cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7936895.v1
title: Identification and characterization of a novel rodent bocavirus from different rodent species in China

description: Members in the genus <i>Bocaparvovirus</i> are closely related to human health and have a wide host range. The diverse hosts raise the possibility of crossing species barrier, which is a feature of emerging viruses. Among the mammalian hosts, rodents are generally acknowledged to be important reservoirs of emerging viruses. Here, rodent samples collected from six provinces and autonomous regions of China (Liaoning, Inner Mongolia, Tibet, Xinjiang, Guangxi and Yunnan) were used to investigate the prevalence and distribution of bocaparvoviruses. By using next-generation sequencing first, a partial non-structural protein 1 (NS1) gene belonging to a possible novel bocaparvovirus was discovered. Following this, PCR-based screening of NS1 gene was conducted in 485 rodent samples, with 106 positive results found in seven rodent species (<i>Rattus norvegicus</i>, <i>Mus musculus</i>, <i>Apodemus agrarius</i>, <i>Cricetulus barabensis</i>, <i>Rattus flavipectus</i>, <i>Rattus rattus</i> and <i>Rhombomys opimus</i>). Finally, six nearly full-length genomes and three complete CDS were obtained and the newly identified bocaparvovirus was tentatively named rodent bocavirus (RoBoV). RoBoV has three ORFs: NS1, NP1, and VP, which are characteristics of bocaparvoviruses. Phylogenetic analyses revealed that porcine bocavirus isolate PBoV-KU14, a member of <i>Ungulate bocaparvovirus 4</i>, was the most related virus to RoBoV, with 92.1–92.9% amino acid identities in NS1 protein. Alignments of RoBoV-related sequences showed RoBoV isolates could be classified into two clades, demonstrating an inter-host genetic diversity. The results indicate a potential interspecies transmission of RoBoV between rodents and swine and expand our knowledge on bocaparvoviruses in rodent populations.
DOI: 10.6084/m9.figshare.7937816
title: Genetic and evolutionary analysis of emerging H3N2 canine influenza virus

description: The H3N2 canine influenza virus (CIV) originated from an avian species. Since its emergence, it has circulated in multiple states and has caused pandemics among dog populations; however, no comprehensive studies have explored the causes driving these ongoing cases. The study of the codon usage patterns of viruses can reveal the genetic changes required for the viruses to adapt to new hosts and the external environment. Here we performed a thorough genetic, evolutionary, and codon usage analysis. We identified three evolutionary H3N2 CIV clades from a timescaled phylogenetic tree, namely, Origin, China, and Korea/USA, by principal component analysis (PCA). Additionally, we found a low codon usage bias and that mutation pressure, natural selection, and dinucleotide abundance shape the codon usage bias of H3N2 CIVs, with natural selection being more crucial than the others. Moreover, the human codon adaptation index was similar to that of dogs (the natural host) and cats. In addition, the H3N2 CIV similarity index values were higher than those of the avian influenza virus (AIV), suggesting viral adaptation to the host. Therefore, H3N2 CIVs may pose a potential risk to public health in the future, and further epidemiologic, evolutionary, and pathogenetic studies are required.
DOI: 10.15468/dl.8qwgbz
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Setaria pseudaristata (Peter) Pilg."
 ]
}

 The dataset includes 27 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127103-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.7937000
title: A novel sheet-like virus particle array is a hallmark of Zika virus infection

description: Zika virus (ZIKV) is an emerging flavivirus that caused thousands of human infections in recent years. Compared to other human flaviviruses, ZIKV replication is not well understood. Using fluorescent, transmission electron, and focused ion beam-scanning electron microscopy, we examined ZIKV replication dynamics in Vero 76 cells and in the brains of infected laboratory mice. We observed the progressive development of a perinuclear flaviviral replication factory both in vitro and in vivo. In vitro, we illustrated the ZIKV lifecycle from particle cell entry to egress. ZIKV particles assembled and aggregated in an induced convoluted membrane structure and ZIKV strain-specific membranous vesicles. While most mature virus particles egressed via membrane budding, some particles also likely trafficked through late endosomes and egressed through membrane abscission. Interestingly, we consistently observed a novel sheet-like virus particle array consisting of a single layer of ZIKV particles. Our study further defines ZIKV replication and identifies a novel hallmark of ZIKV infection.
DOI: 10.6084/m9.figshare.7937000.v2
title: A novel sheet-like virus particle array is a hallmark of Zika virus infection

