新发现的水禽星状病毒、微RNA病毒和嵌杯病毒的分子检测与鉴定
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摘要
近20年来,新的水禽疫病不断出现,对我国水禽业构成了巨大威胁。因此,筛查水禽群体中可能存在的新病毒对于水禽新现疾病的防控具有十分重要的意义。
2011-2012年间,从我国四个省采集水禽样品155份,包括来自江西的2月龄健康朗德鹅粪便样品19份和健康麻鸭粪便样品18份、来自广东和湖北的活禽市场采集的北京鸭粪便样品90份以及从山东采集的出壳前死亡北京鸭胚的肠道样品28份。利用星状病毒ORF1b通用引物进行RT-PCR检测,检出阳性样品20份(12.9%)。对扩增产物的序列进行比较分析的结果显示,20株星状病毒分属两类(A和B),彼此间核苷酸和氨基酸序列同源性分别为55%-58%和57-59%,它们与已知禽星状病毒的核苷酸和氨基酸序列同源性分别为52%-72%和35-79%。进化分析进-步证实,这些毒株均不同于已知的禽星状病毒,属于两类新的星状病毒。A类星状病毒共7株,均来白广东的北京鸭；B类星状病毒包括来自广东的北京鸭源毒株1株、从山东的北京鸭胚中检出的毒株3株、来自江西的麻鸭源毒株2株和朗德鹅源毒株7株。这些结果表明,星状病毒感染的地区分布已很广泛,且至少有三种水禽可感染星状病毒。研究结果还表明,两类星状病毒感染水禽后均可经粪便排毒,其中B类星状病毒具有较广泛的宿主范围。
在部分ORF1b区,B类毒株与本室最近检出的鸭星状病毒(duck astrovirus, DAstV) CPH株具有相近的遗传进化关系,其核苷酸与氨基酸序列同源性分别达95%-96%和97-99%,表明它们属于同一个类型,因此,从A类中选DAstV/YP2株,用随机扩增、RT-PCR、5'RACE和3'RACE技术测定了其基因组序列。序列分析表明,不计poly(A)尾,DAstV/YP2基因组长度为7287nt,由12nt的5’UTR、3363nt的ORFla、1545nt的ORF1b、2184nt的ORF2和177nt的5'UTR组成。结果表明,DAstV/YP2具有典型的星状病毒基因组结构。用三个蛋白的全长氨基酸序列进行同源性分析和进化分析的结果表明,DAstV/YP2与已知的禽星状病毒具有较远的遗传进化关系。在衣壳蛋白区,DAstV/YP2与已知的禽星状病毒之间的遗传距离为0.599-0.801,据此可将DAstV/YP2鉴定为星状病毒科禽星状病毒属的一个新病毒种。
采用不依赖序列的随机扩增法,并经测序和序列相似性检索,从一份来自广东的北京鸭粪便样品检测到一种新的微RNA病毒(LY株)。随后,采用RT-PCR、5'RACE和3’RACE技术测定了该病毒的基因组序列。序列同源性和进化分析结果表明,该病毒LY与微RNA病毒科Megrivirus属成员间的遗传进化关系最近,在P1、P2、P3、polyprotein和2C+3CD区,该病毒与Megrivirus成员间的氨基酸序列同源性分别为32-68%、35-45%、51-57%、41-50%和61-63%,据此将该病毒鉴定为Megrivirus属内的一个新成员,暂称之为Duck megrivirus (DMV)。序列分析表明,DMV具有类似于MeV-A的基因组结构,但亦有自身的特点。不计poly(A)尾,DMVLY株基因组长度为9700nt,是微RNA病毒科中最长的。最显著的特点位于2A区,该区由两个功能未知的蛋白(2A1和2A2)以及一个parachovirus样的2A3组成。DMV的5'UTR所含内部核糖体进入位点(internal ribosome entry site, IRES)属于IVB IRES的变异型,即其Ⅲ域含有一个很长的Ⅲ4螺旋,且Ⅲ域的顶端是一个20-nt长的“8”样保守结构。比较分析显示,所预测的DMV IRES Ⅲ域的二级结构亦见于Me V-A、Mesivirus、鹌鹑微RNA病毒和鸽子微RNA病毒B。以往在IVA和IVC型IRES的、域所见到的保守的内部和顶环在DMV IRES的Ⅱ域高度保守。另外,在不同的基因区,DMV分别与Megrivirus属的两个成员具有相近的遗传进化关系。这些结果表明,在进化过程中,DMV的编码区和非编码区可能发生过基因重组。为了解DMV感染的流行情况,检测了2011-2012年间从山东、广东、湖北和海南采集的另外117份北京鸭样品,从4个地区的样品中均检测到DMV,阳性率为23.9%,结果表明,我国鸭群中DMV的感染率较高,且地区分布较广。
