一种新型冠状病毒基因的克隆和序列分析与传染性非典型肺炎病原学的调查

目的 探讨冠状病毒感染与传染性非典型肺炎发病的关系，分析冠状病毒基因序列变异的临床意义，建立诊断冠状病毒变异株感染的分子生物学方法。方法 收集非典型肺炎(SARS)患者的不同临床标本，采用PCR技术分别进行衣原体、甲肺炎病毒以及冠状病毒等的基因检测。以冠状病毒相对保守的依赖RNA的RNA多聚酶基因为靶基因，采用Nested RT—PCR技术从非典型肺炎患者的鼻咽吸取物标本和濑喉液标本中扩增出冠状病毒基因，将PCR产物直接克隆到T载体，进行序列测定，进一步比较不同分离株间的核苷酸和氨基酸序列同源性。结果 在27例非典型肺炎患者中检出冠状病毒基因阳性6例，阳性率为22．2％。而在15例健康对照中，全部阴性。采用BLAST软件将所获得的冠状病毒的基因序列与基因库(GenBank)登记的序列比较，结果显示本次分离克隆的冠状病毒基因与既往报道的所有冠状病毒在核苷酸水平没有相关性，核苷酸同源性最高不超过40％。但在氨基酸水平的同源性为80％左右(70％-82％)。从不同患者中分离的冠状病毒基因之间在核苷酸水平的同源性在98％以上。与刚刚公布的加拿大、中国香港、英国等SARS冠状病毒的核苷酸序列同源性在99％以上。结论 相当部分非典型肺炎患者存在冠状病毒的感染，提示本次的非典型肺炎发病与感染冠状病毒有关。序列分析结果表明从本次非典型肺炎患者中分离的冠状病毒为一种新的冠状病毒，并与世界其他地区分离的SARS冠状病毒同源性达99％以上。以RNA多聚酶为靶基因Nested RT—PCR技术可以用于诊断这一新种冠状病毒感染。     

SARS患者咽拭标本中新分离呼肠病毒部分基因组序列分析

目的 研究SARS患者中多病原感染状况，测定并分析新分离呼肠病毒基因组序列，从病毒的分子生物学角度研究其分类学位置。方法 SARS患者咽拭子标本经处理后接种Hep-2细胞，提取分离到的病毒RNA，以随机引物逆转录PCR扩增，PCR产物经克隆、测序，将其核苷酸序列及推断的氨基酸序列与GenBank（数据库中基因进行比较分析并建立系统进化树。结果 从4份SARS患者咽拭子标本中分离到3株呼肠病毒，部分基因片段测序结果显示为同一病毒，其病毒基因与呼肠病毒1、2、3型有较高的同源性，尤其是与呼肠病毒1、3型，相应片段的核苷酸序列同源性达82％～92％，推断相应氨基酸序列同源性高达94％～99％，而与其他病毒不存在有意义的同源性；系统进化树分析显示新分离呼肠病毒属于呼肠病毒科呼肠病毒属，且可能为哺乳动物呼肠病毒中的新血清型。结论 SARS患者咽拭子标本中存在呼肠病毒，新分离呼肠病毒核苷酸和氨基酸序列与呼肠病毒1、3型同源性最高，由于尚未得到决定病毒血清型的S1片段基因序列，故该病毒的确切分型有待进一步确定，与SARS患者病情的关系有待进一步研究。     

海南岛两株甲病毒基因组3′末端核苷酸序列的克隆与分析

目的　从分子水平鉴定海南省分离的两株甲病毒 (HBb17和M1病毒 )。方法　采用RT-PCR方法 ,分别扩增两株病毒基因组的 3′末端核苷酸序列 ,扩增产物经亚克隆 ,筛选重组子并测定核苷酸序列对序列进行分析。结果　HBb17和M1病毒分别扩增出约 1 6kb和 1 3kb的特异片段。序列分析表明 ,在 3′末端非翻译区HBb17病毒与罗斯河病毒 (国际标准株T48病毒 )核苷酸同源性为99 % ,M1病毒与鹭山病毒 (SAG)同源性为 98% ;两病毒结构基因的E1区序列 ,HBb17病毒与罗斯河病毒核苷酸 (氨基酸 )同源性为 99% (99% ) ,M1病毒与鹭山病毒核苷酸 (氨基酸 )同源性为 97% (99% ) ,M1病毒与盖塔病毒同源性为 94% (98% )。结论　序列分析表明 ,海南岛分离的HBb17病毒属于罗斯河病毒 ,M1病毒可能是鹭山病毒或盖塔病毒的变异株     

