duke University, Duke University Medical Center Durham, NC, USA.



In 2014, a sentinel chicken surveillance for avian influenza viruses was conducted in aquatic bird habitat near Wuxi City, Jiangsu Province, China. Two H7N2, one H5N6, and two H9N2 viruses were isolated. Sequence analysis revealed that the H7N2 virus is a novel reassortant of H7N9 and H9N2 viruses and H5N6 virus is a reassortant of H5N1 clade 2.3.4 and H6N6 viruses. Substitutions V186 and L226 (H3 numbering) in the hemagglutinin (HA) gene protein was found in two H7N2 viruses but not in the H5N6 virus. Two A138 and A160 mutations were identified in the HA gene protein of all three viruses but a P128 mutation was only observed in the H5N6 virus. A deletion of 3 and 11 amino acids in the neuraminidase stalk region was found in two H7N2 and H5N6 viruses, respectively. Moreover, a mutation of N31 in M2 protein was observed in both two H7N2 viruses. High similarity of these isolated viruses to viruses previously identified among poultry and humans, suggests that peridomestic aquatic birds may play a role in sustaining novel virus transmission. Therefore, continued surveillance is needed to monitor these avian influenza viruses in wild bird and domestic poultry that may pose a threat to poultry and human health.

KEYWORDS: H5N6 virus; H7N2 virus; H9N2 virus; avian influenza A virus; sentinel chicken; transmission

PMID: 27899915 DOI: 10.3389/fmicb.2016.01766

[PubMed – in process]

Keywords: Reassortant Strains; Avian Influenza; China; Poultry; H7N2; H9N2; H5N6; H6N6; H5N1.


#Genesis, #Evolution and #Prevalence of #H5N6 #Avian #Influenza Viruses in #China (Cell Host Microbe, abstract)

[Source: Cell Host & Microbe, full page: (LINK). Abstract, edited.]


Genesis, Evolution and Prevalence of H5N6 Avian Influenza Viruses in China

Yuhai Bi21, Quanjiao Chen21, Qianli Wang21, Jianjun Chen21, Tao Jin, Gary Wong, Chuansong Quan, Jun Liu, Jun Wu, Renfu Yin, Lihua Zhao, Mingxin Li, Zhuang Ding, Rongrong Zou, Wen Xu, Hong Li, Huijun Wang, Kegong Tian, Guanghua Fu, Yu Huang, Alexander Shestopalov, Shoujun Li, Bing Xu, Hongjie Yu, Tingrong Luo, Lin Lu, Xun Xu, Yang Luo, Yingxia Liu, Weifeng Shi, Di Liu, George Fu Gao22,

21 Co-first author

22 Lead Contact

Publication stage: In Press Corrected Proof / DOI: http://dx.doi.org/10.1016/j.chom.2016.10.022

Publication History: Published: December 1, 2016 – Accepted: October 28, 2016 – Received in revised form: September 27, 2016 – Received: August 8, 2016



  • Live poultry markets in China surveyed for avian influenza viruses during 2014–2016
  • H5N6 has replaced H5N1 as a dominant AIV subtype in southern China, especially in ducks
  • The HA and NA genes of H5N6 show apparent lineage-specific matching patterns
  • At least 34 distinct H5N6 genotypes noted, one responsible for five human infections



Constant surveillance of live poultry markets (LPMs) is currently the best way to predict and identify emerging avian influenza viruses (AIVs) that pose a potential threat to public health. Through surveillance of LPMs from 16 provinces and municipalities in China during 2014–2016, we identified 3,174 AIV-positive samples and isolated and sequenced 1,135 AIVs covering 31 subtypes. Our analysis shows that H5N6 has replaced H5N1 as one of the dominant AIV subtypes in southern China, especially in ducks. Phylogenetic analysis reveals that H5N6 arose from reassortments of H5 and H6N6 viruses, with the hemagglutinin and neuraminidase combinations being strongly lineage specific. H5N6 viruses constitute at least 34 distinct genotypes derived from various evolutionary pathways. Notably, genotype G1.2 virus, with internal genes from the chicken H9N2/H7N9 gene pool, was responsible for at least five human H5N6 infections. Our findings highlight H5N6 AIVs as potential threats to public health and agriculture.

Keywords: Avian Influenza; China; Human; Poultry; H5N6; H9N2; H7N9; Reassortant Strains.


The #complexity of #human infected AIV #H5N6 isolated from #China (BMC Infect Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

BMC Infect Dis. 2016 Oct 25;16(1):600.

The complexity of human infected AIV H5N6 isolated from China.

Zhang Z1,2, Li R1,2, Jiang L2,3, Xiong C4,5,6, Chen Y7, Zhao G1,2, Jiang Q2.