采用上述方法,从一份来自江西的朗德鹅粪便样品检测到一种嵌杯病毒。随后,采用RT-PCR.5’RACE和3’RACE技术测定了该病毒的基因组序列。序列分析表明,鹅嵌杯病毒(Goose calicivirus,GoCV)基因组全长8103nt,编码2个ORF,即ORF1和ORF2,这两个ORF位于同一个读框,间隔3nt,这一特性与火鸡嵌杯病毒(Tukey caliivirus, TuCV)类似。长度为6960-nt的ORF1编码一个大的聚蛋白,预测该聚蛋白裂解为非结构蛋白Nterm、NTPase、3A、VPg和Pro-pol以及主要结构蛋白VP1；长度为825-nt的ORF2编码次要结构蛋白VP2。结果表明,GoCV拥有类似于TuCV的基因组结构。与其他嵌杯病毒的比较结果表明,在非结构蛋白、VP1和VP2区,GoCV与TuCV的氨基酸序列同源性最高,分别为62%、38%和52%。进化分析表明,GoCV与TuCV具有相近的遗传进化关系,但亦存在明显的区别,因此,将GoCV鉴定为嵌杯病毒科"Nacovirus"属内的一种新病毒。
In the past20years, a number of new diseases have emerged in waterfowl, which have raised serious threat on the Chinese waterfowl industry. It is, therefore, important to screen the potential novel viruses present in waterfowl populations for the controlling of the emerging diseases in waterfowl.
155samples were collected from ducks and geese in the years2011to2012, including19fecal samples from2-month-old healthy Landes geese and18fecal samples from healthy Ma ducks in Jiangxi,90fecal samples from Pekin ducks in live-bird markets in Guangdong and Hubei, and28intestinal samples from dead-in-shell Pekin duckings in Shandong. Using an open reading frame (ORF)1b-based astrovirus-specific reverse transcription (RT)-PCR assay, astroviruses were detected in20(12.9%) of the samples. Comparative analyses based on the ORF1b amplicon sequences showed that the astroviruses could be divided into two groups (A and B) which shared low nucleotide (55-58%) and amino acid (57-59%) identities with one another. The nucleotide and amino acid identities shared by the20astroviruses with previously known avastroviruses were55-58%and57-59%respectively. Phylogenetic analysis of the partial ORFlb sequence demonstrated that the astroviruses in this study were distinct from previously known avastroviruses, suggesting the presence of two novel astroviruses in waterfowl. Group A included7isolates, all of which were detected in Pekin ducks. Group B included one strain detected in Pekin duck,3strains detected in Pekin duck embryos,2strains detected in Ma ducks, and7strains detected in Landes geese. These investigations demonstrated that astrovirus infections were geographically widespread and that at least three waterfowl species could be infected by astroviruses. The results also suggested that astroviruses in the two groups could be shed in waterfowl feces and that astrovirus in group B have a broad host range.
