We report a bioinformatic analysis of the datasets of sequences of all ten genes from the 2009 H1N1 influenza A pandemic in the state of Wisconsin. The gene with the greatest summed information entropy was found to be...We report a bioinformatic analysis of the datasets of sequences of all ten genes from the 2009 H1N1 influenza A pandemic in the state of Wisconsin. The gene with the greatest summed information entropy was found to be the hemagglutinin (HA) gene. Based upon the viral ID identifier of the HA gene sequence, the sequences of all of the genes were sorted into two subsets, depending upon whether the nucleotide occupying the position of maximum entropy, position 658 of the HA sequence, was either A or U. It was found that the information entropy (H) distributions of subsets differed significantly from each other, from H distributions of randomly generated subsets and from the H distributions of the complete datasets of each gene. Mutual information (MI) values facilitated identification of nine nucleotide positions, distributed over seven of the influenza genes, at which the nucleotide subsets were disjoint, or almost disjoint. Nucleotide frequencies at these nine positions were used to compute mutual information values that subsequently served as weighting factors for edges in a graph net-work. Seven of the nucleotide positions in the graph network are sites of synonymous mutations. Three of these sites of synonymous mutation are within a single gene, the M1 gene, which occupied the position of greatest graph centrality. It is proposed that these bioinformatic and network graph results may reflect alterations in M1-mediated viral packaging and exteriorization, known to be susceptible to synonymous mutations.展开更多
Mutations of influenza virus associated with adaptation occurring during passage in embryonated chicken eggs could result in antigenic change or reduced vaccine effectiveness.In this study,we investigated the mutation...Mutations of influenza virus associated with adaptation occurring during passage in embryonated chicken eggs could result in antigenic change or reduced vaccine effectiveness.In this study,we investigated the mutations of influenza A(H1N1)pdm09 egg isolates from the Chinese National Influenza Surveillance Network between 2009 and 2016.Thirteen mutations were identified in the hemagglutinin(HA)protein from viruses passaged in eggs,in comparing to those in cells.After scanning public database,four mutations,D127E,L191I,D222G/N and Q223R in HA1,which may alter the receptor-binding specificity,were observed frequently.Although the A(H1N1)pdm09 virus has evolved in human for nearly ten years,most egg-cultured viruses acquired one or more further mutations.Using the egg isolates for influenza surveillance requires extra caution because of these selected mutations,and their impacts on antigenicity and receptor-binding property need further evaluation.Currently,most of the influenza vaccines are produced using egg isolates,particularly in China.Thus,there is an urge to promote the establishment of an alternative influenza vaccine production platform.展开更多
As part of the USA’s National Strategy for Pandemic Influenza,an Interagency Strategic Plan for the Early Detection of Highly Pathogenic H5N1 Avian Influenza in Wild Migratory Birds was developed and implemented.From...As part of the USA’s National Strategy for Pandemic Influenza,an Interagency Strategic Plan for the Early Detection of Highly Pathogenic H5N1 Avian Influenza in Wild Migratory Birds was developed and implemented.From1April2006 through 31 March 2009,261946 samples fromwild birds and 101457 wild bird fecalsamples were collected in the USA;no highly pathogenic avian influenza was detected.The United States Department of Agriculture,and state and tribal cooperators accounted for 213115(81%)of the wild bird samples collected;31,27,21 and 21%of the samples were collected from theAtlantic,Pacific,Central and Mississippi flyways,respectively.More than 250 species of wild birds in all 50 states were sampled.The majority of wild birds(86%)were dabbling ducks,geese,swans and shorebirds.The apparent prevalence of low pathogenic avian influenza viruses during biological years 2007 and 2008 was 9.7 and 11.0%,respectively.The apparent prevalence of H5 and H7 subtypes across all species sampled were 0.5 and 0.06%,respectively.The pooled fecal samples(n=101539)positive for low pathogenic avian influenza were 4.0,6.7 and 4.7%for biological years 2006,2007 and 2008,respectively.The highly pathogenic early detection system for wild birds developed and implemented in the USA represents the largest coordinated wildlife disease surveillance system ever conducted.This effort provided evidence that wild birds in the USA were free of highly pathogenic avian influenza virus(given the expected minimum prevalence of 0.001%)at the 99.9%confidence level during the surveillance period.展开更多
This paper demonstrates that the susceptible-infected-removed （SIR） model applied to the early phase of an epidemic can be used to determine epidemic parameters reliably. As a case study, the SIR model is applied to...This paper demonstrates that the susceptible-infected-removed （SIR） model applied to the early phase of an epidemic can be used to determine epidemic parameters reliably. As a case study, the SIR model is applied to the fatality data of the 2009 fall wave cycle of the A（H1N1） pandemic in 12 European countries. It is observed that the best estimates of the basic reproduction number R0 and the mean duration of the infection period l/r/ lie on a curve in the scatterplots, indicating the existence of a nearly-invariant quantity which corresponds to the duration of the epidemic. Spline interpolation applied to the early phase of the epidemic, an approximately 10-week period, together with a future control point in the stabilization region, is sufficient to estimate model parameters. The SIR model is run over a wide range of parameters and estimates of R0 in the range 1.2- 2.0 match the values in the literature. The duration of the infection period, 1/η is estimated to be in the range 2.0-7.0 days. Longer infection periods are tied to spatial characteristics of the spread of the epidemic.展开更多
文摘We report a bioinformatic analysis of the datasets of sequences of all ten genes from the 2009 H1N1 influenza A pandemic in the state of Wisconsin. The gene with the greatest summed information entropy was found to be the hemagglutinin (HA) gene. Based upon the viral ID identifier of the HA gene sequence, the sequences of all of the genes were sorted into two subsets, depending upon whether the nucleotide occupying the position of maximum entropy, position 658 of the HA sequence, was either A or U. It was found that the information entropy (H) distributions of subsets differed significantly from each other, from H distributions of randomly generated subsets and from the H distributions of the complete datasets of each gene. Mutual information (MI) values facilitated identification of nine nucleotide positions, distributed over seven of the influenza genes, at which the nucleotide subsets were disjoint, or almost disjoint. Nucleotide frequencies at these nine positions were used to compute mutual information values that subsequently served as weighting factors for edges in a graph net-work. Seven of the nucleotide positions in the graph network are sites of synonymous mutations. Three of these sites of synonymous mutation are within a single gene, the M1 gene, which occupied the position of greatest graph centrality. It is proposed that these bioinformatic and network graph results may reflect alterations in M1-mediated viral packaging and exteriorization, known to be susceptible to synonymous mutations.
