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.     

H9N2亚型禽流感病毒血凝素和神经氨酸酶基因的遗传分析

H9N2亚型禽流感病毒自1994年在中国首次发现以来,一直在家禽中流行,其导致的产蛋下降和发病死亡给养禽业发展带来严重危害。以前的研究发现中国的H9N2亚型禽流感病毒在进化过程中形成多个基因型,其表面抗原蛋白血凝素基因(HA)可被划分为以A/chicken/Beijing/1/94、A/quail/Hong Kong/G1/97(G1)和A/chicken/Heilongjiang/35/01等为代表的3个亚群,神经氨酸酶基因(NA)可被划分为以A/chicken/Beijing/1/94、A/quail/Hong Kong/G1/97(G1)和A/chicken/Hong Kong/G9/97(G9)等为代表的3个亚群。其中类G1病毒的HA基因只在香港分离株中出现。本研究对我国2003年～2004年从禽类中分离的H9N2亚型禽流感病毒血凝素(HA)和神经氨酸酶(NA)基因进行测定和遗传演化分析,结果表明其中11株病毒的HA基因属于CK/BJ/1/94群系,NA基因属于CK/BJ/1/94或DK/HK/G9/97群系,并首次发现两株病毒含有类G1病毒HA和NA基因,而且这些类G1病毒具有不同的抗原性以及人流感病毒的受体结合位点。本研究结果提示应对H9N2病毒的防治及其公共卫生意义予以高度重视。     

Phylogenetic analysis of the hemagglutinin genes of twenty-six avian influenza viruses of subtype H9N2 isolated from chickens in China during 1996-2001

The complete coding region of hemagglutinin genes from 26 influenza A viruses of H9N2 subtype isolated from chicken flocks in China during 1996-2001 was amplified and sequenced. Sequence analysis and phylogenetic studies of H9N2 subtype viruses on the basis of data of 26 viruses in this study and 71 selected strains available in the GenBank were conducted. The results revealed that all the mainland China isolates showed high homology (94.19%-100%) and were assigned to a special sublineage in the major Eurasian lineage, in contrast to the high heterogeneity of Hong Kong SAR isolates. All the 29 mainland China isolates and six Hong Kong SAR strains also had the following common characteristics: sharing the same sequence of proteolytic cleavage site with one additional basic amino acid, RSSR, with only two exceptions; having the same amino acid motif of the receptor-binding site, YWTNV/ALY; 23 of 28 isolates bearing seven potential glycosylation sites and the remaining five having six; and sharing characteristic deduced amino acid residues Asn-183 at the receptor-binding site and Ser-130 at the potential glycosylation site. We concluded that the H9N2 subtype influenza viruses circulating in chicken flocks in China since the 1990s and Ck/HK/G9/97-like viruses isolated in Hong Kong SAR should have a common origin, whereas Qu/HK/G1/97-like viruses including human strains isolated in Hong Kong SAR might originate from other places. The available evidence also suggests that the H9N2 viruses of special lineage themselves and factors prone to secondary infections may contribute to the widespread and dominant distribution of viruses of this subtype in chicken flocks in China and other Asian countries.     

福建省H9N2亚型禽流感病毒HA和NA基因的进化分析

为进一步了解福建省H9N2亚型禽流感病毒的基因遗传进化关系,本研究将福建省2011年分离的毒株FZ-04、FZ-11与GenBank上登录的2000～2011年福建省分离的H9N2毒株及国内外典型代表株进行HA、NA基因的序列比对和遗传进化分析。结果表明,分离株FZ-04和FZ-11的HA基因与CK/FJ/G9/09株核苷酸同源性最高,属于国内常见的CK/BJ/1/94亚系。HA裂解位点处的氨基酸序列为-PSRSSR/GL-,符合低致病性禽流感病毒的分子特征。NA基因在遗传进化关系上呈现独立的分支,与CK/FJ/10954/05毒株核苷酸序列同源性最高,属于CK/HK/G9/97亚系,且NA基因推导的469个氨基酸序列中没有缺失。同时,从HA和NA基因的遗传进化树上可知,2000～2011年福建省H9N2禽流感病毒进化相对比较稳定,可能有一个共同的起源。     

Molecular characterization of the surface glycoprotein genes of highly pathogenic H5N1 avian influenza viruses detected in Iran in 2011

