Molecular characterization and phylogenetic analysis of new Newcastle disease virus isolates from the mainland of China

Seventy-nine velogenic Newcastle disease virus (NDV) isolates were obtained from infected chicken flocks during the outbreaks of Newcastle disease (ND) in various regions of the mainland of China in 2006. The F gene fragment (535 bp, from nt 47 to 581 of the F gene) which codes the main functional region of the F protein was obtained by RT-PCR and sequenced. All sequences obtained in this study have been submitted to GenBank. All the isolates have the motif ¹¹²R-R-Q/R-K/R-R-F¹¹⁷ at the cleavage site of the fusion protein, which is typical of velogenic NDV isolates. For genotyping, a phylogenetic tree based on nucleotides 47–435 of the F gene was constructed, and the 79 isolates could be divided into two genotypes, namely VIId and III. Most of the isolates proved to be of genotype VIId; only two isolates were of genotype III. Genotype VIId NDV has been the predominant pathogen responsible for most Newcastle disease outbreaks in China. The proportion of isolates of genotype VIId NDV shows an increasing trend, according to studies on the molecular epidemiology of NDV in China from 2002 to 2006.     

Molecular characterization and phylogenetic analysis of new Newcastle disease virus isolates from the mainland of China

Seventy-nine velogenic Newcastle disease virus (NDV) isolates were obtained from infected chicken flocks during the outbreaks of Newcastle disease (ND) in various regions of the mainland of China in 2006. The F gene fragment (535 bp, from nt 47 to 581 of the F gene) which codes the main functional region of the F protein was obtained by RT-PCR and sequenced. All sequences obtained in this study have been submitted to GenBank. All the isolates have the motif ¹¹²R-R-Q/R-K/R-R-F¹¹⁷ at the cleavage site of the fusion protein, which is typical of velogenic NDV isolates. For genotyping, a phylogenetic tree based on nucleotides 47–435 of the F gene was constructed, and the 79 isolates could be divided into two genotypes, namely VIId and III. Most of the isolates proved to be of genotype VIId; only two isolates were of genotype III. Genotype VIId NDV has been the predominant pathogen responsible for most Newcastle disease outbreaks in China. The proportion of isolates of genotype VIId NDV shows an increasing trend, according to studies on the molecular epidemiology of NDV in China from 2002 to 2006.     

Characterization of pigeon-origin Newcastle disease virus isolated in China

Fourteen pigeon-origin Newcastle disease virus (NDV) isolates were obtained from sick pigeons in China between 1996 and 2005. The mean death time (MDT) of embryonated eggs and the intracerebral pathogenicity indices (ICPI) were tested to determine the virulence of the field isolates. The result indicated that most isolates were proved to be mesogenic (MDT 60-90 hr and ICPI > 1.2). The main function regions of F protein gene of the isolates were amplified and sequenced for phylogenetic and residue substitutive analysis. The fusion protein cleavage site sequences of most isolates had multiple basic amino acids R/KRQKRF at positions 112-116 and a phenyl alanine at position 117, characteristic of velogenic isolates. In the phylogenetic tree, the majority of the isolates were clustered into a single genetic lineage, termed genotype VIb, and were typical pigeon paramyxovirus type 1, whereas a small number of recent isolates (three strains) were grouped into genotype VIId, a predominant genotype responsible for most Newcastle disease outbreaks in chickens and geese since the end of last century. One isolate, PK9901, was proved to be a lentogenic strain, of genotype II NDV, to which the vaccine strain La Sota belongs.     

Newcastle disease outbreaks in western China were caused by the genotypes VIIa and VIII

Twelve Newcastle disease virus (NDV) strains were isolated from chickens involved in outbreaks of Newcastle disease (ND) in western China (Shaanxi, Gansu, Xinjiang, Qinghai and Guangxi provinces) between 1979 and 1999. All strains were determined to be velogenic by plaque formation, the mean death time (MDT) of embryonated eggs, and the intracerebral pathogenicity index (ICPI). For preparation of virus RNA, the acid guanidinium-thiocyanate method was used. A 908bp fragment of nucleotide was amplified by RT-PCR starting from the N terminal of the F gene and the PCR segments were cloned into the PGEM-T vector and sequenced. The similarities of the nucleotide sequences (1-519bp) and predicted amino acid sequences of the F gene (1-125) were analyzed by comparing the 12 NDV isolates with the NDV vaccine strains Lasota, B1, H1 and V4, with classical NDV strains and recent epizootic strains. Phylogenetic analysis demonstrated that all strains were of two novel genotypes; the NDV strains that caused the outbreak of ND in western China during 1998-1999 was of the genotype VIIa, whereas the strains from the Qinghai province (1979-1985) were of genotype VIII, which has been found predominately in southern Africa.     

