We report the near full genome sequences of 18 isolates of foot-and-mouth disease virus serotype ... more We report the near full genome sequences of 18 isolates of foot-and-mouth disease virus serotype O and 6 isolates of serotype A obtained from outbreaks in Pakistan between 2011 and 2012. The scarcity of full-length FMDV sequences from this region enhances the importance of these genomes for understanding regional molecular epidemiology.
<p>The 100 probes with the largest difference in expression between non-carriers and carrie... more <p>The 100 probes with the largest difference in expression between non-carriers and carriers (out of a total of 867 with q<0.1) are shown ordered by decreasing difference. Genes that were expressed higher in carriers are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162750#pone.0162750.g001" target="_blank">Fig 1</a>, and genes that were higher expressed in non-carriers are shown in Fig 2. For each probe, the fold change relative to the naïve controls is shown on the x-axis with the vertical dashed line representing no change compared to the naïve animals. Fold changes in signal intensity between non-carriers and naïve controls are marked with blue squares, and the fold changes between carriers and naïve animals are marked with red circles. Filled blue or red symbols indicate a significant difference in intensity (q<0.1) compared to the naïve animals. The horizontal distance between each square and circle represents the difference in signal intensity between non-carriers and carriers, and the color of the label indicates the group in which the signal intensity was higher (blue for non-carriers, red for carriers). The difference between non-carriers and carriers is significant (q<0.1) for all probes shown, independent of whether the difference between each infected group and the controls is significant.</p
We report the near-full-genome sequences of 49 isolates of serotype Asia-1 foot-and-mouth disease... more We report the near-full-genome sequences of 49 isolates of serotype Asia-1 foot-and-mouth disease virus obtained from subclinically infected Asian buffalo in Islamabad Capital Region, Pakistan, in 2011 to 2012. Sequences from subclinically infected animals are exceedingly rare and complement the more commonly available sequences acquired from clinical cases.
We report the near-full-length genome sequences of 22 isolates of foot-and-mouth disease virus (F... more We report the near-full-length genome sequences of 22 isolates of foot-and-mouth disease virus (FMDV) serotype Asia-1, lineage Sindh-08, obtained from foot-and-mouth disease outbreaks in Pakistan between 2011 and 2012. The scarcity of full-length FMDV sequences from this region enhances the importance of these new genomes for understanding the regional molecular epidemiology.
We report the genome sequences of 12 recombinant foot-and-mouth disease virus isolates from Vietn... more We report the genome sequences of 12 recombinant foot-and-mouth disease virus isolates from Vietnam. The recombinant strain has a capsid region from an A/Sea-97 strain and a nonstructural segment from an O/ME-SA/PanAsia strain. The isolates were obtained from two outbreak samples collected in June 2017 and 10 subclinical samples collected between 2017 and 2019.
We report the genomes of four foot-and-mouth disease virus (FMDV) serotype SAT 1 topotype X isola... more We report the genomes of four foot-and-mouth disease virus (FMDV) serotype SAT 1 topotype X isolates from Cameroon. The viruses were isolated from bovine epithelium collected during an outbreak in 2016. These novel sequences update knowledge of FMDV diversity in Central Africa and contribute to regional FMDV molecular epidemiology.
We report the genome sequence of a foot-and-mouth disease virus (FMDV) serotype A topotype Africa... more We report the genome sequence of a foot-and-mouth disease virus (FMDV) serotype A topotype Africa isolate collected from bovine vesicular epithelium from Kenya in 2016. This novel sequence updates the knowledge of FMDV diversity in eastern Africa and has important implications for FMDV epidemiology and molecular analyses.
This is the first report of two near-complete genome sequences of foot-and-mouth disease virus (F... more This is the first report of two near-complete genome sequences of foot-and-mouth disease virus (FMDV) serotype O from Kenya. The viruses were isolated from bovine epithelium collected in 2014 and 2016 from local FMD outbreaks. These full-genome sequences are critical for improving the understanding of regional FMDV molecular epidemiology.