In the partial ORFlb region, the virus strains in group B was shown to be closely related to duck astrovirus (DastV) strain CPH detected recently in our laboratory, with nucleotide and amino acid identities of95%-96%and97-99%. This result showed that they may belong to the same avastrovirus species. Thus, DAstV/YP2in the group A was selected for full-length sequencing, using sequence-independent PCR amplification, RT-PCR and5'/3' rapid amplification of cDNA ends (RACE) strategies. Sequence analysis revealed that the complete genome of DAstV/YP2was7287nt, excluding the poly (A) tail. The polyadenylated genome was organized into three overlapping ORFs of3363(ORF1a),1545(ORF1b) and2184nt (ORF2) as well as a short5' untranslated region (UTR) of12nt and a3'UTR of177nt. The findings indicated that DAstV/YP2possessed a typical astrovirus organization. Sequence identity and phylogenetic analyses demonstrated that the DAstV/YP2was distinct from all known avastroviruses. Genetic analysis of the complete ORF2region revealed that mean amino acid genetic distances between DAstV/YP2and previously known avastroviruses were between0.599and0.801, suggesting that DAstV/YP2may be classified as an additional species in the genus Avastrovirus of the family Astroviridae.
Using sequence-independent PCR amplification, sequencing, and sequence similarity searches, a novel picomavirus (designated LY) was detected from a fecal sample collected from a Pekin duck located in Guangdong. Subsequently, the complete genome sequence of the LY isolate was determined using RT-PCR and5'/'RACE. The virus was shown to be most closely related to the genus Mergivirus of the family Picornaviridae, with average amino acid identities of32%to68%,35%to45%,51%to57%,41%to50%, and61%to63%in the P1, P2, P3, polyprotein and2C+3CD regions, respectively. The virus was thus identified as an additional species in the genus Megrivirus and tentatively named Duck megrivirus (DMV). Sequence analyses indicated that the DMV genome possessed a MeV-A-like organization and also exhibited several unique features. The polyadenylated genome comprised9700nt, the largest among known picoraviruses. A notable feature was the2A region, which had an association of two distinct, function-unknown2As (2A1and2A2) and a parechovirus-like2A3. The5'UTR contained a variant type IVB internal ribosome entry site (IRES), which possessed a long helix Ⅲ4ending with the "8"-like20-nt-long conserved structure at the top of domain III. The secondary structure model of inferred domain III of DMV-like IRES was also conserved in MeV-A, Mesivirus, Quail picornavirus, and Pigeon picornavirus B. Domain II in DMV contained the conserved internal and apical loops previously identified in groups A and C of type IV IRESs. Moreover, DMV was closely related to different megriviruses in different genomic regions. These findings suggest that recombination events involving exchange of coding and noncoding regions may have occurred during the evolution of the virus. To understand the prevalence of DMV infection, additional117duck samples collected from Guangdong, Shandong, Hubei and Hainan provinces between2011and2012were tested using the RT-PCR method. DMV-specific RNA was found in23.9%samples from domestic ducks, reflecting a high prevalence of DMV in duck populations. The positive samples were detected from four provinces, suggesting that DMV infections were geographically widespread.
Using the strategy described above, a novel calicivirus was detected in a Landes goose from Jiangxi and then completely sequenced. Sequence analysis revealed that the Goose calicivirus (GoCV) genome comprised8013nt, which was organized into two ORFs, ORF1and ORF2. The two ORFs were in the same frame and separated by3nt, most similar to the case for turkey calicivirus (TuCV). The6960-nt ORF1was predicted to encode a large polyprotein which was predicted to be cleaved into nonstructural proteins Nterm, NTPase,3A-like protein, VPg and Pro-Pol as well as major structural protein VP1. The825-nt-long ORF2was predicted to encode a minor structural protein VP2. These findings indicated that GoCV possessed a TuCV-like genome organization. Comparison of GoCV with other caliciviruses showed that it shared the highest amino acid identities of62%,38%, and52%in nonstructural protein, VP1, and VP2, respectively, with TuCV. Phylogenetic analyses based on amino acid sequences of nonstructural protein and VP1both demonstrated that GoCV was most closely related to but distinct from TuCV. Thus, GoCV was identified as a novel member in the proposed genus "Nacovirus" of the family Caliciviridae.
