Isolation and pathotyping of H9N2 avian influenza viruses in Indian poultry

A total of 1246 faecal and tissue samples collected/received from 119 farms located in various states of India were processed for isolation of avian influenza viruses (AIV) during 2003-2004 as part of a program to monitor AIV infection in Indian poultry population. Avian influenza virus was isolated for the first time in India from poultry farms with history of drop in egg production, respiratory illness and increased mortality in Haryana state. A total of 29 H9N2 AIV isolates were obtained from the states of Punjab, Haryana, Uttar Pradesh, Gujarat, and Orissa and Union Territory Delhi. Subtyping was done by HI, RT-PCR and neuraminidase inhibition assay. Pathotyping of six representative isolates by intravenous pathogenicity index (0.0/3.0) in 6-8 weeks old chicken, trypsin dependency in cell culture and HA cleavage site analysis (335RSSR*GLF341) confirmed that these isolates are low pathogenic. Nucleotide sequence analysis of the HA gene showed that the Indian isolates are very closely related (95.0-99.6%) and shared a homology of 92-96% with H9N2 isolates from Germany and Asian regions other than that of mainland China. Deduced amino acid sequences showed the presence of L226 (234 in H9 numbering) which indicates a preference to binding of alpha (2-6) sialic acid receptors. Two of the six isolates had 7 glycosylation sites in the HA1 cleaved protein and the remaining four had 5 sites. Phylogenetic analysis showed that they share a common ancestor Qa/HK/G1/97 isolate which had contributed internal genes of H5N1 virus circulating in Vietnam. Further characterization of Indian H9N2 isolates is required to understand their nature and evolution.     

Sequence analysis of related low-pathogenic and highly pathogenic H5N2 avian influenza isolates from United States live bird markets and poultry farms from 1983 to 1989

The last highly pathogenic outbreak of avian influenza in the United States was caused by an H5N2 influenza virus in Pennsylvania and New Jersey in 1983-84. Through a combined federal and state eradication effort, the outbreak was controlled. However, in 1986-89, multiple H5N2 viruses were isolated from poultry farms and the live bird markets (LBMs) in the United States. To determine the epidemiologic relationships of these viruses, the complete coding sequence of the nonstructural gene and the hemagglutinin protein subunit 1 of the hemagglutinin gene was determined for 11 H5N2 viruses and compared with previously available influenza sequences. The H5N2 isolates from 1986-89 were all closely related to the isolates from the 1983-84 Pennsylvania outbreak by nucleotide and amino acid sequence analysis for both genes, providing additional evidence that the Pennsylvania/83 (PA/83) virus lineage was not completely eradicated. The PA/83 lineage also had a large number of unique amino acid changes not found in other avian influenza viruses, which was suggestive that this lineage of virus had been circulating in poultry for an extended period of time before the first isolation of virus in 1983. High substitution and evolutionary rates were measured by examining the number of nucleotide or amino acid substitutions over time as compared with the index case, CK/PA/21525/83. These rates, however, were similar to other outbreaks of avian influenza in poultry. This study provides another example of the long-term maintenance and evolution of influenza viruses in the U.S. LBMs and provides further evidence of the connection of the LBMs and the Pennsylvania 1983 H5N2 outbreak.     

Genetic characterization of the H9N2 influenza viruses circulated in the poultry population in Israel

The partial nucleotide sequences of the hemagglutinin (HA) genes of 72 H9N2 influenza viruses isolated from chickens and turkeys in Israel during the period 2000-2005 were genetically analyzed. The isolates possessed the three types of amino acid motif -R-S-S-R/G-L-, -R-S-N-R/G-L-, and -R-S-K-R/G-L- at the cleavage site of HA. Phylogenetic analyses showed that all Israeli isolates belonged to the same group which further divided into three closely related sub-groups. The HA genes of these isolates were related to the HA gene of A/chicken/Germany/R45/98 isolated from chicken in Germany in 1998.     