Highly pathogenic avian influenza (HPAI) H5N1 virus is causing the death of a large number of wild birds and poultry. HPAI H5N1 was reported in the north of Iran in 2011. In this study, two A/Chicken/Iran/271/2011 and A/Duck/Iran/178/2011 viruses were genetically characterized by sequence analysis of Hemagglutinin (HA) and Neuraminidase (NA) genes. Phylogenetic analysis revealed that these viruses were different from previous Iranian isolates (Clade 2.2) and belonged to the subclade 2.3.2.1. The results showed that the detected viruses are almost identical to each other and closely related to HPAI H5N1 strains isolated in Mongolia in 2010. Based on the amino acid sequence analysis, these viruses at their HA cleavage sites contained the multibasic amino acid motif PQRERRRK-R/GLF lacking a lysine residue compared with the previous reports of the same motif. There is also a 20-amino acid deletion (resides 49–69) in the NA stalk similar to other viruses isolated after 2000. It seems that introduction of HPAI H5N1 to Iran might have happened by wild birds from Mongolian origin virus.     

An H9N2 influenza virus vaccine prepared from a non-pathogenic isolate from a migratory duck confers protective immunity in mice against challenge with an H9N2 virus isolated from a girl in Hong Kong

H9N2 influenza viruses circulate in wild birds and poultry in Eurasian countries, and have been isolated from pigs and humans in China. H9N2 viruses isolated from birds, pigs and humans have been classified into three sublineages based on antigenic and genetic features. Chicken antisera to H9N2 viruses of the Korean sublineage reacted with viruses of different sublineages by the hemagglutination-inhibition test. A test vaccine prepared from a non-pathogenic A/duck/Hokkaido/49/1998 (H9N2) strain of the Korean sublineage, obtained from our influenza virus library, induced immunity in mice to reduce the impact of disease caused by the challenge with A/Hong Kong/1073/1999 (H9N2), which is of a different sublineage. The present results indicate that an inactivated whole virus vaccine prepared from a non-pathogenic influenza virus from the library could be used as an emergency vaccine during the early stage of a pandemic caused by H9N2 infection.     

禽流感病毒分离株A/Goose/Guangdong/1/96(H5N1)全基因克隆及序列分析

本研究用无特定病原体（ＳＰＦ）鸡胚增殖禽流感病毒鹅体分离株Ａ／Ｇｏｏｓｅ／Ｇｕａｎｇｄｏｎｇ／１／９６（Ｈ５Ｎ１）（ＧＤ１／９６）,提取病毒基因组总ＲＮＡ,运用反转录－聚合酶链反应（ＲＴ－ＰＣＲ）技术分别扩增该病毒分离株的８个基因片段的ｃＤＮＡ,分别克隆后进行序列测定。序列分析结果表明,所扩增到的８个片段均包含相应的病毒基因的完整开放阅读框架。ＧＤ１／９６株与１９９７年香港禽流感事件中的４株香港流感病毒分离株（分别来自人、鸡、鸭和鹅）的ＨＡ基因的高度同源性说明它们可能起源于同一种系,但ＮＳ基因的差异说明它们分属于不同的基因群系。ＧＤ１／９６株与香港流感病毒分离株的核苷酸和推导的氨基酸序列的同源性较低（６３．９％￣９８．１％）,而香港流感病毒分离株之间的核苷酸和氨基酸序列的同源性很高（９６．５％￣１００％）,且香     

Neurotropism of the 1997 Hong Kong H5N1 influenza virus in mice

The direct transmission of H5N1 influenza A viruses from chickens to humans in Hong Kong in 1997 emphasized the need to have information on the pathogenesis of avian influenza virus infection in mammals. H5N1 influenza viruses isolated from patients during the incident killed experimentally infected mice. The principal lesions of the mice were broncho-interstitial pneumonia and nonsuppurative encephalitis. Infectious viruses and/or viral antigens were detected in the brain as well as in the trigeminal and vagal ganglia but not in the blood of the mice. These findings suggest that the virus reached the brain through the vagus and/or trigeminal nerves following replication in the respiratory mucosa. The results imply that neurotropism of the H5N1 virus in mice is a novel characteristic in the pathogenesis of infection by human influenza virus isolates.     