基金supported by the National Key Research and Development Program of China(2016YFD0500208 to Dayan Wang and 2016YFC1200200 to Yuelong Shu)the National Mega-projects for Infectious Diseases(2017ZX10303401-004).
文摘Mutations of influenza virus associated with adaptation occurring during passage in embryonated chicken eggs could result in antigenic change or reduced vaccine effectiveness.In this study,we investigated the mutations of influenza A(H1N1)pdm09 egg isolates from the Chinese National Influenza Surveillance Network between 2009 and 2016.Thirteen mutations were identified in the hemagglutinin(HA)protein from viruses passaged in eggs,in comparing to those in cells.After scanning public database,four mutations,D127E,L191I,D222G/N and Q223R in HA1,which may alter the receptor-binding specificity,were observed frequently.Although the A(H1N1)pdm09 virus has evolved in human for nearly ten years,most egg-cultured viruses acquired one or more further mutations.Using the egg isolates for influenza surveillance requires extra caution because of these selected mutations,and their impacts on antigenicity and receptor-binding property need further evaluation.Currently,most of the influenza vaccines are produced using egg isolates,particularly in China.Thus,there is an urge to promote the establishment of an alternative influenza vaccine production platform.
文摘As part of the USA’s National Strategy for Pandemic Influenza,an Interagency Strategic Plan for the Early Detection of Highly Pathogenic H5N1 Avian Influenza in Wild Migratory Birds was developed and implemented.From1April2006 through 31 March 2009,261946 samples fromwild birds and 101457 wild bird fecalsamples were collected in the USA;no highly pathogenic avian influenza was detected.The United States Department of Agriculture,and state and tribal cooperators accounted for 213115(81%)of the wild bird samples collected;31,27,21 and 21%of the samples were collected from theAtlantic,Pacific,Central and Mississippi flyways,respectively.More than 250 species of wild birds in all 50 states were sampled.The majority of wild birds(86%)were dabbling ducks,geese,swans and shorebirds.The apparent prevalence of low pathogenic avian influenza viruses during biological years 2007 and 2008 was 9.7 and 11.0%,respectively.The apparent prevalence of H5 and H7 subtypes across all species sampled were 0.5 and 0.06%,respectively.The pooled fecal samples(n=101539)positive for low pathogenic avian influenza were 4.0,6.7 and 4.7%for biological years 2006,2007 and 2008,respectively.The highly pathogenic early detection system for wild birds developed and implemented in the USA represents the largest coordinated wildlife disease surveillance system ever conducted.This effort provided evidence that wild birds in the USA were free of highly pathogenic avian influenza virus(given the expected minimum prevalence of 0.001%)at the 99.9%confidence level during the surveillance period.
文摘This paper demonstrates that the susceptible-infected-removed （SIR） model applied to the early phase of an epidemic can be used to determine epidemic parameters reliably. As a case study, the SIR model is applied to the fatality data of the 2009 fall wave cycle of the A（H1N1） pandemic in 12 European countries. It is observed that the best estimates of the basic reproduction number R0 and the mean duration of the infection period l/r/ lie on a curve in the scatterplots, indicating the existence of a nearly-invariant quantity which corresponds to the duration of the epidemic. Spline interpolation applied to the early phase of the epidemic, an approximately 10-week period, together with a future control point in the stabilization region, is sufficient to estimate model parameters. The SIR model is run over a wide range of parameters and estimates of R0 in the range 1.2- 2.0 match the values in the literature. The duration of the infection period, 1/η is estimated to be in the range 2.0-7.0 days. Longer infection periods are tied to spatial characteristics of the spread of the epidemic.
