454高通量测序技术应用于粪便中病毒的发现与分析
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摘要
背景：
新发传染病始终威胁着人类的健康。发现和鉴定新病毒以及确定新病毒与疾病的关系是预防、诊断和治疗新发病毒性传染病的首要任务。高通量测序技术突破了传统技术方法的局限,可以直接以标本中所有的遗传物质为研究对象,从而能够快速地鉴定出标本中存在的病毒,形成了一门研究特定环境中病毒群落的新兴学科：病毒宏基因组学。传统意义上有很多用于发现新病毒的方法,但利用高通量测序发现新病毒具有信息量大、对标本所含信息无偏倚等独特优点,使得该技术已成为目前病毒发现最为重要的前沿技术之一。在短短的几年里,人们依靠这种技术发现了很多有意义的病毒,研究领域涉及到人类、动物、环境、水体等,充分显示出其在病毒诊断、溯源、预警等方面的实用意义。
腹泻是各个年龄段的人类和动物中常见的疾病,可由细菌、病毒和寄生虫等病原引起,而轮状病毒、杯状病毒、肠道腺病毒和星状病毒是引起人类腹泻最主要的病毒性病原。在世界范围内,每年有200多万5岁以下腹泻儿童死亡,并且发展中国家占有较大的比例。现有的检测技术只能发现60%的腹泻病例的病原,仍有近40%的病例查不出具体病原。其中部分腹泻的未知病因可能是目前暂未被发现的病毒。腹泻在儿童中的发生率远高于成人,严重影响了儿童的健康,分析腹泻儿童与健康对照儿童粪便标本中的病毒群落差异以及发掘潜在的新病毒将为诊断不明腹泻的病因提供新的途径。此外,猪作为与人类接触最为密切的经济动物之一是人兽共患病的重要宿主,被认为是天然的病原体库。因此,开展其粪便中病毒谱的研究对预警潜在的人类新发病毒病也具有重要意义。
方法：
1、以猪的粪便标本为研究对象,摸索并建立适用于454高通量测序的粪便标本处理方法；通过对海量序列进行生物信息分析,研究猪粪便中的病毒谱,发现潜在的新病毒；进一步利用生物信息学、分子生物学与免疫学等方法,了解新病毒的基因结构、分子流行病学及血清流行学等特点,初步探索新病毒在人类中存在感染的潜在可能。
2、应用454高通量测序分析了腹泻与健康儿童粪便标本中的病毒性病原组成情况；采用统计学方法分析了主要病毒性病原的种类与序列数量在两类标本中的差异；通过序列同源性比对分析,发现潜在的新病毒序列,并了解其在两类不同标本中的检出情况。
结果：
从9份健康猪的粪便标本中共获得40万余条序列,平均长度达361bp,其中病毒序列为5437条,涉及病毒种类达20余种；基因序列与进化树分析表明标本中存在多株不同的新型星状病毒、博卡病毒和类双埃可病毒,且这些病毒在健康猪粪便标本中广泛存在,检出率分别为：51.5%、72%和13.5%。对新型的类双埃可病毒PLV-CHN进行深入分析显示,该株病毒基因组全长为6832bp,编码一个长为2132个氨基酸的完整多聚蛋白,与已知双埃可病毒属的Ljungan病毒有最大同源性(氨基酸同源性为32%)。值得注意的是,在本研究整理相关结果时,法国报道了一株与PLV-CHN极为类似的病毒SPaV1,核苷酸与氨基酸同源性分别达到82%和89%,基因特点与进化分析均显示PLV-CHN与SPaV1最为相近,二者形成了小RNA病毒科的一个新的属——Pasivirus。对该病毒3D区进行的分子流行病学显示,健康猪粪便标本的检出率为20%；腹泻与正常儿童粪便以及脑炎儿童脑脊液中均未检出该病毒。但ELISA结果表明健康人群的血清中该病毒或与该病毒相关的抗体阳性率高达63.5%,其中12岁之前的绝大部分儿童显示血清阳性。
腹泻与对照儿童粪便标本中获得的序列数量分别为385288条与290647条,两类标本中的病原组成种类无明显差别,除去未分类序列,细菌、噬菌体与病毒序列的数量在两类标本中均占据前三位。而对病毒宏基因组分析显示,病毒的序列在两类标本中的数量差别较大,分别为7744条和1949条；主要病毒序列组成也不尽相同：腹泻组标本中前三位的病毒依次为Anellovirus、杯状病毒和Salivirus,正常组标本中前三位的病毒依次为Anellovirus、 Tymovirus和HPeV;其中Anellovirus在两类标本中的阳性率和序列数量的差异均无统计学意义,而诺如病毒、札如病毒和Salivirus的阳性率和序列数量在两类标本中均具有统计学差异,显示了与儿童腹泻的相关性；而其中的GIV型诺如病毒是首次在中国腹泻儿童粪便标本中发现。此外,在腹泻儿童标本中,出现大量与已知病毒同源性很低的序列,其中5个序列读长为具有潜在意义新病毒的序列,分别与Densovirus、鼠细小病毒、未分类densovirus、蛙腺病毒和乳头瘤病毒最匹配,且氨基酸同源性均<50%。
结论：
1、猪粪便中存在多种新病毒序列,表明猪是病毒多样型的生物库,在人类病毒病的预警研究中要给与重视。
2.我国健康猪中发现了全新的类双埃可病毒PLV-CHN,它与法国同期发现的SPaV1形成了小RNA病毒科的一个新的属——Pasivirus。
3、人类儿童早期可能存在全新的小RNA病毒科新属(Pasivirus)成员(如PLV-CHN)的感染。
4、腹泻与对照儿童粪便标本中的病原组成、种类与数量存在差异,其中部分病毒的潜在意义还需要深入探讨。
5、儿童腹泻标本中发现了五个新病毒序列,其生物学意义及与腹泻的相关性有有待深入研究。
6、中国腹泻儿童中第一次报道诺如病毒GIV型的存在。
Background:
New emerging infectious diseases is a constant threat for people's health. Discovery, identification of the new viruses, as well as determination of the relationship between new viruses and diseases is a priority for the prevention, diagnosis and treatment of new viral infectious diseases. High-throughput sequencing technology has broken the limitations of traditional technologies, and could work directly on the genetic material of the pathogens in the specimens, to quickly identify all the viruses, and itself has formed a new discipline, Viral Metagenomics, for studying virus community in a specific environment. Traditionally, there are many methods for the discovery of new viruses, but the use of high-throughput sequencing is characterized by large quantity of information, unbiased towards information contained in specimen, which has made the technique become the most important forefront technique for discovery of viruses. In just a few years, by this method people have discovered many meaningful viruses involving human intestinal, animal tissue, blood, water, and etc., clearly demonstrating the practical significance of the technique in virus diagnosis, pathogen tracing, biological warning and etc.
Diarrhea is a common disease in humans of all ages and in animals, which could be caused by bacteria, viruses and parasites and other pathogens, while rotavirus, calicivirus, enteric adenovirus and astroviruses are the main viral pathogens for human diarrhea. Each year more than2million children under5-year-old die from diarrhea, and developing countries account for a large proportion. At present, existing detection techniques can only find pathogens in60%of diarrhea cases, still nearly40%of cases can not be find specific pathogen. Part of the unknown etiology may be temporarily undiscovered viruses. The incidence of diarrhea in children is much higher than that of adults, which seriously affected children's health, analysis of virus community differences in stool specimens of the diarrhea and healthy children, and discovery of potential new viruses will provide a new way for diagnose the cause of unknown diarrhea. In addition, pig, as one of the most closely related to human economic animals, is an important host for zoonosis, and is considered to be a natural pathogen base. Therefore, to carry out research on the viral spectrum of its feces is of important significance for the early warning of potential emerging human viral diseases.