Pathogenicity of a Hong Kong-origin H5N1 highly pathogenic avian influenza virus for emus, geese, ducks, and pigeons

The H5N1 type A influenza viruses that emerged in Hong Kong in 1997 are a unique lineage of type A influenza viruses with the capacity to transmit directly from chickens to humans and produce significant disease and mortality in both of these hosts. The objective of this study was to ascertain the susceptibility of emus (Dramaius novaehollandiae), domestic geese (Anser anser domesticus), domestic ducks (Anas platyrhynchos), and pigeons (Columba livia) to intranasal (i.n.) inoculation with the A/chicken/Hong Kong/220/97 (H5N1) highly pathogenic avian influenza virus. No mortality occurred within 10 days postinoculation (DPI) in the four species investigated, and clinical disease, evident as neurologic dysfunction, was observed exclusively in emus and geese. Grossly, pancreatic mottling and splenomegaly were identified in these two species. In addition, the geese had cerebral malacia and thymic and bursal atrophy. Histologically, both the emus and geese developed pancreatitis, meningoencephalitis, and mild myocarditis. Influenza viral antigen was demonstrated in areas with histologic lesions up to 10 DPI in the geese. Virus was reisolated from oropharyngeal and cloacal swabs and from the lung, brain, and kidney of the emus and geese. Moderate splenomegaly was observed grossly in the ducks. Viral infection of the ducks was pneumotropic, as evidenced by mild inflammatory lesions in the respiratory tract and virus reisolation from oropharyngeal swabs and from a lung. Pigeons were resistant to HK/220 infection, lacking gross and histologic lesions, viral antigen, and reisolation of virus. These results imply that emus and geese are susceptible to i.n. inoculation with the HK/220 virus, whereas ducks and pigeons are more resistant. These latter two species probably played a minimal epidemiologic role in the perpetuation of the H5N1 Hong Kong-origin influenza viruses.     

10株H9N2亚型禽流感病毒血凝素基因的序列分析

为了解中国目前H9N2亚型禽流感病毒(avian influenza virus,AIV)血凝素(HA)基因的遗传变异情况,对中国不同地区分离的10株H9N2亚型AIV的HA基因进行扩增、克隆和测序,并对所获得的HA全序列进行同源性和遗传进化分析。结果表明,10个分离株的裂解位点均为RSSR↓GLF,符合低致病性AIV的分子特征;10个分离株有7~9个潜在糖基化位点,由于基因突变有些HA基因出现了新的糖基化位点;与参考株相比,发现了4个抗原表位的突变,这些表位的突变可能引起病毒致病性的改变;受体结合位点除198位有变异外,其他位点均较保守;6株病毒234位氨基酸均为L,具有与哺乳动物唾液酸α,2-6受体结合的特征;10个分离株HA基因与国内疫苗株的核苷酸及氨基酸序列同源性分别为90.4%~99.2%和92.2%~98.7%;10个分离株同属于欧亚谱系中的A/duck/Hong Kong/Y280/97群,但差异显著,为此本试验又将其分为4个不同的亚群。人工感染排毒试验结果表明,BJ15和NJ17分离株在鸡体内具有较强的复制能力,排毒周期较长且排毒量也较大,而S145N的漂变导致在145-147位氨基酸多出1个糖基化位点NGT,可能是分离株复制能力增强的原因。     

2株H3N8亚型禽流感病毒HA和NA基因遗传变异分析

采用RT-PCR技术扩增了2株H3N8亚型流感毒株A/duck/Guangxi/69/2009和A/chicken/Guangxi/2117/2010的HA和NA基因,并与GenBank中收录的其他毒株序列进行比较分析和遗传进化分析.结果表明,分离株的HA与NA基因全长分别为1 733 bp、1 432 bp.A/du...     

Coexpression of avian influenza virus H5 and N1 by recombinant Newcastle disease virus and the impact on immune response in chickens