Evolutionary characterization of hemagglutinin gene of H9N2 influenza viruses isolated from Asia

The full length hemagglutinin (HA) genes of 287 H9N2 AI strains isolated from chickens in Asia during the period 1994-2009 were genetically analyzed. Phylogenetic analysis showed that G1-like viruses circulated in the Middle East and Indian sub-continent countries, whereas other sublineages existed in Far East countries. It also revealed G1-like viruses with an average 96.7% identity clustered into two subgroups largely based on their time of isolation. The Ka/Ks ratio was calculated 0.34 for subgroup 1 and 0.57 for subgroup 2 indicates purifying/stabilizing selection, but despite this there is evidence of localized positive selection when comparing the subgroups 1 and 2 protein sequences. Five sites in HA H9N2 viruses had a posterior probability >0.5 using the Bayesian method, indicating these sites were under positive selection. These sites were found to be associated with the globular head region of HA. To identify sites under positive selection; amino acid substitution classified depends on their radicalism and neutrality. The results indicate that, although most positions in HAs were under purifying selection and can be eliminated, a few positions located in the antigenic regions and receptor binding sites were subject to positive selection.     

广东一株重组H9N2亚型禽流感病毒的鉴定及全基因组序列分析

本研究于2013年从广东某发病鸡场分离到一株H9N2亚型AIV,命名为A/chicken/Guangdong/LG1/2013.对病毒进行全基因组克隆测序和进化分析,其HA基因裂解基序为333pSRSSR ↓ GLF341,呈典型低致病性AIV分子特征.其HA基因发生Q226突变和A316S突变,NA基因出现第63～65位氨基酸缺失.该病毒株HA、NA和NS基因属于类BJ/1/94分支,PB2属于类SD/H/09分支,PB1、PA、NP基因属于类SH/F/98分支,M基因属于类HK/G1/97分支,该基因型在广东地区未见报道,其内部基因与H7N9亚型人流感病毒SH/02/2013株核苷酸同源性在95.6 ％～98.6％之间.本研究表明我国H9N2亚型AIV呈现遗传演化的多样性及基因重组的复杂性,对该亚型病毒的监测和研究具有重要的兽医和公共卫生意义.     

我国长三角和珠三角地区活禽市场H9N2亚型禽流感流行病学调查

为了解目前我国活禽市场H9N2亚型禽流感病毒(avian influenza virus,AIV)流行和增殖情况,2014年在上海、江苏、安徽和广东随机选取58个活禽市场,采集12 635份活禽拭子样品进行病毒分离、RT-PCR和序列测定分析。结果:15.11%拭子样品和98.28%的活禽市场是H9N2亚型AIV阳性。鸡、鸭、鹅、鸽样品阳性率分别为22.98%(1730/7529)、3.62%(94/2594)、4.08%(67/1643)、2.09%(18/861);上海、江苏、安徽和广东的样品阳性率分别为24.11%(688/2853)、8.43%(284/3368)、15.27%(475/3110)、13.95%(461/3304)。活禽零售市场阳性率(34.40%)显著高于活禽批发市场感染率(12.24%)。随着家禽在批发市场内停留时间的延长,H9N2亚型AIV阳性率从11.45%(停留8 h内)上升到29.13%(停留48 h以上)。遗传进化分析表明:所检出的H9N2亚型AIV均属于2007年以来我国H9亚型AIV主要流行分支,即h9.4.2.5分支。这些流行病学调查结果提示我国长三角和珠三角活禽市场的家禽(尤其是鸡)H9N2亚型AIV感染率很高,并且随着活禽在批发市场内停留时间延长,以及向零售市场转移,H9N2亚型AIV存在一个显著增殖和扩散的过程。     

中国猪源HSN1和H9N2亚型流感病毒的分离鉴定

猪是禽流感病毒"禽-猪-人"传播链中重要的中间宿主,了解猪流感的疫情动态将为动物流感及人流感的疾病预测及防制提供重要依据.1999～2001年间进行的血清学和病毒学监测发现我国猪群存在大范围的H1和H3亚型猪流感感染(李海燕等,2002).2002～2003年,我们进一步对来自全国14个省市的1936份血清进行了H9亚型猪流感的检测,同时在广东、福建等省进行了H5亚型猪流感的检测.2002年辽宁、广东、山东及重庆猪血清中出现H9亚型流感抗体,阳性率分别为7.3%、6.8%、5.1%和1.6%.2003年采集的猪血清H9亚型流感抗体均为阴性,同时发现广东、福建两省2003年出现H5亚型流感阳性猪群,阳性率分别为4.7%和8.2%.从2001～2003年收集和送检的样品中分离鉴定了6株H9N2亚型和2株H5N1亚型猪流感病毒,部分序列分析发现H9和H5亚型猪流感病毒均与我国分离的禽流感病毒高度同源.本研究进一步确证了我国猪群中存在H9N2亚型流感病毒,并且首次发现我国猪群已出现H5N1亚型流感病毒,为人类流感及动物流感的防制敲响了警钟.对这两个亚型流感病毒所具有的公共卫生和兽医公共卫生危害性应予以高度重视.     