We report the full polyprotein-coding sequences and partial untranslated regions (UTRs) of 18 foo... more We report the full polyprotein-coding sequences and partial untranslated regions (UTRs) of 18 foot-and-mouth disease (FMD) viruses from 4 outbreaks in India in 2013 and 2014. All strains grouped within the O/ME-SA/Ind2001d sublineage. These genomes update knowledge of FMD virus (FMDV) diversity in South Asia and may contribute to molecular epidemiology studies and vaccine selections.
We report the polyprotein coding sequence of the newly defined Ind2001e sublineage of foot-and-mo... more We report the polyprotein coding sequence of the newly defined Ind2001e sublineage of foot-and-mouth disease virus (FMDV) serotype O, isolated from a bovine epithelial tissue sample collected in 2017 in Kon Tum Province, Vietnam. This discovery updates FMDV diversity in Vietnam, has implications for FMDV epidemiology, and influences future vaccine selections.
In 2018, senecavirus A was detected for the first time in Vietnam. This report contains the first... more In 2018, senecavirus A was detected for the first time in Vietnam. This report contains the first complete genome of a senecavirus A isolate collected from pigs in Kon Tum Province, Vietnam.
African swine fever virus (ASFV) is the etiological agent of an often lethal disease of domestic ... more African swine fever virus (ASFV) is the etiological agent of an often lethal disease of domestic pigs. Disease control strategies have been hampered by the unavailability of vaccines against ASFV. Since its introduction in the Republic of Georgia, a highly virulent virus, ASFV Georgia 2007 (ASFV-G), has caused an epizootic that spread rapidly into Eastern European countries. Currently no vaccines are available or under development to control ASFV-G. In the past, genetically modified ASFVs harboring deletions of virulence-associated genes have proven attenuated in swine, inducing protective immunity against challenge with homologous parental viruses. Deletion of the gene 9GL (open reading frame [ORF] B119L) in highly virulent ASFV Malawi-Lil-20/1 produced an attenuated phenotype even when administered to pigs at 10 6 50% hemadsorption doses (HAD 50 ). Here we report the construction of a genetically modified ASFV-G strain (ASFV-G-Δ9GLv) harboring a deletion of the 9GL (B119L) gene. L...
Viral recombination contributes to the emergence of novel strains with the potential for altered ... more Viral recombination contributes to the emergence of novel strains with the potential for altered host range, transmissibility, virulence, and immune evasion. For foot-and-mouth disease virus (FMDV), cell culture experiments and phylogenetic analyses of field samples have demonstrated the occurrence of recombination. However, the frequency of recombination and associated virus–host interactions within an infected host have not been determined. We have previously reported the detection of interserotypic recombinant FMDVs in oropharyngeal fluid (OPF) samples of 42% (5/12) of heterologously superinfected FMDV carrier cattle. The present investigation consists of a detailed analysis of the virus populations in these samples including identification and characterization of additional interserotypic minority recombinants. In every animal in which recombination was detected, recombinant viruses were identified in the OPF at the earliest sampling point after superinfection. Some recombinants...
African buffalo are the natural reservoirs of the SAT serotypes of foot-and-mouth disease virus (... more African buffalo are the natural reservoirs of the SAT serotypes of foot-and-mouth disease virus (FMDV) in sub-Saharan Africa. Most buffalo are exposed to multiple FMDV serotypes early in life, and a proportion of them become persistently infected carriers. Understanding the genetic diversity and evolution of FMDV in carrier animals is critical to elucidate how FMDV persists in buffalo populations. In this study, we obtained oropharyngeal (OPF) fluid from naturally infected African buffalo, and characterized the genetic diversity of FMDV. Out of 54 FMDV-positive OPF, 5 were co-infected with SAT1 and SAT2 serotypes. From the five co-infected buffalo, we obtained eighty-nine plaque-purified isolates. Isolates obtained directly from OPF and plaque purification were sequenced using next-generation sequencing (NGS). Phylogenetic analyses of the sequences obtained from recombination-free protein-coding regions revealed a discrepancy in the topology of capsid proteins and non-structural pro...