Molecular epidemiology of Newcastle disease viruses in Vietnam

Newcastle disease virus (NDV) causes significant economic losses to the poultry industry in Southeast Asia. In the present study, 12 field isolates of NDV were recovered from dead village chickens in Vietnam between 2007 and 2012, and were characterized. All the field isolates were classified as velogenic. Based on the sequence analysis of the F variable region, two distinct genetic groups (Vietnam genetic groups G1 and G2) were recognized. Phylogenetic analysis revealed that all the 12 field isolates fell into the class II genotype VII cluster. Ten of the field isolates, classified as Vietnam genetic group G1, were closely related to VIIh viruses that had been isolated from Indonesia, Malaysia, and Cambodia since the mid-2000s, while the other two field isolates, of Vietnam genetic group G2, clustered with VIId viruses, which were predominantly circulating in China and Far East Asia. Our results indicate that genotype VII viruses, especially VIIh viruses, are predominantly responsible for the recent epizootic of the disease in Vietnam.     

Molecular characterization of Newcastle disease viruses in Ostriches (Struthio camelus L.): further evidences of recombination within avian paramyxovirus type 1

Newcastle disease virus (NDV) strains isolated from ostriches have been genotyped for the first time by partial sequencing of the F gene to determine the epidemiologic role that this species can play within ND outbreaks. Fifteen additional NDV strains, mostly isolated from chickens but also from pigeons and penguins, were also included in the study to determine genetic relationships with ostriches NDV isolates. High genetic diversity was demonstrated in ostrich NDV isolates, as the 10 isolates were grouped in four distinct NDV genotypes. In agreement with the results obtained when chicken isolates have been molecularly characterized, the predominant genotype in ostriches was the genotype VII. More interestingly, evidences of recombination between genotype II and VII were observed in one ostrich isolate and in two further chicken isolates. Therefore, it seems that ostriches may play a relevant role in the ecology and epidemiology of ND particularly in those regions where they have an increasing farming importance as minor poultry species.     

Molecular characterization of a recent Newcastle disease virus outbreak in Jordan

Newcastle disease (ND) is a highly contagious viral disease and is a continuous threat to the poultry industry worldwide. In the early months of 2011, several devastating ND outbreaks occurred in Jordan affecting broilers, layers and breeders. The fusion gene of the isolated Newcastle disease virus (NDV) was partially amplified by RT-PCR, then directly sequenced. The NDV isolates were found to have the motif(112)RRQKRF(117). This motif and a mean death time (MDT) of 46h are indicative of the velogenic nature of these NDV isolates. Phylogenetic analysis showed that the new NDV strain belongs to the lineage 5d (Aldous et al., 2003) and is closely related to the Chinese strain SG/Liaoning/2009. NDV outbreaks in 2010 and 2011 have been noted in neighboring countries. Based on the high nucleotide similarity between our isolated NDV isolates and the Chinese NDV strain, the origin of these recent NDV isolates might be from China.     

Newcastle disease virus isolated from recent outbreaks in Taiwan phylogenetically related to viruses (genotype VII) from recent outbreaks in western Europe

Three major outbreaks of Newcastle disease (ND) occurred in Taiwan in the last three decades (in 1969, 1984, and 1995). Newcastle disease viruses (NDVs) isolated in the three outbreaks, together with those isolated in 1998, were sequenced between nucleotides 47 and 435 of the fusion gene. A phylogenetic tree based on sequences obtained showed that the NDV isolated in 1969 was similar to the genotype III viruses. In contrast, all isolates in 1984 and seven of the eight isolates in 1995, together with all isolates in 1998, fell into the genotype VII. These results suggest that the 1969 outbreak of ND in Taiwan was caused by the genotype III virus, whereas the 1984 and 1995 outbreaks were caused by the genotype VII viruses. To date, the genotype VII viruses have caused many outbreaks in east Asia and western Europe. We suspect that these outbreaks have constituted the fourth panzootic of ND, which is distinct from the third panzootic caused by the "pigeon PMV-1 viruses." NDV isolated in Taiwan in 1984 was the earliest isolation of the genotype VII virus.     