2011-2012年间,从我国四个省采集水禽样品155份,包括来自江西的2月龄健康朗德鹅粪便样品19份和健康麻鸭粪便样品18份、来自广东和湖北的活禽市场采集的北京鸭粪便样品90份以及从山东采集的出壳前死亡北京鸭胚的肠道样品28份。利用星状病毒ORF1b通用引物进行RT-PCR检测,检出阳性样品20份(12.9%)。对扩增产物的序列进行比较分析的结果显示,20株星状病毒分属两类(A和B),彼此间核苷酸和氨基酸序列同源性分别为55%-58%和57-59%,它们与已知禽星状病毒的核苷酸和氨基酸序列同源性分别为52%-72%和35-79%。进化分析进-步证实,这些毒株均不同于已知的禽星状病毒,属于两类新的星状病毒。A类星状病毒共7株,均来白广东的北京鸭；B类星状病毒包括来自广东的北京鸭源毒株1株、从山东的北京鸭胚中检出的毒株3株、来自江西的麻鸭源毒株2株和朗德鹅源毒株7株。这些结果表明,星状病毒感染的地区分布已很广泛,且至少有三种水禽可感染星状病毒。研究结果还表明,两类星状病毒感染水禽后均可经粪便排毒,其中B类星状病毒具有较广泛的宿主范围。
在部分ORF1b区,B类毒株与本室最近检出的鸭星状病毒(duck astrovirus, DAstV) CPH株具有相近的遗传进化关系,其核苷酸与氨基酸序列同源性分别达95%-96%和97-99%,表明它们属于同一个类型,因此,从A类中选DAstV/YP2株,用随机扩增、RT-PCR、5'RACE和3'RACE技术测定了其基因组序列。序列分析表明,不计poly(A)尾,DAstV/YP2基因组长度为7287nt,由12nt的5’UTR、3363nt的ORFla、1545nt的ORF1b、2184nt的ORF2和177nt的5'UTR组成。结果表明,DAstV/YP2具有典型的星状病毒基因组结构。用三个蛋白的全长氨基酸序列进行同源性分析和进化分析的结果表明,DAstV/YP2与已知的禽星状病毒具有较远的遗传进化关系。在衣壳蛋白区,DAstV/YP2与已知的禽星状病毒之间的遗传距离为0.599-0.801,据此可将DAstV/YP2鉴定为星状病毒科禽星状病毒属的一个新病毒种。
采用不依赖序列的随机扩增法,并经测序和序列相似性检索,从一份来自广东的北京鸭粪便样品检测到一种新的微RNA病毒(LY株)。随后,采用RT-PCR、5'RACE和3’RACE技术测定了该病毒的基因组序列。序列同源性和进化分析结果表明,该病毒LY与微RNA病毒科Megrivirus属成员间的遗传进化关系最近,在P1、P2、P3、polyprotein和2C+3CD区,该病毒与Megrivirus成员间的氨基酸序列同源性分别为32-68%、35-45%、51-57%、41-50%和61-63%,据此将该病毒鉴定为Megrivirus属内的一个新成员,暂称之为Duck megrivirus (DMV)。序列分析表明,DMV具有类似于MeV-A的基因组结构,但亦有自身的特点。不计poly(A)尾,DMVLY株基因组长度为9700nt,是微RNA病毒科中最长的。最显著的特点位于2A区,该区由两个功能未知的蛋白(2A1和2A2)以及一个parachovirus样的2A3组成。DMV的5'UTR所含内部核糖体进入位点(internal ribosome entry site, IRES)属于IVB IRES的变异型,即其Ⅲ域含有一个很长的Ⅲ4螺旋,且Ⅲ域的顶端是一个20-nt长的“8”样保守结构。比较分析显示,所预测的DMV IRES Ⅲ域的二级结构亦见于Me V-A、Mesivirus、鹌鹑微RNA病毒和鸽子微RNA病毒B。以往在IVA和IVC型IRES的、域所见到的保守的内部和顶环在DMV IRES的Ⅱ域高度保守。另外,在不同的基因区,DMV分别与Megrivirus属的两个成员具有相近的遗传进化关系。这些结果表明,在进化过程中,DMV的编码区和非编码区可能发生过基因重组。为了解DMV感染的流行情况,检测了2011-2012年间从山东、广东、湖北和海南采集的另外117份北京鸭样品,从4个地区的样品中均检测到DMV,阳性率为23.9%,结果表明,我国鸭群中DMV的感染率较高,且地区分布较广。
采用上述方法,从一份来自江西的朗德鹅粪便样品检测到一种嵌杯病毒。随后,采用RT-PCR.5’RACE和3’RACE技术测定了该病毒的基因组序列。序列分析表明,鹅嵌杯病毒(Goose calicivirus,GoCV)基因组全长8103nt,编码2个ORF,即ORF1和ORF2,这两个ORF位于同一个读框,间隔3nt,这一特性与火鸡嵌杯病毒(Tukey caliivirus, TuCV)类似。长度为6960-nt的ORF1编码一个大的聚蛋白,预测该聚蛋白裂解为非结构蛋白Nterm、NTPase、3A、VPg和Pro-pol以及主要结构蛋白VP1；长度为825-nt的ORF2编码次要结构蛋白VP2。结果表明,GoCV拥有类似于TuCV的基因组结构。与其他嵌杯病毒的比较结果表明,在非结构蛋白、VP1和VP2区,GoCV与TuCV的氨基酸序列同源性最高,分别为62%、38%和52%。进化分析表明,GoCV与TuCV具有相近的遗传进化关系,但亦存在明显的区别,因此,将GoCV鉴定为嵌杯病毒科"Nacovirus"属内的一种新病毒。