We report the near full genome sequences of 18 isolates of foot-and-mouth disease virus serotype ... more We report the near full genome sequences of 18 isolates of foot-and-mouth disease virus serotype O and 6 isolates of serotype A obtained from outbreaks in Pakistan between 2011 and 2012. The scarcity of full-length FMDV sequences from this region enhances the importance of these genomes for understanding regional molecular epidemiology.
<p>The 100 probes with the largest difference in expression between non-carriers and carrie... more <p>The 100 probes with the largest difference in expression between non-carriers and carriers (out of a total of 867 with q<0.1) are shown ordered by decreasing difference. Genes that were expressed higher in carriers are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162750#pone.0162750.g001" target="_blank">Fig 1</a>, and genes that were higher expressed in non-carriers are shown in Fig 2. For each probe, the fold change relative to the naïve controls is shown on the x-axis with the vertical dashed line representing no change compared to the naïve animals. Fold changes in signal intensity between non-carriers and naïve controls are marked with blue squares, and the fold changes between carriers and naïve animals are marked with red circles. Filled blue or red symbols indicate a significant difference in intensity (q<0.1) compared to the naïve animals. The horizontal distance between each square and circle represents the difference in signal intensity between non-carriers and carriers, and the color of the label indicates the group in which the signal intensity was higher (blue for non-carriers, red for carriers). The difference between non-carriers and carriers is significant (q<0.1) for all probes shown, independent of whether the difference between each infected group and the controls is significant.</p
We report the near-full-genome sequences of 49 isolates of serotype Asia-1 foot-and-mouth disease... more We report the near-full-genome sequences of 49 isolates of serotype Asia-1 foot-and-mouth disease virus obtained from subclinically infected Asian buffalo in Islamabad Capital Region, Pakistan, in 2011 to 2012. Sequences from subclinically infected animals are exceedingly rare and complement the more commonly available sequences acquired from clinical cases.
We report the near-full-length genome sequences of 22 isolates of foot-and-mouth disease virus (F... more We report the near-full-length genome sequences of 22 isolates of foot-and-mouth disease virus (FMDV) serotype Asia-1, lineage Sindh-08, obtained from foot-and-mouth disease outbreaks in Pakistan between 2011 and 2012. The scarcity of full-length FMDV sequences from this region enhances the importance of these new genomes for understanding the regional molecular epidemiology.
We report the genome sequences of 12 recombinant foot-and-mouth disease virus isolates from Vietn... more We report the genome sequences of 12 recombinant foot-and-mouth disease virus isolates from Vietnam. The recombinant strain has a capsid region from an A/Sea-97 strain and a nonstructural segment from an O/ME-SA/PanAsia strain. The isolates were obtained from two outbreak samples collected in June 2017 and 10 subclinical samples collected between 2017 and 2019.
We report the genomes of four foot-and-mouth disease virus (FMDV) serotype SAT 1 topotype X isola... more We report the genomes of four foot-and-mouth disease virus (FMDV) serotype SAT 1 topotype X isolates from Cameroon. The viruses were isolated from bovine epithelium collected during an outbreak in 2016. These novel sequences update knowledge of FMDV diversity in Central Africa and contribute to regional FMDV molecular epidemiology.
We report the genome sequence of a foot-and-mouth disease virus (FMDV) serotype A topotype Africa... more We report the genome sequence of a foot-and-mouth disease virus (FMDV) serotype A topotype Africa isolate collected from bovine vesicular epithelium from Kenya in 2016. This novel sequence updates the knowledge of FMDV diversity in eastern Africa and has important implications for FMDV epidemiology and molecular analyses.
This is the first report of two near-complete genome sequences of foot-and-mouth disease virus (F... more This is the first report of two near-complete genome sequences of foot-and-mouth disease virus (FMDV) serotype O from Kenya. The viruses were isolated from bovine epithelium collected in 2014 and 2016 from local FMD outbreaks. These full-genome sequences are critical for improving the understanding of regional FMDV molecular epidemiology.