Newcastle disease virus outbreaks: Vaccine mismatch or inadequate application?

Newcastle disease (ND) is one of the most important diseases of poultry, and may cause devastating losses in the poultry industry worldwide. Its causative agent is Newcastle disease virus (NDV), also known as avian paramyxovirus type 1. Many countries maintain a stringent vaccination policy against ND, but there are indications that ND outbreaks can still occur despite intensive vaccination. It has been argued that this may be due to antigenic divergence between the vaccine strains and circulating field strains. Here we present the complete genome sequence of a highly virulent genotype VII virus (NL/93) obtained from vaccinated poultry during an outbreak of ND in the Netherlands in 1992-1993. Using this strain, we investigated whether the identified genetic evolution of NDV is accompanied by antigenic evolution. In this study we show that a live vaccine that is antigenically adapted to match the genotype VII NL/93 outbreak strain does not provide increased protection compared to a classic genotype II live vaccine. When challenged with the NL/93 strain, chickens vaccinated with a classic vaccine were completely protected against clinical disease and mortality and virus shedding was significantly reduced, even with a supposedly suboptimal vaccine dose. These results suggest that it is not antigenic variation but rather poor flock immunity due to inadequate vaccination practices that may be responsible for outbreaks and spreading of virulent NDV field strains.     

新城疫病毒贵州不同鸡源分离株F基因的克隆与序列分析

应用PCR技术扩增NDV贵州不同鸡源分离株,包括肉鸡源P1株与BY株、蛋鸡源H2株与FW株、七彩山鸡源N98株和越南斗鸡源DQ株的F蛋白基因,将该基因片段分别进行克隆和测序,并与国内外NDV参考株的对应序列进行比较分析。结果表明:6株NDV贵州不同鸡源分离株的F基因长度均为1 662 bp,编码553个氨基酸;分离株间核苷酸同源性为86.9%~99.7%,氨基酸同源性为91.0%~99.3%;与国内外NDV代表株(LaSota株、B1株、F48E9株、CH2000株和TW 2000株)的核苷酸同源性为84.0%~98.9%,氨基酸同源性为87.2%~98.6%;经系统发育进化树分析,DQ株、N98株、P1株和H2株为基因VIId型,而BY株和FW株为基因IX型。这些结果提示贵州省不同鸡群间存在相同NDV毒株感染的可能性,不同年份间NDV毒株发生基因型改变,而近年来贵州省流行的ND疫情主要是由NDV基因VII型引起。     

Molecular epidemiological investigation of Newcastle disease virus from domestic ducks in Korea

To expand the epidemiological understanding of Newcastle disease virus (NDV) found in domestic ducks in Korea, 14 NDV isolates from apparently healthy domestic ducks were biologically and genetically characterized. Thirteen and 1 isolates of NDV were categorized into lentogenic and velogenic viruses, respectively, based on in vivo pathogenicity tests. Twelve lentogenic viruses showed HA activity to horse RBCs, while 1 lentogenic virus and the velogenic virus were negative. Lentogenic viruses (n=13) had sequence motifs of (112)ERQERL(117) (n=1) or (112)GRQGRL(117) (n=12) at the F0 cleavage site, while the velogenic virus (n=1) had a sequence motif of (112)RRQKRF(117) at the same site. Phylogenetic analysis revealed that at least three distinct genotypes may exist in domestic ducks in Korea; one class I genotype (genotype 2), and two class II (genotypes I and VII) genotypes. The class I virus was most closely related to strains of genotype 2 which were isolated in birds from the USA, Germany and Denmark. Twelve lentogenic class II viruses were grouped together in genotype I, and were then divided into at least three clusters, namely Aomori-like, Ulster2C-like, and V4-like. The velogenic class II virus was assigned to genotype VII which represents viruses responsible for recent epidemics in many Asian countries including Korea. The epidemiological importance of domestic duck isolates of NDV in Korea is discussed.     