To analyze the contribution of neuraminidase (NA) toward protection against avian influenza virus (AIV) infection, three different recombinant Newcastle disease viruses (NDVs) expressing hemagglutinin (HA) or NA, or both, of highly pathogenic avian influenza virus (HPAIV) were generated. The lentogenic NDV Clone 30 was used as backbone for the insertion of HA of HPAIV strain A/chicken/Vietnam/P41/05 (H5N1) and NA of HPAIV strain A/duck/Vietnam/TG24-01/05 (H5N1). The HA was inserted between the genes encoding NDV phosphoprotein (P) and matrixprotein (M), and the NA was inserted between the fusion (F) and hemagglutinin-neuraminidase protein (HN) genes, resulting in NDVH5VmPMN1FHN. Two additional recombinants were constructed carrying the HA gene between the NDV P and M genes (NDVH5VmPM) or the NA between F and HN (NDVN1FHN). All recombinants replicated well and stably expressed the HA gene, the NA gene, or both. Chickens immunized with NDVH5VmPMN1FHN or NDVH5VmPM were protected against two different HPAIV H5N1 and also against HPAIV H5N2. In contrast, immunization of chickens with NDVN1FHN induced NDV- and AIV N1-specific antibodies but did not protect the animals against a lethal dose of HPAIV H5N1. Furthermore, expression of AIV N1, in addition to AIV H5 by NDV, did not increase protection against HPAIV H5N1.     

Genetic characterization of H7N2 influenza virus isolated from pigs

Because pigs have respiratory epitheliums which express both α2-3 and α2-6 linked sialic acid as receptors to influenza A viruses, they are regarded as mixing vessel for the generation of pandemic influenza viruses through genetic reassortment. A H7N2 influenza virus (A/swine/KU/16/2001) was isolated from pig lungs collected from the slaughterhouse. All eight genes of the influenza virus were sequenced and phylogenetic analysis indicated that A/swine/KU/16/2001 originated in Hong Kong and genetic reassortment had occurred between the avian H7N2 and H5N3 influenza viruses. The first isolation of H7 influenza virus in pigs provides the opportunity for genetic reassortment of influenza viruses with pandemic potential and emphasizes the importance of surveillance for atypical swine influenza viruses.     

中国流行的2009甲型H1N1猪源流感病毒HA和NA基因的分子和遗传特征

目前流行的甲型H1N1流感病毒是一个复杂的基因重配病毒。对病毒的分子生物学研究,尤其是病毒囊膜蛋白血凝素（haemagglutini,HA）基因和神经氨酸酶（neuraminidase,NA）基因的研究,为控制和预防H1N1流感病毒具有重要的意义。本研究对中国流行的2009甲型H1N1猪源流感病毒的HA和NA基因与疫苗株A/California/07/2009（H1N1）,以及不同国家和地区的病毒株进行核苷酸和氨基酸序列分析。从NCBI的GenBank数据库下载所需要毒株的序列,采用Lasergene 6.0软件包中的EditSeq和MegAlign进行序列分析,进化树分析采用MEGA4.1软件。进化分析表明,中国流行的2009 H1N1流感病毒与疫苗株的核苷酸同源率分别在98.8%~99.7%和98.6%~99.6%之间;裂解位点处为I/VPSIQSR↓G,不具备高致病性流感病毒的特征;有1株NA抗性病毒。尽管与疫苗株相比,中国流行株2009甲型H1N1猪源流感病毒的HA和NA基因有部分突变,但这些突变并不是重要的。本研究首次详细分析了中国流行的2009甲型H1N1猪源流感病毒株与疫苗株的HA和NA基因的分子特征,对实时监测流感病毒HA和NA基因的变化具有重要意义。     

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.     

H4亚型家养水禽流感病毒分离株的表面膜蛋白基因的序列测定和遗传进化分析

采用常规的血清学试验和特异性RT-PCR方法对华东地区家养水禽中流感病毒的带毒状况进行4年多的监测，分离鉴定出多株H4亚型禽流感病毒。对其中的A／Duck／Yangzhou／216／2002（简称Dk／YZ／216／02）、A／Duck／Yangzhou／526／2003（简称Dk／YZ／526／03）、A／Duck／Yangzhou／36／2004（简称Dk／YZ／36／04）的血凝素基因和Dk／YZ／526／03、Dk／YZ／36／04的神经氨酸酶基因进行了克隆测序，并与GenBank中收录的其它序列进行了比较，遗传进化结果表明Dk／YZ／216／02的血凝素基因（HA）与毒株Tk／Minnesota／833／80（H4N2）同源性最高，而Dk／YZ／526／03和Dk／YZ／36／04的血凝素基因（HA）均与Budgerigar／Hokkaido／1／77（H4N6）同源性最高；而神经氨酸酶基因（NA）遗传进化分析结果表明Dk／YZ／36／04（H4N6）的NA基因与毒株Pigeon／Nanchang／8-142／2000（H3N6）同源性最高，而Dk／YZ／526／03（H4N2）的NA基因与Dk／Hokkaido／13／00（H9N2）同源性最高，3株禽流感病毒的HA推导的氨基酸剪切位点序列均为P-E-K-A-S-R，为典型低致病性禽流感病毒的特征序列，与对SPF鸡的致病力试验相吻合。     