Methods:
1. Use of pig manure specimens as the study subject, explore and construct stool specimen processing method to prepare for454high-throughput sequencing; Study of the virus spectrum in pig manure through bioinformatics analysis on massive amount of sequences, and to identify potential new virus; Further use of bioinformatics, molecular biology and immunology methods to understand the genetic structure, molecular epidemiology and seroprevalence characteristics of the virus, so as to conduct preliminary exploration on the infection of new viruses in humans.
2. Application of454high-throughput sequencing for the analysis of viral pathogen composition of the stool specimens from both diarrhea and healthy children; Statistical analysis was employed to analyze the difference in respect to the type and sequence quantity of the major viral pathogens between the two group of specimens; Discovery of potential new viral sequences through sequence homology comparative analysis and to learn the detection of the them in the two group of specimens.
Results:
More than400,000reads were obtained from manure specimens of9healthy pigs, with an average length of361bp, in which5437were viral reads, involving more than20kinds of virus types; Gene sequences and phylogenetic tree analysis showed that there are many strains of different novel astroviruses, bocavirus and parecho-like virus in the specimens, and that these viruses are widely present in manure specimens of healthy pigs, with the detection rates be51.5%,72%and13.5%respectively. In-depth analysis on the novel type of parecho-like virus, PLV-CHN, showed that the total length of the viral genome was6832bp, encoding a complete polyglutamine protein of2132amino acids long, which shared the maximum homology to the known Ljungan virus, parecho virus genus (32%amino acid homology). It is noteworthy that, while preparing results of the study, France reported SPaV1, an extremely similar virus to PLV-CHN, with the nucleotide and amino acid homology be82%and89%respectively, and both of them had formed a new genus in picornaviridae, i.e. Pasivirus. Molecular epidemiological analysis of the viral3D region showed that the detection rate of the virus in healthy pigs manure specimens was20%; the virus was not detected in stool samples of diarrhea and normal children, neither in cerebrospinal fluid of children with encephalitis. However, ELISA results showed that the virus (or the related) antibody positive rate in the serum of healthy people was as high as63.5%, and the vast majority of children were infected before the age of12.
The number of sequence obtained from diarrhea and control children stool specimens was385,288and290,647respectively, and no significant difference was observed in the pathogenic species composition in the two groups of specimens. With unsorted sequences removed, the top three most sequences were from bacteria, phage and virus. Viral metagenome analysis showed that the difference was big in the number of sequences from virus between the two groups of specimens, which was7744and1949respectively; Composition of the major viral sequences was also not the same in that the top three in the diarrhea group were anellovirus, calicivirus, and Salivirus, while in the normal group were Anellovirus, Tymovirus and HPeV; The differences in positive rate and number of sequence of Anellovirus between the two groups of specimens were not statistically significant, while they were significant for norovirus, Sapporovirus and Salivirus, demonstrating their association with diarrhea in children; Among the viruses detected, Norovirus GIV was the first discovery in stool specimens of children with diarrhea in China. In addition, a large number of sequences with very low homology with known viruses was detected in specimens of diarrhea children, in which5sequences had a read length bearing the potential of new virus sequences, which matching the most with Densovirus, Rat parvovirus, unclassified densovirus, frog adenovirus and papillomavirus, respectively, and the amino acid homology of them were all<50%.
Conclusions:
1. A variety of new viral sequences existed in pig manure, showing that pig is a biobank for viral diversity, which should be given importance in early warning study of human viral diseases.
2. A brand new parecho-like virus, PLV-CHN, was detected in healthy piglets in China, which, together with SPaV1identified in France at the same period, formed a new genus in Picornaviridae.
3. Infection of new members (Pasivirus) of small RNA virus family, such as PLV-CHN, might exist in the early childhood of human development.
4. Differences existed in pathogen composition, type, and quantity in stool specimens between diarrhea and control children, and the potential significance of some of the viruses still need to be discussed further.
5. Five new viral sequences were discovered in specimens of diarrhea children, and their true existence and association with diarrhea necessitate an in-depth study.