Molecular characterization of Newcastle disease viruses isolated from rural chicken in northwest Ethiopia reveals the circulation of three distinct genotypes in the country

Newcastle disease (ND) is a highly contagious disease that affects many species of birds and causes significant economic losses to the poultry industry worldwide. Fifteen Newcastle disease virus (NDV) isolates obtained from rural chickens in northwest Ethiopia in 2011 and 2012 were characterized genotypically. The main functional region of the F gene was amplified and sequenced (260 nucleotides). Among the Ethiopian NDV isolates, 2 isolates had the virulent motif ¹¹²R-R-Q-K-R-F¹¹⁷ at the cleavage site of the fusion protein while 13 isolates contained the lentogenic motif ¹¹²G-G/R-Q-G-R-L¹¹⁷. Phylogenetic analysis based on the variable region of the F gene indicated that the two isolates exhibiting the virulent motif belonged to lineage 5 (genotype VII) subgenotype d and the remaining 13 isolates were grouped into lineage 2 (genotype II). The nucleotide sequences of lineage 5 isolates were genetically related to the Sudanese NDV isolates, suggesting potential epidemiological link of ND outbreaks between neighbouring countries. The lentogenic strains shared similarities with La Sota vaccine strain and probably originated from the vaccine strain either through direct exposure of birds to the live vaccine or to infectious La Sota-like strains circulating in rural poultry. This study provides genetic evidence on the existence of different NDV genotypes circulating in the rural poultry in Ethiopia. The virulent NDV continues to be a problem in poultry sector in Ethiopia, and their continuous circulation in rural and commercial poultry calls for improved surveillance and intensified vaccination and other control measures.     

华东地区健康水禽携带新城疫病毒情况调查

近年来,新城疫逐渐成为了一种严重的家养水禽疾病。尽管如此,目前对于我国水禽新城疫的流行和分布情况依然知之甚少。本研究采集了2011-2012年中国华东6省1市的部分活禽市场和养殖场表观健康家鸭和家鹅泄殖腔棉拭样品,进行新城疫病毒的分离和毒力检测工作。通过测定分离株F基因高变区nt47-420,对其进行遗传进化分析。结果显示,在1200份样品中,检测到阳性样品23份,分离率为1．92％,表明眼观健康家鸭和家鹅中携带新城疫病毒。对比寒冷的春冬两季和炎热的夏季,新城疫病毒的分离率存在明显的差别。在中国家鸭和鹅中流行的新城疫毒株依然对温度敏感,高温天气不利于新城疫疫情蔓延。对分离株的鸡胚平均死亡时间和脑内接种指数进行了测定。参考76株GenBank中已发表并鉴定基因型毒株的F基因高变区nt47～420,对23株家养水禽分离株进行了遗传进化分析,结果发现分离株与流行的强毒株和疫苗株遗传距离较远。其中,13株与ClassII基因Ib亚型遗传距离最近;3株属于ClassI基因2型;7株与ClassI基因3b亚型遗传距离最近。     

鸡新城疫病毒河北分离株F基因的分子特性分析

通过毒力测定、RT-PCR及F基因的序列测定与遗传进化分析,对2005-2008年从河北省部分地区的发病鸡群中分离到的10株新城疫病毒（NDV）进行了研究。各分离株经典毒力测定结果显示：MDT在37.6～54.4h之间,ICPI在1.71～2.0之间,IVPI值在2.16～2.8之间,均为新城疫病毒强毒株特征。F基因的序列测定表明,分离株之间的核苷酸序列具有77.4%～98.0%的同源性,与疫苗株Lasota的同源性为87.0%～98.9%,与国内标准强毒株F48E9同源性为89.7%～98.9%。推导其氨基酸序列分析表明,8个分离株的F蛋白的裂解位点氨基酸组成为112 R-R-Q-K-R-F117,具有NDV强毒株特征,与毒力测定结果相符,2个分离株的F蛋白的裂解位点氨基酸组成为112 G-R-Q-G-R-L117,与弱毒株特征相符。F基因分型和同源性比较显示：目前河北新城疫的流行以基因Ⅶ型为主（占70%）,同时兼有基因Ⅱ型（占20%）和基因Ⅸ型（占10%）。     