In the past20years, a number of new diseases have emerged in waterfowl, which have raised serious threat on the Chinese waterfowl industry. It is, therefore, important to screen the potential novel viruses present in waterfowl populations for the controlling of the emerging diseases in waterfowl.
155samples were collected from ducks and geese in the years2011to2012, including19fecal samples from2-month-old healthy Landes geese and18fecal samples from healthy Ma ducks in Jiangxi,90fecal samples from Pekin ducks in live-bird markets in Guangdong and Hubei, and28intestinal samples from dead-in-shell Pekin duckings in Shandong. Using an open reading frame (ORF)1b-based astrovirus-specific reverse transcription (RT)-PCR assay, astroviruses were detected in20(12.9%) of the samples. Comparative analyses based on the ORF1b amplicon sequences showed that the astroviruses could be divided into two groups (A and B) which shared low nucleotide (55-58%) and amino acid (57-59%) identities with one another. The nucleotide and amino acid identities shared by the20astroviruses with previously known avastroviruses were55-58%and57-59%respectively. Phylogenetic analysis of the partial ORFlb sequence demonstrated that the astroviruses in this study were distinct from previously known avastroviruses, suggesting the presence of two novel astroviruses in waterfowl. Group A included7isolates, all of which were detected in Pekin ducks. Group B included one strain detected in Pekin duck,3strains detected in Pekin duck embryos,2strains detected in Ma ducks, and7strains detected in Landes geese. These investigations demonstrated that astrovirus infections were geographically widespread and that at least three waterfowl species could be infected by astroviruses. The results also suggested that astroviruses in the two groups could be shed in waterfowl feces and that astrovirus in group B have a broad host range.