山东省部分HIV-1流行株的亚型分析和序列特征研究

目的　对山东省HIV 1流行毒株进行亚型分析 ,并研究其变异特征。方法　采集 2 6份HIV 1感染者的外周静脉抗凝血 ,提取前病毒DNA进行体外扩增 ,获得包膜蛋白 (env)基因的核酸片段 ,并对其C2 V3及邻区的核苷酸进行测定和分析。结果　基因和氨基酸序列分析表明 ,2 6份标本中存在 4种亚型和重组毒株 (B′、C、A、A/E) ,其中B′ 17株 ,其组内基因距离为 11.6 9± 4 .19。V3环顶端四肽有 6种形式 ,最多的是GPGQ(15株 )、GPGR(6株 )。V3环第 11、2 5位氨基酸出现变异 ,并有 1株呈电荷双阳性。结论　山东省HIV 1流行株亚型较多 ,有重组毒株出现的可能 ,基因发生较大变异 ,HIV 1传播在山东省有加快的趋势。     

登革2型病毒广东流行株结构蛋白基因序列测定及分析

目的 对广东省90年代以来流行的3株登革2型病毒(DEN2)的结构蛋白基因序列测定及分析，了解流行株之间的相互关系、变异及基因型：方法 应用RT-PCR技术扩增广东省不同年份流行的3株DEN2型病毒的结构蛋白基因(C、PrM、E基因)。分别克隆到pMD18T载体，转化JM109宿主菌，挑取阳性克隆进行鉴定及序列测定。结果 3株DEN2病毒结构蛋白基因序列长度均为2325bv，编码775个氨基酸。三者核苷酸(氨基酸)的同源性分别是：GD06／93与GD19／2001为96％(97％)、GD06／93与GD08／98为94％(97％)、GD08／98与GD19／2001为92％(94％)。其在相关毒力位点E383～385处均为GLU—PRO-GLY、E126处均为GLU。3株DEN2与国际参考株比较表明：GD06／93与GD19／2001和澳大利亚TSV01株共享序列非常接近，核苷酸(氨基酸)的同源性为98％(98％)；GD08／98与泰国株ThNH-P28／93核苷酸(氨基酸)同源性为98％(98％)。此3株DEN2二级结构与对乳鼠不致病的04株比较，主要差别位于其393～400氨基酸处，本室分离的3株对乳鼠致病毒株为EEEEHHHH，而04株为EEEE----；337～343处本室分离的3株对乳鼠致病毒株为HH-------HHHHH，而04株为--------HHHHE-，恰好位于Dengue病毒E基因的Ⅲ区：结论 GD06／93、GD19／2001与TSV01亲缘关系较近，属同一基因型。GD08／98与ThNH—P28／93共享序列非常接近，属同一基因型。3株DEN2病毒在E蛋白Ⅲ区结构有一定变异，可能与毒力有关。     

重庆流行性乙型脑炎病毒分离株CQ11-66在PrM/C及E基因区的分子特征

目的 分析重庆地区儿童流行性乙型脑炎(简称乙脑)病毒分离株CQ11-66在PrM/C及E基因区的分子特征.方法 采集重庆医科大学附属儿童医院感染消化科诊断的流行性乙脑患者血液及脑脊液标本,通过接种BHK-21细胞检测并分离乙脑病毒,并对其PrM/C及E基因区测序.使用Clustal X(1.8)、MEGA5等生物学软件进行核苷酸序列、氨基酸序列及系统进化分析.结果 本研究仅从儿童乙脑患者脑脊液标本中分离到1株乙脑病毒,命名为CQ11-66.CQ11-66和其他国家及地区的乙脑病毒分离株相比,PrM/C基因区总体核苷酸及氨基酸序列同源性分别为74.8％～97.4％及85.6％～98.7％,而E基因区总体核苷酸及氨基酸序列同源性分别为81.6％ ～ 99.6％及94.8％ ～99.6％;CQ11-66株与福建省乙脑病毒人分离株相比较,在PrM/C、E基因核苷酸及氨基酸序列同源性均很高.基于PrM/C及E基因区核苷酸序列进行系统进化分析,CQ11-66株属于基因Ⅲ型.结论 在重庆市儿童乙脑患者标本中分离到1株乙脑病毒CQ11-66,CQ11-66株在PrM/C和F基因区核苷酸序列和氨基酸序列同其他乙脑病毒分离株存在一定的差异,且系统进化分析显示CQ11-66株属于乙脑病毒基因Ⅲ型.     