Phylogenetic analysis of Newcastle disease viruses isolated from wild birds in the Poyang Lake region of China

Newcastle disease virus (NDV) causes a highly contagious viral disease in poultry and wild birds, and it can cause significant economic loss worldwide. Eight viral strains were isolated by inoculating embryonated chicken eggs from the Poyang Lake region of China with swab samples. All eight of the NDV isolates were identified as class I genotype 3 strains, but they diverged notablely from class II viruses. Further analysis revealed that all eight NDV isolates were lentogenic strains containing the ¹¹²ERQER↓L¹¹⁷ motif at the F protein cleavage site. The strains were highly identical and were more species specific (chicken and waterfowl) than site specific (Nanchang and Duchang regions). The close phylogenetic proximity of these isolates indicates that viral transmission may happen between poultry and wild birds. Our study demonstrates that lentogenic class I NDVs exist in clinically healthy wild waterfowl and poultry within the Poyang Lake region. Active surveillance of these viruses to determine their evolution and origin is one of the most realistic strategies for preventing and controlling NDV outbreaks.     

Characterisation of genotype VII Newcastle disease virus (NDV) isolated from NDV vaccinated chickens,and the efficacy of LaSota and recombinant genotype VII vaccines against challenge with velogenic NDV

A Newcastle disease virus (NDV) isolate designated IBS002 was isolated from a commercial broiler farm in Malaysia. The virus was characterised as a virulent strain based on the multiple basic amino acid motif of the fusion (F) cleavage site ¹¹²RRRKGF¹¹⁷ and length of the C-terminus extension of the hemagglutinin-neuraminidase (HN) gene. Furthermore, IBS002 was classified as a velogenic NDV with mean death time (MDT) of 51.2 h and intracerebral pathogenicity index (ICPI) of 1.76. A genetic distance analysis based on the full-length F and HN genes showed that both velogenic viruses used in this study, genotype VII NDV isolate IBS002 and genotype VIII NDV isolate AF2240-I, had high genetic variations with genotype II LaSota vaccine. In this study, the protection efficacy of the recombinant genotype VII NDV inactivated vaccine was also evaluated when added to an existing commercial vaccination program against challenge with velogenic NDV IBS002 and NDV AF2240-I in commercial broilers. The results indicated that both LaSota and recombinant genotype VII vaccines offered full protection against challenge with AF2240-I. However, the LaSota vaccine only conferred partial protection against IBS002. In addition, significantly reduced viral shedding was observed in the recombinant genotype VII-vaccinated chickens compared to LaSota-vaccinated chickens.     

NDV subgenotype VII(L) is currently circulating in commercial broiler farms of Iran, 2017–2018

Background

Based on our previous work, it was discovered that some Newcastle disease virus (NDV) isolates from backyard poultry between 2011 and 2013 in Iran formed a new separate cluster when phylogenetic analysis based on the complete F gene sequence was carried out. The novel cluster was designated subgenotype VII(L) and published.

Aim

In the current study, for further validation, we initiated a comprehensive epidemiological study to identify the dominant NDV genotype(s) circulating within the country. Collection of samples was executed between October 2017 and February 2018 from 108 commercial broiler farms which reported clinical signs of respiratory disease in their broilers.

Result

We report that 38 of the farms (> 35%) tested positive for NDV. The complete F gene sequences of seven of the isolates are shown as representative sequences in this study. According to the phylogenetic tree constructed, the recent broiler farm isolates clustered into the newly designated cluster VII(L) together with the older Iranian backyard poultry isolates in our previous work. All the sequences shared the same virulence-associated F cleavage site of ₁₁₂RRQKR↓F₁₁₇.

Conclusion

Our phylogenetic analysis suggested that the NDV subgenotype VII(L) may have been derived from subgenotype VIId, and contrary to popular belief, subgenotype VIId may not be the dominant subgenotype in Iran. Tracking of the subgenotype on BLAST suggested that the NDV subgenotype VII(L), although previously unidentified, may have been circulating in this region as an endemic virus for at least a decade. Other NDV genotypes, however, have also been reported in Iran in recent years. Hence, ongoing study is aimed at determining the exact dominant NDV genotypes and subgenotypes in the country. This will be crucial in effective mitigation of outbreaks in Iranian broiler farms.