6. Norovirus GIV infection was first reported in Chinese children with diarrhea.
新发传染病始终威胁着人类的健康。发现和鉴定新病毒以及确定新病毒与疾病的关系是预防、诊断和治疗新发病毒性传染病的首要任务。高通量测序技术突破了传统技术方法的局限,可以直接以标本中所有的遗传物质为研究对象,从而能够快速地鉴定出标本中存在的病毒,形成了一门研究特定环境中病毒群落的新兴学科：病毒宏基因组学。传统意义上有很多用于发现新病毒的方法,但利用高通量测序发现新病毒具有信息量大、对标本所含信息无偏倚等独特优点,使得该技术已成为目前病毒发现最为重要的前沿技术之一。在短短的几年里,人们依靠这种技术发现了很多有意义的病毒,研究领域涉及到人类、动物、环境、水体等,充分显示出其在病毒诊断、溯源、预警等方面的实用意义。
腹泻是各个年龄段的人类和动物中常见的疾病,可由细菌、病毒和寄生虫等病原引起,而轮状病毒、杯状病毒、肠道腺病毒和星状病毒是引起人类腹泻最主要的病毒性病原。在世界范围内,每年有200多万5岁以下腹泻儿童死亡,并且发展中国家占有较大的比例。现有的检测技术只能发现60%的腹泻病例的病原,仍有近40%的病例查不出具体病原。其中部分腹泻的未知病因可能是目前暂未被发现的病毒。腹泻在儿童中的发生率远高于成人,严重影响了儿童的健康,分析腹泻儿童与健康对照儿童粪便标本中的病毒群落差异以及发掘潜在的新病毒将为诊断不明腹泻的病因提供新的途径。此外,猪作为与人类接触最为密切的经济动物之一是人兽共患病的重要宿主,被认为是天然的病原体库。因此,开展其粪便中病毒谱的研究对预警潜在的人类新发病毒病也具有重要意义。
方法：
1、以猪的粪便标本为研究对象,摸索并建立适用于454高通量测序的粪便标本处理方法；通过对海量序列进行生物信息分析,研究猪粪便中的病毒谱,发现潜在的新病毒；进一步利用生物信息学、分子生物学与免疫学等方法,了解新病毒的基因结构、分子流行病学及血清流行学等特点,初步探索新病毒在人类中存在感染的潜在可能。
2、应用454高通量测序分析了腹泻与健康儿童粪便标本中的病毒性病原组成情况；采用统计学方法分析了主要病毒性病原的种类与序列数量在两类标本中的差异；通过序列同源性比对分析,发现潜在的新病毒序列,并了解其在两类不同标本中的检出情况。
结果：
从9份健康猪的粪便标本中共获得40万余条序列,平均长度达361bp,其中病毒序列为5437条,涉及病毒种类达20余种；基因序列与进化树分析表明标本中存在多株不同的新型星状病毒、博卡病毒和类双埃可病毒,且这些病毒在健康猪粪便标本中广泛存在,检出率分别为：51.5%、72%和13.5%。对新型的类双埃可病毒PLV-CHN进行深入分析显示,该株病毒基因组全长为6832bp,编码一个长为2132个氨基酸的完整多聚蛋白,与已知双埃可病毒属的Ljungan病毒有最大同源性(氨基酸同源性为32%)。值得注意的是,在本研究整理相关结果时,法国报道了一株与PLV-CHN极为类似的病毒SPaV1,核苷酸与氨基酸同源性分别达到82%和89%,基因特点与进化分析均显示PLV-CHN与SPaV1最为相近,二者形成了小RNA病毒科的一个新的属——Pasivirus。对该病毒3D区进行的分子流行病学显示,健康猪粪便标本的检出率为20%；腹泻与正常儿童粪便以及脑炎儿童脑脊液中均未检出该病毒。但ELISA结果表明健康人群的血清中该病毒或与该病毒相关的抗体阳性率高达63.5%,其中12岁之前的绝大部分儿童显示血清阳性。
腹泻与对照儿童粪便标本中获得的序列数量分别为385288条与290647条,两类标本中的病原组成种类无明显差别,除去未分类序列,细菌、噬菌体与病毒序列的数量在两类标本中均占据前三位。而对病毒宏基因组分析显示,病毒的序列在两类标本中的数量差别较大,分别为7744条和1949条；主要病毒序列组成也不尽相同：腹泻组标本中前三位的病毒依次为Anellovirus、杯状病毒和Salivirus,正常组标本中前三位的病毒依次为Anellovirus、 Tymovirus和HPeV;其中Anellovirus在两类标本中的阳性率和序列数量的差异均无统计学意义,而诺如病毒、札如病毒和Salivirus的阳性率和序列数量在两类标本中均具有统计学差异,显示了与儿童腹泻的相关性；而其中的GIV型诺如病毒是首次在中国腹泻儿童粪便标本中发现。此外,在腹泻儿童标本中,出现大量与已知病毒同源性很低的序列,其中5个序列读长为具有潜在意义新病毒的序列,分别与Densovirus、鼠细小病毒、未分类densovirus、蛙腺病毒和乳头瘤病毒最匹配,且氨基酸同源性均<50%。
结论：
1、猪粪便中存在多种新病毒序列,表明猪是病毒多样型的生物库,在人类病毒病的预警研究中要给与重视。
2.我国健康猪中发现了全新的类双埃可病毒PLV-CHN,它与法国同期发现的SPaV1形成了小RNA病毒科的一个新的属——Pasivirus。
3、人类儿童早期可能存在全新的小RNA病毒科新属(Pasivirus)成员(如PLV-CHN)的感染。
4、腹泻与对照儿童粪便标本中的病原组成、种类与数量存在差异,其中部分病毒的潜在意义还需要深入探讨。
5、儿童腹泻标本中发现了五个新病毒序列,其生物学意义及与腹泻的相关性有有待深入研究。
6、中国腹泻儿童中第一次报道诺如病毒GIV型的存在。
Background:
New emerging infectious diseases is a constant threat for people's health. Discovery, identification of the new viruses, as well as determination of the relationship between new viruses and diseases is a priority for the prevention, diagnosis and treatment of new viral infectious diseases. High-throughput sequencing technology has broken the limitations of traditional technologies, and could work directly on the genetic material of the pathogens in the specimens, to quickly identify all the viruses, and itself has formed a new discipline, Viral Metagenomics, for studying virus community in a specific environment. Traditionally, there are many methods for the discovery of new viruses, but the use of high-throughput sequencing is characterized by large quantity of information, unbiased towards information contained in specimen, which has made the technique become the most important forefront technique for discovery of viruses. In just a few years, by this method people have discovered many meaningful viruses involving human intestinal, animal tissue, blood, water, and etc., clearly demonstrating the practical significance of the technique in virus diagnosis, pathogen tracing, biological warning and etc.
Diarrhea is a common disease in humans of all ages and in animals, which could be caused by bacteria, viruses and parasites and other pathogens, while rotavirus, calicivirus, enteric adenovirus and astroviruses are the main viral pathogens for human diarrhea. Each year more than2million children under5-year-old die from diarrhea, and developing countries account for a large proportion. At present, existing detection techniques can only find pathogens in60%of diarrhea cases, still nearly40%of cases can not be find specific pathogen. Part of the unknown etiology may be temporarily undiscovered viruses. The incidence of diarrhea in children is much higher than that of adults, which seriously affected children's health, analysis of virus community differences in stool specimens of the diarrhea and healthy children, and discovery of potential new viruses will provide a new way for diagnose the cause of unknown diarrhea. In addition, pig, as one of the most closely related to human economic animals, is an important host for zoonosis, and is considered to be a natural pathogen base. Therefore, to carry out research on the viral spectrum of its feces is of important significance for the early warning of potential emerging human viral diseases.