Recombinant Strain A/HK/Otar/6:2/2010 (H3N8) for Development of a Live Intranasal Equine Influenza Vaccine

Recombinant cold-adapted strain A/HK/Otar/6:2/2010 (H3N8) constructed by the method of classic genetic reassortment, inherited the hemagglutinin and neuraminidase genes from the epizootic A/equine/Otar/764/2007 (Н3N8) virus and genes of nonglycosylated proteins from attenuation donor A/Hong Kong/1/68/162/35 (H3N2). The resulted virus was of cold-adapted (efficient growth at 25°C) and temperature-sensitive (restricted replication at 39°C) phenotype. Like the parental virus of subtype H3N2, the resulted reassortant was attenuated, with limited replication in lungs of mice (1.75 lgEID₅₀/mL) versus replication in turbinate (2.5 lgEID₅₀/mL). Intranasal immunization of mice with A/HK/Otar/6:2/2010 (H3N8) reassortant did not induce animal weight reduction in contrast to epizootic A/equine/Otar/764/2007 (Н3N8) virus.     

Antigenic and genetic analyses of H5 influenza viruses isolated from ducks in Asia.

The hemagglutinin (HA) of six H5 influenza virus strains isolated from ducks in Japan and China in 1976 to 1996 were analyzed antigenically and genetically. Antigenic analysis using a panel of monoclonal antibodies revealed that the HA of H5 influenza viruses isolated from ducks are antigenically closely related to each other. Phylogenetic analysis indicates that the isolates from ducks in Hokkaido were derived from an ancestor common with the highly pathogenic isolates from chickens and humans in Hong Kong in 1997.     

Molecular characterization of low pathogenic avian influenza viruses, isolated from food products imported into Singapore

We have completed the genetic characterization of all eight gene segments for four low pathogenic avian influenza (LPAI) viruses. The objective of this study was to detect the presence of novel signatures that may serve as early warning indicators of the conversion of LPAI viruses to high pathogenic avian influenza (HPAI) viruses. This study included three H5N2 and one H5N3 viruses that were isolated from live poultry imported into Singapore as part of the national avian influenza virus (AIV) surveillance program. Based on the molecular criterion of the World Organisation for Animal Health (OIE), sequence analysis with the translated amino acid (aa) sequence of the hemagglutinin (HA) gene revealed the absence of multibasic aa at the HA cleavage site, identifying all four virus isolates as LPAI. Detailed phylogenetic tree analyses using the HA and neuraminidase (NA) genes clustered these isolates in the Eurasian H5 lineage, but away from the HPAI H5 subtypes. This analysis further revealed that the internal genes clustered to different avian and swine subtypes, suggesting that the four isolates may possibly share their ancestry with these different influenza subtypes. Our results suggest that the four LPAI isolates in this study contained mainly avian signatures, and the phylogenetic tree for the internal genes further suggests the potential for reassortment with other different circulating avian subtypes. This is the first comprehensive report on the genetic characterization of LPAI H5N2/3 viruses isolated in South-East Asia.     

两株H6N2亚型鸡源禽流感病毒的分离鉴定

本研究利用血凝抑制试验(HI)、反转录-聚合酶链式反应(RT-PCR)、基因测序等方法,对广东省某活禽交易市场进行流行病学调查时获得的两株非H5、H9亚型禽流感病毒65株和C7株进行了亚型鉴定。结果表明这两株病毒均具有血凝活性,且能被抗H6亚型禽流感病毒标准阳性血清特异性抑制。用针对禽流感病毒的M基因、H6亚型禽流感病毒HA基因、N2亚型禽流感病毒NA基因特异性鉴定引物对65株和C7株进行RT-PCR扩增,分别获得特异性目的片段。测序及BLAST分析表明两株分离株与H6N2亚型禽流感广东分离株的HA基因和NA基因核苷酸序列相似性均高达95%以上。将该两分离株鉴定为H6N2亚型禽流感病毒,并命名为A/Chicken/Guangdong/65/2009、A/Chicken/Guangdong/C7/2009。