2009年泉州市H1N1流感监测及基因特性分析

目的 了解2009年泉州地区H1N1流感监测情况,分析泉州市H1N1流感病毒的HA和NA基因特征,探讨该病毒的遗传变异及分子特性.方法 对泉州市H1N1流感监测期间的病人咽拭子采用real-time RT-PCR方法检测病毒核酸,MDCK细胞培养进行病毒分离、鉴定,并提取其中2株代表性毒株病毒RNA;采用RT-PCR扩增病毒HA和NA基因,纯化产物进行核苷酸序列测定;用DNAStar Megalign软件进行序列分析.结果 1020份咽拭子中有200份为H1N1流感病毒核酸阳性,70份季节性流感病毒核酸阳性,其中53份为H3N2亚型,14份为H1N1亚型,3份为B型,并分离到29株甲型H1N1流感病毒株.HA基因经核苷酸序列测定显示,该毒株与北美流行株高度同源,由HA基因核苷酸序列推导的氨基酸系列与疫苗株A/Brisbane/59/2007相比,有22个位于抗原决定簇的氨基酸位点发生变异,但受体结合特异性仍为人样受体.NA基因耐药性位点分析,显示对达菲药物依然敏感.结论 2009年泉州市H1N1流感流行毒株与北美流行株高度同源,相对于疫苗代表株出现了HA蛋白抗原性的改变.     

新疆地区克里米亚刚果出血热病毒M片段的遗传分析

目的 为进一步了解克里米亚刚果出血热病毒（CCHFV）M基因的特征，对新疆地区4侏克里米亚刚果出血热病毒分离株亚东璃眼蜱的部分M片段核苷酸序列进行测定及分析。方法 从感染CCHF病毒的鼠脑中提取RNA，应用逆转录聚合酶链反应扩增，测定CCHF病毒的部分M片段核苷酸序列，与GenBank中的已登录的部分CCHF病毒M基因的同源序列进行比较分析和种系进化分析。结果 经测序得到了4株病毒的3962～4385nt位点的424bp核苷酸序列（位点依据IbAr10200的M基因序列），该序列共编码139个氨基酸。前3株病毒序列有相当高的核苷酸同源性（99．5％～99．8％），将所得到的序列与已发表的中国、尼日利亚、巴基斯坦、乌兹别克斯坦、塔吉克斯坦和俄罗斯病毒株相比，中国株之间的核苷酸同源性为78．1％～99．8％，而非中国株则为42．9％～94．8％。但它们所编码的氨基酸序列变异不大，同源性非常高。系统发生树表明，所有的毒株被分为5个进化支（所比较的M基因长度为3962～4385nt核苷酸），来自新疆南部和东部的YT05099、YL04041和YL05035共处于同一分支。结论 相比于新疆其他分离株，YT05099、YL04041和YL05035的部分M基因特征有极高的相似性。新疆株CCHF病毒M基因与中东和远东病毒株之间有较近的亲缘关系。     

一例输入性非典型肺炎患者病原体的分离鉴定及其变异性研究

目的 对一例输入性非典型肺炎病例的病原体进行分离鉴定，研究其变异情况，为该病的诊断和防治提供依据。方法 用Vero E6细胞对病人的咽拭标本进行分离培养，并对分离物使用电镜、间接免疫荧光(IFA)、巢式PCR及S基因核苷酸序列测定等方法进行分析。结果 在该病人的咽拭标本中，成功地分离到一株冠状病毒(R69)，将部分S基因测序并与不同地区非典型肺炎病人分离株进行比较，表明分离到的毒株为一种新型冠状病毒。结论 目前存在冠状病毒的变异株，病毒核苷酸序列与广东省原发性SABS病人分离到的冠状病毒有所不同。     

中国部分甲肝病毒流行株结构蛋白VP3-VP1区基因特点分析

目的 分析中国部分甲肝病毒流行株结构蛋白VP3-VP1区基因特点.方法 收集42份甲肝患者急性期血清标本,经核酸提取、逆转录及巢氏PCR,测得结构-非结构蛋白VP3-VP1-2A区序列,进行序列同源性比较并分析其基因特点.结果 42株HAV病毒株在VP1-2A连接处核苷酸和氨基酸序列同源性分别为89.1%～100%和97.3%～100%;在全长结构蛋白VP3-VP1区的核苷酸和氨基酸序列同源性分别为87.6%～100%和98.8%～100%.VP1-2A连接处序列相同的病毒株在全长结构蛋白VP3-VP1区的核苷酸同源性为98.4%～100%,0～2个氨基酸位点不同.本实验所得序列在中和抗原位点处氨基酸序列均未变异.结论 42株病毒株均属于I型,40株是IA亚型,2株IB亚型.本实验所用HAV流行株在结构蛋白VP3-VP1区的核苷酸存在差异但是氨基酸序列高度保守且没有中和抗原位点处的变异.VP1-2A结合处核苷酸序列相同的分离株在全长结构蛋白VP3-VP1区核苷酸序列相同或相近,氨基酸序列保守.     