Critical control points for avian influenza A H5N1 in live bird markets in low resource settings

Live bird markets can become contaminated with and become a source of transmission for avian influenza viruses including the highly pathogenic H5N1 strain. Many countries affected by the H5N1-virus have limited resources for programs in environmental health, sanitation and disease control in live bird markets. This study proposes five critical control points (CCPs) to reduce the risk of H5N1-virus contamination in markets in low resource settings. The CCPs were developed based on three surveys conducted in Indonesia: a cross-sectional survey in 119 markets, a knowledge, attitudes and practice survey in 3 markets and a microbiological survey in 83 markets. These surveys assessed poultry workflow, market infrastructure, hygiene and regulatory practices and microbiological contamination with the H5N1-virus. The five CCPs identified were (1) reducing risk of receiving infected birds into the market, (2) reducing the risk of virus spread between different bird flocks in holding cages, (3) reducing surface contamination by isolating slaughter processes from other poultry-related processes, (4) minimizing the potential for contamination during evisceration of carcasses and (5) reducing the risk of surface contamination in the sale zone of the market. To be relevant for low resource settings, the CCPs do not necessitate large infrastructure changes. The CCPs are suited for markets that slaughter poultry and have capacity for daily disposal and removal of solid waste from the market. However, it is envisaged that the CCPs can be adapted for the development of risk-based programs in various settings.     

吉林省长春市城乡活禽市场H9N2亚型禽流感病毒的检测与分子遗传进化分析

H9N2亚型禽流感病毒(Avian influenza virus, AIV)通过为其他流感病毒提供内部基因或直接跨越种间屏障感染人,而活禽市场是H9N2亚型AIV传播的主要传播途径之一。为了解吉林省长春地区城乡活禽市场H9N2亚型AIV流行特点和趋势,对2021年9月至2023年4月在4个城乡活禽市场分离到3株代表性H9N2亚型AIV进行了分子遗传进化分析。结果显示3株毒株HA蛋白裂解位点均为PSKSSR↓GLF,其受体结合位点的第226位氨基酸由Q突变为L,可与α,2-6唾液酸受体结合,具有感染人的特性。分子遗传进化分析显示3株毒株的HA基因归属于BJ-94谱系中h9.4.2.5亚分支;NA基因归属Y280谱系;PB2、M基因均属于G1谱系;剩余内部基因均属于F-98谱系。研究结论丰富当前国内H9N2亚型AIV的流行病学研究,提示需加强病毒变异监控和新疫苗研发。     

Sequence and phylogenetic analysis of the haemagglutinin genes of H9N2 avian influenza viruses isolated from commercial chickens in Iran

To determine the genetic relationship of Iranian viruses, the haemagglutinin (HA) genes from ten isolates of H9N2 viruses isolated from commercial chickens in Iran during 1998–2002 were amplified and sequenced. Sequence analysis and phylogenetic studies were conducted by comparing each isolate with those of the available H9N2 strains at GenBank. All these ten isolates had the same sequence –R-S-S-R/G-L– of proteolytic cleavage site of the HA. Nucleotide sequence comparisons of HA gene from Iranian isolates showed 95.2–99.1% identity within the group. Five isolates had leucine (L) at position 226 instead of glutamine (Q). Phylogenetic analysis showed that all our isolates belonged to the G1-like sublineage. Also these isolates showed some degree of homology with other H9N2 isolates e.g., 94.3–96.9% with qu/HK/G1/97, 96.1–98.6% with pa/Chiba/1/97, 95.6–98.2% with pa/Narita/92A/98, and 94.0–96.3% with HK/1073/99. On the basis of phylogenetic and molecular characterization evidence, we concluded that the H9N2 subtype influenza viruses circulating in chicken flocks in Iran since 1998–2002 had a common origin. The results of this study indicated that all Iranian viruses have the potential to emerge as highly pathogenic influenza virus, and considering the homology of these isolates with human H9N2 strains, it seems that the potential of these avian influenza isolates to infect human should not be overlooked.     