Methods:
1. Use of pig manure specimens as the study subject, explore and construct stool specimen processing method to prepare for454high-throughput sequencing; Study of the virus spectrum in pig manure through bioinformatics analysis on massive amount of sequences, and to identify potential new virus; Further use of bioinformatics, molecular biology and immunology methods to understand the genetic structure, molecular epidemiology and seroprevalence characteristics of the virus, so as to conduct preliminary exploration on the infection of new viruses in humans.
2. Application of454high-throughput sequencing for the analysis of viral pathogen composition of the stool specimens from both diarrhea and healthy children; Statistical analysis was employed to analyze the difference in respect to the type and sequence quantity of the major viral pathogens between the two group of specimens; Discovery of potential new viral sequences through sequence homology comparative analysis and to learn the detection of the them in the two group of specimens.
Results:
More than400,000reads were obtained from manure specimens of9healthy pigs, with an average length of361bp, in which5437were viral reads, involving more than20kinds of virus types; Gene sequences and phylogenetic tree analysis showed that there are many strains of different novel astroviruses, bocavirus and parecho-like virus in the specimens, and that these viruses are widely present in manure specimens of healthy pigs, with the detection rates be51.5%,72%and13.5%respectively. In-depth analysis on the novel type of parecho-like virus, PLV-CHN, showed that the total length of the viral genome was6832bp, encoding a complete polyglutamine protein of2132amino acids long, which shared the maximum homology to the known Ljungan virus, parecho virus genus (32%amino acid homology). It is noteworthy that, while preparing results of the study, France reported SPaV1, an extremely similar virus to PLV-CHN, with the nucleotide and amino acid homology be82%and89%respectively, and both of them had formed a new genus in picornaviridae, i.e. Pasivirus. Molecular epidemiological analysis of the viral3D region showed that the detection rate of the virus in healthy pigs manure specimens was20%; the virus was not detected in stool samples of diarrhea and normal children, neither in cerebrospinal fluid of children with encephalitis. However, ELISA results showed that the virus (or the related) antibody positive rate in the serum of healthy people was as high as63.5%, and the vast majority of children were infected before the age of12.
The number of sequence obtained from diarrhea and control children stool specimens was385,288and290,647respectively, and no significant difference was observed in the pathogenic species composition in the two groups of specimens. With unsorted sequences removed, the top three most sequences were from bacteria, phage and virus. Viral metagenome analysis showed that the difference was big in the number of sequences from virus between the two groups of specimens, which was7744and1949respectively; Composition of the major viral sequences was also not the same in that the top three in the diarrhea group were anellovirus, calicivirus, and Salivirus, while in the normal group were Anellovirus, Tymovirus and HPeV; The differences in positive rate and number of sequence of Anellovirus between the two groups of specimens were not statistically significant, while they were significant for norovirus, Sapporovirus and Salivirus, demonstrating their association with diarrhea in children; Among the viruses detected, Norovirus GIV was the first discovery in stool specimens of children with diarrhea in China. In addition, a large number of sequences with very low homology with known viruses was detected in specimens of diarrhea children, in which5sequences had a read length bearing the potential of new virus sequences, which matching the most with Densovirus, Rat parvovirus, unclassified densovirus, frog adenovirus and papillomavirus, respectively, and the amino acid homology of them were all<50%.
Conclusions:
1. A variety of new viral sequences existed in pig manure, showing that pig is a biobank for viral diversity, which should be given importance in early warning study of human viral diseases.
2. A brand new parecho-like virus, PLV-CHN, was detected in healthy piglets in China, which, together with SPaV1identified in France at the same period, formed a new genus in Picornaviridae.
3. Infection of new members (Pasivirus) of small RNA virus family, such as PLV-CHN, might exist in the early childhood of human development.
4. Differences existed in pathogen composition, type, and quantity in stool specimens between diarrhea and control children, and the potential significance of some of the viruses still need to be discussed further.
5. Five new viral sequences were discovered in specimens of diarrhea children, and their true existence and association with diarrhea necessitate an in-depth study.
6. Norovirus GIV infection was first reported in Chinese children with diarrhea.
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