Deduced amino acid sequences of the haemagglutinin of H5N1 avian influenza virus isolates from an outbreak in turkeys in Norfolk,England

Summary The deduced amino acid sequences of the haemagglutinins of avian influenza viruses, isolated from an outbreak in turkeys in Norfolk, England in 1991/92, were determined by PCR amplification and cycle sequencing. Both the highly pathogenic and avirulent isolates had the same cleavage site sequence with multiple-basic amino acids, which normally would be expected only for the former. Clones derived by plaque picking from the highly pathogenic isolate ranged from low to very high pathogenicity in vivo and these, and the original isolates, showed nucleotide and amino acid variation at one or more of five possible sites, none of which were at the cleavage site. None of these site variations correlated with pathogenicity, suggesting that the factor responsible for the suppression of the expected effects of the multiple-basic amino acid haemagglutnin cleavage site in the avirulent isolate may not have been part of the haemagglutinin amino acid sequence.     

A variant serotype G3 rotavirus isolated from an unusually severe outbreak of diarrhoea in piglets.

About 80% of faecal samples from severe outbreak of porcine diarrhoea (scours) were positive for rotavirus. Rotavirus positive samples were analyzed for their antigenic properties and amino acid sequences of the glycoprotein genes. These viruses could not be assigned to any serotypes using serotyping monoclonal antibodies (MAbs) developed for porcine rotaviruses [Nagesha and Holmes: Journal of Medical Virology 35:206-211, 1991b]. When two such viruses were isolated in cell culture and analyzed by neutralization tests using hyperimmune sera they showed only one way antigenic relation with both human and porcine viruses belonging to serotype G3. In addition none of the serotyping MAbs neutralized these two virus isolates. There was no base variation between VP7 genes of faecal and cell culture isolates. Predicted amino acid sequences of the VP7 gene showed marked epitope variation from other porcine type G3 isolates with amino acid substitutions and an additional glycosylation site at residue 238. This antigenic variation seen in rotaviruses appears similar to that of influenza viruses undergoing antigenic drift.     

5株SARS-CoV部分基因序列比较分析

目的　分析SARS CoV部分结构区的基因序列 ,了解其变异程度。方法　采用套式PCR法扩增各结构区基因 ,对阳性PCR产物进行克隆和测序 ,并对序列进行分析。结果　完成了LC1株病毒的M、N、E和S基因的扩增和克隆 ,对LC2、LC3、LC4和LC5株病毒的M区基因进行了扩增和克隆。序列分析显示各结构基因的核苷酸序列与已报道的 18株序列的同源性在 99%以上。结论SARS CoV的基因序列较保守 ,有利于PCR诊断试剂和预防用疫苗的研制。     

Genetic diversity among type emm28 group A Streptococcus strains causing invasive infections and pharyngitis

Genome sequencing of group A Streptococcus (GAS) has revealed that prophages account for the vast majority of gene content differences between strains. Serotype M28 strains are a leading cause of pharyngitis and invasive infections, but little is known about genetic diversity present in natural populations of these organisms. To study this issue, population-based samples of 568 strains from Ontario, Canada; Finland; and Houston, Texas, were analyzed. Special attention was given to analysis of variation in prophage-encoded virulence gene content by a PCR-based method. Thirty and 29 distinct prophage-encoded virulence gene profiles were identified among pharyngitis and invasive infection isolates. Thirteen profiles, representing the majority of the strains, were shared between these two classes of isolates. Significant differences were observed in the frequency of occurrence of certain prophage toxin gene profiles and infection type. M28 strains are highly diverse in prophage-encoded virulence gene content and integration site, supporting the key concept that prophages are critical contributors to GAS genetic diversity and population biology. Nucleotide sequence variation in the emm gene (encodes M protein) was also examined. Only three allelic variants were identified in the hypervariable portion of the emm28 gene. All but one strain had the same inferred amino acid sequence in the first 100 amino acids of the mature M28 protein. In contrast, size differences in the emm28 gene and inferred protein due to variable numbers of C-terminal repeats were common. The presence of macrolide resistance genes (mefA, ermB, and ermTR) was analyzed by PCR, and less than 2% of the strains were positive.     