2015—2016年广州市部分活禽市场H9N2亚型禽流感病毒的流行病学调查

为了解广州市活禽市场禽流感病毒(AIV)的流行和变异情况,本研究于2015年5月至2016年6月从广州市部分活禽市场采集禽咽喉拭子1 579份,对样品处理之后进行分离和RT-PCR鉴定,通过对HA、NA基因进行遗传进化分析后,共检测到9株H9N2亚型禽源流感病毒。9株分离株的HA基因属于BJ/94-like分支,核苷酸相似性为93.2%~99.7%;有8株分离株的HA基因裂解位点的序列为P-S-R-S-S-R,1株的HA基因裂解位点的序列发生了P/L-S-R-S-S-R的替换。HA蛋白第226受体结合位点的氨基酸均为亮氨酸(Leu),具有人流感受体结合的特征。6株分离株的NA基因属于BJ/94-like分支,3株属于HK/G9-like分支,说明不同分支的病毒开始出现重组。本研究通过对广州市部分活禽市场分离到的禽流感病毒序列分析,掌握活禽市场流感病毒的流行变异趋势,为流感病毒的综合防控及保障公共卫生健康提供参考。     

Isolation and genetic characterization of avian origin H9N2 influenza viruses from pigs in China

As pigs are susceptible to infection with both avian and human influenza A viruses, they have been proposed to be an intermediate host for the adaptation of avian influenza viruses to humans. In April 2006, a disease caused by highly pathogenic porcine reproductive and respiratory syndrome virus (PRRSV) occurred in several pig farms and subsequently overwhelmed almost half of China with more than 2,000,000 cases of pig infection. Here we report a case in which four swine H9N2 influenza viruses were isolated from pigs infected by highly pathogenic PRRSVs in Guangxi province in China. All the eight gene segments of the four swine H9N2 viruses are highly homologous to A/Pigeon/Nanchang/2-0461/00 (H9N2) or A/Wild Duck/Nanchang/2-0480/00 (H9N2). Phylogenetic analyses of eight genes show that the swine H9N2 influenza viruses are of avian origin and may be the descendants of A/Duck/Hong Kong/Y280/97-like viruses. Molecular analysis of the HA gene indicates that our H9N2 isolates might have high-affinity binding to the alpha2,6-NeuAcGal receptor found in human cells. In conclusion, our finding provides further evidence about the interspecies transmission of avian influenza viruses to pigs and emphasizes the importance of reinforcing swine influenza virus (SIV) surveillance, especially after the emergence of highly pathogenic PRRSVs in pigs in China.     

2011年中国北方H9N2亚型禽流感病毒分离株HA基因进化分析及受体结合性检测

为了解近期中国北方禽源H9N2亚型禽流感病毒(AIV)流行规律及分子遗传进化特征,本实验对2011年在中国北方家禽中分离到的11株H9N2亚型AIV通过RT-PCR扩增病毒的HA基因片段,进行测序及遗传进化分析,并对这些病毒的受体结合性进行了检测.结果表明:11株H9N2亚型AIV分离株的HA基因在HA1和HA2的氨基酸裂解位点均为PSRSSR/GLF基序,符合低致病性病毒株氨基酸序列特征.多数病毒HA潜在糖基化位点为8个,所有分离株病毒的受体结合位点226位均为L,经红细胞受体结合性试验验证表明这些病毒均同时具有α-2,3和α-2,6受体结合特性,表明目前北方地区流行的H9N2亚型AIV具有感染哺乳动物的潜在威胁.本研究结果对加强H9N2病毒的分子流行病学监测具有重要意义.     