We report the full polyprotein-coding sequences and partial untranslated regions (UTRs) of 18 foo... more We report the full polyprotein-coding sequences and partial untranslated regions (UTRs) of 18 foot-and-mouth disease (FMD) viruses from 4 outbreaks in India in 2013 and 2014. All strains grouped within the O/ME-SA/Ind2001d sublineage. These genomes update knowledge of FMD virus (FMDV) diversity in South Asia and may contribute to molecular epidemiology studies and vaccine selections.
We report the polyprotein coding sequence of the newly defined Ind2001e sublineage of foot-and-mo... more We report the polyprotein coding sequence of the newly defined Ind2001e sublineage of foot-and-mouth disease virus (FMDV) serotype O, isolated from a bovine epithelial tissue sample collected in 2017 in Kon Tum Province, Vietnam. This discovery updates FMDV diversity in Vietnam, has implications for FMDV epidemiology, and influences future vaccine selections.
In 2018, senecavirus A was detected for the first time in Vietnam. This report contains the first... more In 2018, senecavirus A was detected for the first time in Vietnam. This report contains the first complete genome of a senecavirus A isolate collected from pigs in Kon Tum Province, Vietnam.
African swine fever virus (ASFV) is the etiological agent of an often lethal disease of domestic ... more African swine fever virus (ASFV) is the etiological agent of an often lethal disease of domestic pigs. Disease control strategies have been hampered by the unavailability of vaccines against ASFV. Since its introduction in the Republic of Georgia, a highly virulent virus, ASFV Georgia 2007 (ASFV-G), has caused an epizootic that spread rapidly into Eastern European countries. Currently no vaccines are available or under development to control ASFV-G. In the past, genetically modified ASFVs harboring deletions of virulence-associated genes have proven attenuated in swine, inducing protective immunity against challenge with homologous parental viruses. Deletion of the gene 9GL (open reading frame [ORF] B119L) in highly virulent ASFV Malawi-Lil-20/1 produced an attenuated phenotype even when administered to pigs at 10 6 50% hemadsorption doses (HAD 50 ). Here we report the construction of a genetically modified ASFV-G strain (ASFV-G-Δ9GLv) harboring a deletion of the 9GL (B119L) gene. L...
Viral recombination contributes to the emergence of novel strains with the potential for altered ... more Viral recombination contributes to the emergence of novel strains with the potential for altered host range, transmissibility, virulence, and immune evasion. For foot-and-mouth disease virus (FMDV), cell culture experiments and phylogenetic analyses of field samples have demonstrated the occurrence of recombination. However, the frequency of recombination and associated virus–host interactions within an infected host have not been determined. We have previously reported the detection of interserotypic recombinant FMDVs in oropharyngeal fluid (OPF) samples of 42% (5/12) of heterologously superinfected FMDV carrier cattle. The present investigation consists of a detailed analysis of the virus populations in these samples including identification and characterization of additional interserotypic minority recombinants. In every animal in which recombination was detected, recombinant viruses were identified in the OPF at the earliest sampling point after superinfection. Some recombinants...
African buffalo are the natural reservoirs of the SAT serotypes of foot-and-mouth disease virus (... more African buffalo are the natural reservoirs of the SAT serotypes of foot-and-mouth disease virus (FMDV) in sub-Saharan Africa. Most buffalo are exposed to multiple FMDV serotypes early in life, and a proportion of them become persistently infected carriers. Understanding the genetic diversity and evolution of FMDV in carrier animals is critical to elucidate how FMDV persists in buffalo populations. In this study, we obtained oropharyngeal (OPF) fluid from naturally infected African buffalo, and characterized the genetic diversity of FMDV. Out of 54 FMDV-positive OPF, 5 were co-infected with SAT1 and SAT2 serotypes. From the five co-infected buffalo, we obtained eighty-nine plaque-purified isolates. Isolates obtained directly from OPF and plaque purification were sequenced using next-generation sequencing (NGS). Phylogenetic analyses of the sequences obtained from recombination-free protein-coding regions revealed a discrepancy in the topology of capsid proteins and non-structural pro...
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