In the partial ORFlb region, the virus strains in group B was shown to be closely related to duck astrovirus (DastV) strain CPH detected recently in our laboratory, with nucleotide and amino acid identities of95%-96%and97-99%. This result showed that they may belong to the same avastrovirus species. Thus, DAstV/YP2in the group A was selected for full-length sequencing, using sequence-independent PCR amplification, RT-PCR and5'/3' rapid amplification of cDNA ends (RACE) strategies. Sequence analysis revealed that the complete genome of DAstV/YP2was7287nt, excluding the poly (A) tail. The polyadenylated genome was organized into three overlapping ORFs of3363(ORF1a),1545(ORF1b) and2184nt (ORF2) as well as a short5' untranslated region (UTR) of12nt and a3'UTR of177nt. The findings indicated that DAstV/YP2possessed a typical astrovirus organization. Sequence identity and phylogenetic analyses demonstrated that the DAstV/YP2was distinct from all known avastroviruses. Genetic analysis of the complete ORF2region revealed that mean amino acid genetic distances between DAstV/YP2and previously known avastroviruses were between0.599and0.801, suggesting that DAstV/YP2may be classified as an additional species in the genus Avastrovirus of the family Astroviridae.
Using sequence-independent PCR amplification, sequencing, and sequence similarity searches, a novel picomavirus (designated LY) was detected from a fecal sample collected from a Pekin duck located in Guangdong. Subsequently, the complete genome sequence of the LY isolate was determined using RT-PCR and5'/'RACE. The virus was shown to be most closely related to the genus Mergivirus of the family Picornaviridae, with average amino acid identities of32%to68%,35%to45%,51%to57%,41%to50%, and61%to63%in the P1, P2, P3, polyprotein and2C+3CD regions, respectively. The virus was thus identified as an additional species in the genus Megrivirus and tentatively named Duck megrivirus (DMV). Sequence analyses indicated that the DMV genome possessed a MeV-A-like organization and also exhibited several unique features. The polyadenylated genome comprised9700nt, the largest among known picoraviruses. A notable feature was the2A region, which had an association of two distinct, function-unknown2As (2A1and2A2) and a parechovirus-like2A3. The5'UTR contained a variant type IVB internal ribosome entry site (IRES), which possessed a long helix Ⅲ4ending with the "8"-like20-nt-long conserved structure at the top of domain III. The secondary structure model of inferred domain III of DMV-like IRES was also conserved in MeV-A, Mesivirus, Quail picornavirus, and Pigeon picornavirus B. Domain II in DMV contained the conserved internal and apical loops previously identified in groups A and C of type IV IRESs. Moreover, DMV was closely related to different megriviruses in different genomic regions. These findings suggest that recombination events involving exchange of coding and noncoding regions may have occurred during the evolution of the virus. To understand the prevalence of DMV infection, additional117duck samples collected from Guangdong, Shandong, Hubei and Hainan provinces between2011and2012were tested using the RT-PCR method. DMV-specific RNA was found in23.9%samples from domestic ducks, reflecting a high prevalence of DMV in duck populations. The positive samples were detected from four provinces, suggesting that DMV infections were geographically widespread.
Using the strategy described above, a novel calicivirus was detected in a Landes goose from Jiangxi and then completely sequenced. Sequence analysis revealed that the Goose calicivirus (GoCV) genome comprised8013nt, which was organized into two ORFs, ORF1and ORF2. The two ORFs were in the same frame and separated by3nt, most similar to the case for turkey calicivirus (TuCV). The6960-nt ORF1was predicted to encode a large polyprotein which was predicted to be cleaved into nonstructural proteins Nterm, NTPase,3A-like protein, VPg and Pro-Pol as well as major structural protein VP1. The825-nt-long ORF2was predicted to encode a minor structural protein VP2. These findings indicated that GoCV possessed a TuCV-like genome organization. Comparison of GoCV with other caliciviruses showed that it shared the highest amino acid identities of62%,38%, and52%in nonstructural protein, VP1, and VP2, respectively, with TuCV. Phylogenetic analyses based on amino acid sequences of nonstructural protein and VP1both demonstrated that GoCV was most closely related to but distinct from TuCV. Thus, GoCV was identified as a novel member in the proposed genus "Nacovirus" of the family Caliciviridae.
引文
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