Molecular characterization of the hemagglutinin and neuraminidase genes of H5N1 influenza A viruses isolated from poultry in Vietnam from 2004 to 2005

Highly pathogenic H5N1 avian influenza A viruses have been spreading among domestic poultry, wild aquatic birds, and humans in many Asian countries since 2003. The largest number of patients, to date, infected with the H5N1 viruses are in Vietnam, where these viruses continue to cause outbreaks in domestic poultry. Here, we molecularly characterized the hemagglutinin and neuraminidase genes of nine H5N1 viruses isolated between January 2004 and August 2005 from domestic poultry in Vietnam. We found that several groups of highly pathogenic H5N1 avian influenza viruses are circulating among these birds, which suggests that H5N1 viruses of different lineages have been introduced into Vietnam multiple times.     

2007-2008年同一地点H9N2亚型禽流感病毒连续分离毒株HA基因序列分析

2007年3月到2008年3月,某大型肉鸡养殖场发生H9N2亚型禽流感疫情,临床症状多为呼吸道症状,发病鸡群生长缓慢、死亡率上升较快.在此时间段,我们对此养殖场发病的鸡群进行了连续的病毒的分离和病原鉴定,共分离和鉴定出11株H9N2亚型禽流感病毒.     

宁夏地区H1N1亚型猪流感病毒基因组遗传进化分析

对宁夏地区2011年分离到的5株H1N1亚型猪流感病毒进行了基因组测定和遗传进化分析。结果显示:宁夏地区H1N1亚型猪流感病毒具有多样性,5株分离株可分为3类,其中1株为类人H1N1猪流感病毒,2株为经典猪流感病毒,另外2株为重组猪流感病毒,其PB2、PB1、PA、NP、NS基因来源于北美三元重组猪流感病毒,HA、NA、M基因来源于经典猪流感病毒;HA蛋白裂解位点附近氨基酸分析显示5株H1N1亚型猪流感分离株均为低致病性毒株;序列分析结果显示5株病毒在HA蛋白受体结合位点、抗原位点,以及NA蛋白潜在糖基化位点处氨基酸存在差异,这些差异具有分支特异性。5株病毒在NA和M2蛋白上均未出现与神经氨酸酶抑制剂和金刚烷胺耐药性相关的氨基酸变异,但其中3株病毒的PB2蛋白基因具有哺乳动物适应性变异E627K。     

H9N2亚型禽流感病毒新疆油鸡分离株NS基因序列测定及进化生物信息分析

为了明确新疆油鸡H9N2亚型禽流感病毒(AIV)非结构蛋白基因NS的遗传进化情况,本研究采用RT-PCR方法对新疆油鸡分离株的NS基因进行了克隆和序列测定,获得NS蛋白的完整编码序列。将NS基因的核苷酸序列和对应的氨基酸序列与GenBank中已经公布的参考序列进行同源性比较,结果表明,新疆油鸡分离株的NS基因与国内其他物种稳定存在的H9亚型AIV A/Chicken/Beijing/1/1994的NS基因处于同一分支,在系统进化上属于NS基因的A等位基因群。     

H9N2亚型禽流感病毒抗原性变异的研究

对1998—2002年间在河南省豫北地区分离到的5株H9N2亚型禽流感病毒的抗原性变异进行了研究。经HI试验、鸡胚中和试验、细胞中和试验及攻毒保护试验证明，5株H9N2亚型间已经发生了抗原性漂移。98A5和99S毒株间的保护力接近100％，HI试验、鸡胚中和试验、细胞中和试验的相关性均在0．74以上。表明2毒株间的抗原性相近；用00Y毒株攻击其他4株免疫的鸡，其保护率仅为60％～80％；而02Y株对除00Y株外的4株的免疫保护率分别为60％、75％、80％、100％，与分离年代呈负相关性，HI、鸡胚中和试验、细胞中和试验也取得类似结果，说明2000年后的毒株间已发生抗原性变异。     

6株H9N2禽流感病毒分子进化及对小鼠的致病性

2009年从山东不同地区的规模化肉鸡场中分离到6株H9N2亚型流感病毒,对其分子特征进行分析,发现6株病毒可以分为2个不同的基因型,并且其中一个基因型是CK/SH/F/98（H9N2）和CK/SH/Y2/2008（H9N2）的重组病毒。为阐明H9N2流感病毒对哺乳动物致病性,分别以106 EID50剂量攻毒6周龄BALB/c雌性小鼠,6株病毒都能在小鼠肺脏中复制,而且2株病毒能在攻毒7d后引起小鼠死亡。结果表明,H9N2亚型流感病毒对哺乳动物毒力有增强趋势。