广东省历年流行性脑脊髓膜炎病原体分子特征分析

目的 了解广东省历年流行性脑脊髓膜炎(流脑)病原体的外膜蛋白编码基因porA和porB基因特征,并确定病原体的优势克隆型.方法 对1967-2007年从流脑患者分离的18株脑膜炎奈瑟球菌(Neisseria meningitidis)进行复苏培养和生化鉴定;通过DNA序列测定分析外膜蛋白编码基因porA、porB特征;对菌株进行多位点序列分型(multilocus sequence typing, MLST),采用PHYLIP软件制作进化树,并与脑膜炎余瑟球菌MIST全球数据库(PubMLST)中的菌株比较,确定优势克隆型菌株,探讨广东省历年流脑疫情分离株的看家基因序列多态性.结果 porA可变区(VR)1的型别以20型为主,VR2的型别在2004年前主要为9型,以后呈现多态性;porB可变区Ⅰ、Ⅳ、Ⅴ、Ⅵ主要分别为4、7、11、10型,2004年后可变区Ⅴ、Ⅵ型别增多;除2007年分离的1株W135菌株外,其余菌株的porB基因均无Ⅶ、Ⅷ可变区.在7个看家基因中,abcZ等位基因多态性最低,pgm最高.广东省历年流行性脑脊髓膜炎分离株2004年前的优势克隆为ST-5克隆系,自2004年开始出现高致病性ST-4821克隆系,2007年首次出现高致病性ST-11克降系.结论 广东省历年脑膜炎奈瑟球菌分离株的外膜蛋白编码基冈呈现多态性特征,分离株为多克隆系并存,近期以高致病性克隆系为主.     

Genetic and biological differentiation of dengue 3 isolates obtained from clinical cases in Java,Indonesia, 1976–1978

Summary Previous epidemiological, virological and clinical studies have documented a series of outbreaks of dengue fever and dengue haemorrhagic fever/dengue shock syndrome which occured in Java, Indonesia in 1976–1978. In the current study we compare growth characteristics in cell culture, and nucleotide sequence data for the viral prM and E genes, of five low passage DEN-3 isolates obtained during these epidemics from clinically defined cases. All isolates had the same passage history: human sera were passed twice in mosquitoes and three times in a mosquito cell line (Aedes albopictus, C6/36 cells). Growth differences were observed between individual isolates in Vero cells; growth differences were not observed in C 6/36 cells. Nucleotide sequencing of the prM and E gene region indicated that no two isolates were identical (sequence divergence ranged from 0.4 to 1.6% in pairwise comparisons) but that they were closely enough related to present a single genetic type. There were one or two differences in deduced amino acid sequence in E between isolates. Differences were at residues 65, 187, 298 or 443. One isolate differed from all others at residue 16 in the M protein. No relationship was apparent between the amino acid sequence of M or E and the nature of the disease profile, the year of isolation or the geographic region of isolation. The isolates showed 3.5 to 4.4% nucleotide sequence divergence from the highly-adapted H 87 prototype, isolated in the Philippines in 1956. The isolates showed a total of twelve common amino acid differences in prM and E proteins from H 87. Ten of these twelve residues were at positions which differed between the four dengue serotypes. Two differences (at residues 37 in M and 293 in E) were at positions which are conserved in sequence between the four dengue serotypes. The data are discussed in relation to the dengue outbreaks in Java in the period 1976–1978.     

Comparison of nucleic and amino acid sequences and phylogenetic analysis of the GS protein of various equine arteritis virus isolates

The genetic variation in equine arteritis virus (EAV) G_S protein encoding gene was investigated. Nucleic and deduced amino acid sequences from eight different EAV isolates (one European, two American and five Canadian isolates) were compared with those of the Bucyrus reference strain. Nucleotide and amino acid sequence identities between these isolates and the Bucyrus reference strain ranged from 92.3 to 96.4%, and 93.2 to 95.5%, respectively. However, phylogenetic tree analysis and estimation of genetic distances based on the G_S protein encoding gene sequences showed that the European prototype Vienna strain, the American 87AR-A1 isolate and all other North American EAV isolates could be classified into three genetically divergent groups. Our results showed that the G_S protein-encoding gene can be subjected on the basis of phylogenetic analysis to genetic variation, as previously shown for the other three EAV structural protein (M, N and G_L)-encoding genes.     