Author information: 1Department of Epidemiology and Biostatistics, School of Public Health, Fudan University, Shanghai, People’s Republic of China. 2Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, People’s Republic of China. 3Department of Public Health Microbiology, School of Public Health, Fudan University, Shanghai, People’s Republic of China. 4Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, People’s Republic of China. xiongchenglong@fudan.edu.cn. 5Department of Public Health Microbiology, School of Public Health, Fudan University, Shanghai, People’s Republic of China. xiongchenglong@fudan.edu.cn. 6, Bldg. 8#, Rd. Dong’an 130, Shanghai, 200032, People’s Republic of China. xiongchenglong@fudan.edu.cn. 7School of Epidemiology, Public Health and Preventive Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.




Novel avian influenza viruses (AIVs) of H7N9, H10N8, and H5N6 are currently circulating in China’s poultry flocks, occasionally infecting human and other mammals. Human infected AIV H5N6 in China during 2014-2015 is believed to be a triple reassortant originated from H6N6 and two clades of H5 viruses. The current report suggests that its reassortment history is more complicated.


Genomes of human infected isolates of AIV H5N6 were searched from the NCBI Influenza Virus Sequence Database and the Global Initiative on Sharing Avian Influenza Data. Sequences shared high identities with each segment of their genomes were obtained through the Basic Local Alignment Search Tool. Alignments were done by mafft-7.037-win32 program; 8 large-scale and then 8 gradually converged phylogenetic trees were constructed by using MEGA5.1/5.2/6.0 Software.


The events that each segment of the genomes of human infected AIV H5N6 isolates circulated in China had evolved into its current status might have happened before 2013, and so were they then reassorted into the epidemic AIV H5N6. A/Guangzhou/39715/2014(H5N6) and A/Sichuan/26221/2014(H5N6) had their six internal segments (PB2, PB1, PA, NP, NEP, and M) in common, and were reassorted from AIVs H5N1 in the same period and same region as that of HA, while A/Yunnan/0127/2015(H5N6) derived its six internal segments from AIV H9N2 that has been prevalent in Eastern China since 2008.


AIV H5N6 isolates established from both human and poultry in China during 2014-2015 were heterogeneous; both AIVs H5N1 and H9N2 were involved in the reassortment of AIV H5N6 in China.

KEYWORDS: H5N1; H5N6; H9N2; Reassortment

PMID: 27782815 DOI: 10.1186/s12879-016-1932-1

[PubMed – in process]

Keywords: H5N1; H5N6; H9N2; Avian Influenza; China; Poultry; Human.


Novel #Reassortant #H5N6 #Influenza A Virus from the #Lao People’s Democratic Republic Is Highly Pathogenic in #Chickens (PLoS One, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

PLoS One. 2016 Sep 15;11(9):e0162375. doi: 10.1371/journal.pone.0162375.

Novel Reassortant H5N6 Influenza A Virus from the Lao People’s Democratic Republic Is Highly Pathogenic in Chickens.

Butler J1, Stewart CR1, Layton DS1, Phommachanh P2, Harper J1, Payne J1, Evans RM1, Valdeter S1, Walker S1, Harvey G1, Shan S1, Bruce MP1, Rootes CL1, Gough TJ1, Rohringer A1, Peck GR1, Fardy SJ1, Karpala AJ1, Johnson D1, Wang J1, Douangngeun B2, Morrissy C1, Wong FY1, Bean AG1, Bingham J1, Williams DT1.

Author information: 1CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia. 2National Animal Health Laboratory, Vientiane, Lao People’s Democratic Republic.



Avian influenza viruses of H5 subtype can cause highly pathogenic disease in poultry. In March 2014, a new reassortant H5N6 subtype highly pathogenic avian influenza virus emerged in Lao People’s Democratic Republic. We have assessed the pathogenicity, pathobiology and immunological responses associated with this virus in chickens. Infection caused moderate to advanced disease in 6 of 6 chickens within 48 h of mucosal inoculation. High virus titers were observed in blood and tissues (kidney, spleen, liver, duodenum, heart, brain and lung) taken at euthanasia. Viral antigen was detected in endothelium, neurons, myocardium, lymphoid tissues and other cell types. Pro-inflammatory cytokines were elevated compared to non-infected birds. Our study confirmed that this new H5N6 reassortant is highly pathogenic, causing disease in chickens similar to that of Asian H5N1 viruses, and demonstrated the ability of such clade 2.3.4-origin H5 viruses to reassort with non-N1 subtype viruses while maintaining a fit and infectious phenotype. Recent detection of influenza H5N6 poultry infections in Lao PDR, China and Viet Nam, as well as six fatal human infections in China, demonstrate that these emergent highly pathogenic H5N6 viruses may be widely established in several countries and represent an emerging threat to poultry and human populations.

PMID: 27631618 DOI: 10.1371/journal.pone.0162375

[PubMed – as supplied by publisher]

Keywords: Research; Abstracts; Avian Influenza; H5N6; Poultry; Laos; Reassortant Strain.