The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of trans...The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS- associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to beinvolved in the immunoreactions between the virus and its host. Two amino acid changes have been detected in the Mprotein, which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides noevidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of otherpossible SARS-related pathogen(s).展开更多
In 2011, Shiga toxin-producing Escherichia coli O104 : H4 resulted in a large outbreak of bloody diarrhea and hemolytic uremic syndrome (HUS) in Germany and 15 other countries in Europe and North America. This event r...In 2011, Shiga toxin-producing Escherichia coli O104 : H4 resulted in a large outbreak of bloody diarrhea and hemolytic uremic syndrome (HUS) in Germany and 15 other countries in Europe and North America. This event raised a serious public health crisis and caused more than two billion US dollars in economic losses. In this review, we describe the classification of E. coli, the Germany outbreak, and the characteristics and epidemical source-tracing of the causative agent. We also discuss the genomics analysis of the outbreak organism and propose an open-source genomics analysis as a new strategy in combating the emerging infectious diseases.展开更多
Ebola virus disease （EVD） is an acute, serious and fatal illness caused by the Ebola virus. EVD was first identified in 1976 during two simultaneous outbreaks, one in Nzara, Sudan, and the other in Yambuku, Democrat...Ebola virus disease （EVD） is an acute, serious and fatal illness caused by the Ebola virus. EVD was first identified in 1976 during two simultaneous outbreaks, one in Nzara, Sudan, and the other in Yambuku, Democratic Republic of Congo [1]. The latter occurred in a village near the Ebola River, from which the disease takes its name. Since its emergence, several EVD outbreaks have occurred in Africa. The 2013-2015 Ebola outbreak in West Africa is the largest and the most complex one to date. There have been more cases and deaths resulting from this outbreak than those reported for all previous outbreaks. The disease has also spread between countries, beginning in Guinea and then spreading across land borders to Sierra Leone and Liberia [2]. Of the countries afflicted, Guinea, Liberia and Sierra Leone have been the most severely affected; these countries also have very weak health systems, lack human and infrastructural resources, and have only recently emerged from long periods of conflict and instability, mak- ing control of the outbreak more challenging.展开更多
文摘The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS- associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to beinvolved in the immunoreactions between the virus and its host. Two amino acid changes have been detected in the Mprotein, which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides noevidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of otherpossible SARS-related pathogen(s).
基金supported by the National Basic Research Program of China(2009CB522600)Shenzhen Biological Industry Development Special Foundation-Basic Research Key Projects (JC201005250088A)
文摘In 2011, Shiga toxin-producing Escherichia coli O104 : H4 resulted in a large outbreak of bloody diarrhea and hemolytic uremic syndrome (HUS) in Germany and 15 other countries in Europe and North America. This event raised a serious public health crisis and caused more than two billion US dollars in economic losses. In this review, we describe the classification of E. coli, the Germany outbreak, and the characteristics and epidemical source-tracing of the causative agent. We also discuss the genomics analysis of the outbreak organism and propose an open-source genomics analysis as a new strategy in combating the emerging infectious diseases.
基金supported by the National Key Program for Infectious Diseases of China(2013ZX10004-203,2013ZX10004805-006)
文摘Ebola virus disease （EVD） is an acute, serious and fatal illness caused by the Ebola virus. EVD was first identified in 1976 during two simultaneous outbreaks, one in Nzara, Sudan, and the other in Yambuku, Democratic Republic of Congo [1]. The latter occurred in a village near the Ebola River, from which the disease takes its name. Since its emergence, several EVD outbreaks have occurred in Africa. The 2013-2015 Ebola outbreak in West Africa is the largest and the most complex one to date. There have been more cases and deaths resulting from this outbreak than those reported for all previous outbreaks. The disease has also spread between countries, beginning in Guinea and then spreading across land borders to Sierra Leone and Liberia [2]. Of the countries afflicted, Guinea, Liberia and Sierra Leone have been the most severely affected; these countries also have very weak health systems, lack human and infrastructural resources, and have only recently emerged from long periods of conflict and instability, mak- ing control of the outbreak more challenging.