Characterization by restriction fragment length polymorphism and sequence analysis of field and vaccine strains of infectious laryngotracheitis virus involved in severe outbreaks

At the end of 2002 and throughout 2003, there was a severe outbreak of infectious laryngotracheitis (ILT) in an intensive production area of commercial hens in the São Paulo State of Brazil. ILT virus was isolated from 28 flocks, and 21 isolates were genotyped by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) using four genes and eight restriction enzymes, and by partial sequencing of the infected cell protein 4 (ICP4) and thymidine kinase (TK) genes. Three groups resulted from the combinations of PCR-RFLP patterns: 19 field isolates formed Group I, and the remaining two isolates together with the chicken embryo origin (CEO) vaccine strains formed Group II. Group III comprised the tissue-culture origin (TCO) vaccine strain by itself. The PCR-RFLP results agreed with the sequencing results of two ICP4 gene fragments. The ICP4 gene sequence analysis showed that the 19 field isolates classified into Group I by RFLP-PCR were identical among themselves, but were different to the TCO and CEO vaccines. The two Group II isolates could not be distinguished from one of the CEO vaccines. The nucleotide and amino acid sequence analyses discriminated between the Brazilian and non-Brazilian isolates, as well as between the TCO and CEO vaccines. Sequence analysis of the TK gene enabled classification of the field isolates (Group I) as virulent and non-vaccine. This work shows that the severe ILT outbreak was caused by a highly virulent, non-vaccine strain.     

Extensive sequence variation of feline immunodeficiency virusenv genes in isolates from naturally infected cats

Summary In an investigation of the evolution of feline immunodeficiency virus (FIV) in vivo, sequential isolates from a persistently infected cat were examined by direct sequencing following amplification of selected subgenomic regions by polymerase chain reaction (PCR). Three isolates, T 90, T 91, and T 92, obtained over a three-year period revealed no changes to regions known to be conserved withingag andpol genes. Additionally, no change occurred withingag andpol in an isolate recovered from a second cat which was experimentally infected with T 90. Changes were detected within an N-terminal region of the envelope glycoprotein gp 120 (env). These consisted of point mutations, some of which would result in amino acid substitutions and the predicted amino acid changes tended to cluster within variable domains. Inoculation of T 90 into a second cat resulted in a different pattern of mutations than that observed for the three isolates from the first cat. In all cases, virus isolates derived from the same cat were much more highly related to each other (extent ofenv variation was 0.5–1.5%) than to isolates from other cats (10–12%env variation). The rate of change of FIV was estimated to be 3.4×10^–3 nucleotide substitutions per site per year for theenv gene and less than 10^–4 nucleotide substitutions per site per year for thegag andpol genes, values concordant with that found for human immunodeficiency virus 1. Both nucleotide and amino acid changes in the gp 120 region were found to be directional, suggesting that selective pressures influence FIV envelope gene sequences.     

Phylogenetic relationships among virulent Newcastle disease virus isolates from the 2002-2003 outbreak in California and other recent outbreaks in North America

Isolates from the 2002-2003 virulent Newcastle disease virus (v-NDV) outbreak in southern California, Nevada, Arizona, and Texas in the United States were compared to each other along with recent v-NDV isolates from Mexico and Central America and reference avian paramyxovirus type 1 strains. Nucleotide sequencing and phylogenetic analyses were conducted on a 1,195-base genomic segment composing the 3' region of the matrix (M) protein gene and a 5' portion of the fusion (F) protein gene including the M-F intergenic region. This encompasses coding sequences for the nuclear localization signal of the M protein and the F protein cleavage activation site. A dibasic amino acid motif was present at the predicted F protein cleavage activation site in all v-NDVs, including the California 2002-2003, Arizona, Nevada, Texas, Mexico, and Central America isolates. Phylogenetic analyses demonstrated that the California 2002-2003, Arizona, Nevada, and Texas viruses were most closely related to isolates from Mexico and Central America. An isolate from Texas obtained during 2003 appeared to represent a separate introduction of v-NDV into the United States, as this virus was even more closely related to the Mexico 2000 isolates than the California, Arizona, and Nevada viruses. The close phylogenetic relationship between the recent 2002-2003 U.S. v-NDV isolates and those viruses from countries geographically close to the United States warrants continued surveillance of commercial and noncommercial poultry for early detection of highly virulent NDV.