Currently, three predominant subtypes of influenza virus are prevalent in pig populations worldwide： H1N1, H3N2, and H1N2. European avian-Hke H1N1 viruses, which were initially detected in European pig populations in...Currently, three predominant subtypes of influenza virus are prevalent in pig populations worldwide： H1N1, H3N2, and H1N2. European avian-Hke H1N1 viruses, which were initially detected in European pig populations in 1979, have been circulating in pigs in eastern China since 2007. In this study, six influenza A viruses were isolated from 60 swine lung samples collected from January to April 2011 in eastern China. Based on whole genome sequencing, molecular characteristics of two isolates were determined. Phylogenetic analysis showed the eight genes of the two isolates were closely related to those of the avian-like H1N1 viruses circulating in pig populations, especially similar to those found in China. Four potential glycosylation sites were observed at positions 13, 26, 198, 277 in the HA1 proteins of the two isolates. Due to the presence of a stop codon at codon 12, the isolates contained truncated PB1-F2 proteins. In this study, the isolates contained 591Q, 627E and 701N in the polymerase subunit PB2, which had been shown to be determinants of virulence and host adaptation. The isolates also had a D rather than E at position 92 of the NS1, a marker of mammalian adaptation. Both isolates contained the GPKV motif at the PDZ ligand domain of the 3＇ end of the NS1, a characteristic marker of the European avian-like swine viruses since about 1999, which is distinct from those of avian, human and classical swine viruses. The M2 proteins of the isolates have the mutation （S31N）, a characteristic marker of the European avian-like swine viruses since about 1987, which may confer resistance to amantadine and rimantadine antivirals. Our findings further emphasize the importance of surveillance on the genetic diversity of influenza A viruses in pigs, and raise more concerns about the occurrence of cross-species transmission events.展开更多
Since late 2005, the swine industry in Shandong province has experienced a significant increase in postweaning multisystemic wasting syndrome （PMWS）. Porcine circovirus type 2 （PCV2） is one of the major etiologic ...Since late 2005, the swine industry in Shandong province has experienced a significant increase in postweaning multisystemic wasting syndrome （PMWS）. Porcine circovirus type 2 （PCV2） is one of the major etiologic agents of PMWS. In order to understand the genetic diversity of PCV2 in swine herds in Shandong province, we sequenced six complete genomes of PCV2 between 2005 and 2007. Sequence analysis revealed that all the six PCV2 strains belonged to one genotype （named PCV 2b）. The deduced amino acid sequences of the replication associated protein （coded by ORFI） showed that all the six PCV2 strains belonged to genotype 2a and could be further divided into two clusters. Based on the analysis of the capsid protein （coded by ORF2）, the six PCV2 strains belonged to genotype 2b. All the six strains belonged to recombinant viruses between genotype PCV2a and genotype PCV2b. This study implied that such recombinant PCV2 spread widely in Shandong area and might be the reason that pig death rate associated with PMWS increased in recent years.展开更多
Many viruses can cause respiratory diseases in humans.Although great advances have been achieved in methods of diagnosis,it remains challenging to identify pathogens in unexplained pneumonia(UP) cases.In this study,we...Many viruses can cause respiratory diseases in humans.Although great advances have been achieved in methods of diagnosis,it remains challenging to identify pathogens in unexplained pneumonia(UP) cases.In this study,we applied next-generation sequencing(NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province,China.A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS.An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples.Human rhinovirus C was the virus most frequently detected and was identified in seven samples.Human measles virus,adenovirus B 55 and coxsackievirus A10 were also identified.Metagenomic sequencing also provided virus genomic sequences,which enabled genotype characterization and phylogenetic analysis.For cases of multiple infection,metagenomic sequencing afforded information regarding the quantity of each virus in the sample,which could be used to evaluate each viruses' role in the disease.Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.展开更多
基金Supported by the Natural Science Foundation of Jiangsu Province(BK2009434)the Innovation Platform for Public Health Emergency Preparedness and Response(NO.ZX201109)the Key Medical Talent Foundation of Jiangsu Province(RC2011084)
文摘Currently, three predominant subtypes of influenza virus are prevalent in pig populations worldwide： H1N1, H3N2, and H1N2. European avian-Hke H1N1 viruses, which were initially detected in European pig populations in 1979, have been circulating in pigs in eastern China since 2007. In this study, six influenza A viruses were isolated from 60 swine lung samples collected from January to April 2011 in eastern China. Based on whole genome sequencing, molecular characteristics of two isolates were determined. Phylogenetic analysis showed the eight genes of the two isolates were closely related to those of the avian-like H1N1 viruses circulating in pig populations, especially similar to those found in China. Four potential glycosylation sites were observed at positions 13, 26, 198, 277 in the HA1 proteins of the two isolates. Due to the presence of a stop codon at codon 12, the isolates contained truncated PB1-F2 proteins. In this study, the isolates contained 591Q, 627E and 701N in the polymerase subunit PB2, which had been shown to be determinants of virulence and host adaptation. The isolates also had a D rather than E at position 92 of the NS1, a marker of mammalian adaptation. Both isolates contained the GPKV motif at the PDZ ligand domain of the 3＇ end of the NS1, a characteristic marker of the European avian-like swine viruses since about 1999, which is distinct from those of avian, human and classical swine viruses. The M2 proteins of the isolates have the mutation （S31N）, a characteristic marker of the European avian-like swine viruses since about 1987, which may confer resistance to amantadine and rimantadine antivirals. Our findings further emphasize the importance of surveillance on the genetic diversity of influenza A viruses in pigs, and raise more concerns about the occurrence of cross-species transmission events.
文摘Since late 2005, the swine industry in Shandong province has experienced a significant increase in postweaning multisystemic wasting syndrome （PMWS）. Porcine circovirus type 2 （PCV2） is one of the major etiologic agents of PMWS. In order to understand the genetic diversity of PCV2 in swine herds in Shandong province, we sequenced six complete genomes of PCV2 between 2005 and 2007. Sequence analysis revealed that all the six PCV2 strains belonged to one genotype （named PCV 2b）. The deduced amino acid sequences of the replication associated protein （coded by ORFI） showed that all the six PCV2 strains belonged to genotype 2a and could be further divided into two clusters. Based on the analysis of the capsid protein （coded by ORF2）, the six PCV2 strains belonged to genotype 2b. All the six strains belonged to recombinant viruses between genotype PCV2a and genotype PCV2b. This study implied that such recombinant PCV2 spread widely in Shandong area and might be the reason that pig death rate associated with PMWS increased in recent years.
基金supported by the National Mega-projects for Infectious Diseases(2014ZX10004002)Beijing Municipal Science and Technology Commission grant(D151100002115003)
文摘Many viruses can cause respiratory diseases in humans.Although great advances have been achieved in methods of diagnosis,it remains challenging to identify pathogens in unexplained pneumonia(UP) cases.In this study,we applied next-generation sequencing(NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province,China.A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS.An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples.Human rhinovirus C was the virus most frequently detected and was identified in seven samples.Human measles virus,adenovirus B 55 and coxsackievirus A10 were also identified.Metagenomic sequencing also provided virus genomic sequences,which enabled genotype characterization and phylogenetic analysis.For cases of multiple infection,metagenomic sequencing afforded information regarding the quantity of each virus in the sample,which could be used to evaluate each viruses' role in the disease.Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.