description: Zika virus (ZIKV) is an emerging flavivirus that caused thousands of human infections in recent years. Compared to other human flaviviruses, ZIKV replication is not well understood. Using fluorescent, transmission electron, and focused ion beam-scanning electron microscopy, we examined ZIKV replication dynamics in Vero 76 cells and in the brains of infected laboratory mice. We observed the progressive development of a perinuclear flaviviral replication factory both in vitro and in vivo. In vitro, we illustrated the ZIKV lifecycle from particle cell entry to egress. ZIKV particles assembled and aggregated in an induced convoluted membrane structure and ZIKV strain-specific membranous vesicles. While most mature virus particles egressed via membrane budding, some particles also likely trafficked through late endosomes and egressed through membrane abscission. Interestingly, we consistently observed a novel sheet-like virus particle array consisting of a single layer of ZIKV particles. Our study further defines ZIKV replication and identifies a novel hallmark of ZIKV infection.
DOI: 10.6084/m9.figshare.7937816.v1
title: Genetic and evolutionary analysis of emerging H3N2 canine influenza virus

description: The H3N2 canine influenza virus (CIV) originated from an avian species. Since its emergence, it has circulated in multiple states and has caused pandemics among dog populations; however, no comprehensive studies have explored the causes driving these ongoing cases. The study of the codon usage patterns of viruses can reveal the genetic changes required for the viruses to adapt to new hosts and the external environment. Here we performed a thorough genetic, evolutionary, and codon usage analysis. We identified three evolutionary H3N2 CIV clades from a timescaled phylogenetic tree, namely, Origin, China, and Korea/USA, by principal component analysis (PCA). Additionally, we found a low codon usage bias and that mutation pressure, natural selection, and dinucleotide abundance shape the codon usage bias of H3N2 CIVs, with natural selection being more crucial than the others. Moreover, the human codon adaptation index was similar to that of dogs (the natural host) and cats. In addition, the H3N2 CIV similarity index values were higher than those of the avian influenza virus (AIV), suggesting viral adaptation to the host. Therefore, H3N2 CIVs may pose a potential risk to public health in the future, and further epidemiologic, evolutionary, and pathogenetic studies are required.
DOI: 10.6084/m9.figshare.7937000.v1
title: A novel sheet-like virus particle array is a hallmark of Zika virus infection

description: Zika virus (ZIKV) is an emerging flavivirus that caused thousands of human infections in recent years. Compared to other human flaviviruses, ZIKV replication is not well understood. Using fluorescent, transmission electron, and focused ion beam-scanning electron microscopy, we examined ZIKV replication dynamics in Vero 76 cells and in the brains of infected laboratory mice. We observed the progressive development of a perinuclear flaviviral replication factory both in vitro and in vivo. In vitro, we illustrated the ZIKV lifecycle from particle cell entry to egress. ZIKV particles assembled and aggregated in an induced convoluted membrane structure and ZIKV strain-specific membranous vesicles. While most mature virus particles egressed via membrane budding, some particles also likely trafficked through late endosomes and egressed through membrane abscission. Interestingly, we consistently observed a novel sheet-like virus particle array consisting of a single layer of ZIKV particles. Our study further defines ZIKV replication and identifies a novel hallmark of ZIKV infection.
DOI: 10.6084/m9.figshare.7937132
title: Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium <i>Treponema pallidum</i> subsp. <i>pertenue</i>

description: Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium <i>Treponema pallidum</i> subsp. <i>pertenue</i>
DOI: 10.6084/m9.figshare.7937132.v2
title: Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium <i>Treponema pallidum</i> subsp. <i>pertenue</i>

description: Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium <i>Treponema pallidum</i> subsp. <i>pertenue</i>
DOI: 10.15468/dl.tq77rd
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-83.6757908000000015 43.0293214000000006, -83.6757908000000015 43.0299468799999971, -83.6757908000000015 43.0302596200000025, -83.6757908000000015 43.0307287299999999, -83.6757908000000015 43.0314793100000017, -83.6757908000000015 43.0318858700000035, -83.6757908000000015 43.0324487999999974, -83.6751027800000031 43.0324487999999974, -83.6746336700000057 43.0324487999999974, -83.6737892799999941 43.0324487999999974, -83.6729761699999983 43.0324487999999974, -83.6722881500000000 43.0324487999999974, -83.6718503200000043 43.0324487999999974, -83.6711935699999998 43.0324487999999974, -83.6704117299999979 43.0324487999999974, -83.6698487999999969 43.0324487999999974, -83.6698487999999969 43.0319484199999991, -83.6698487999999969 43.0316669500000017, -83.6698487999999969 43.0310727399999990, -83.6698487999999969 43.0307287299999999, -83.6698487999999969 43.0299781499999980, -83.6698487999999969 43.0293214000000006, -83.6705055500000014 43.0293214000000006, -83.6712873900000034 43.0293214000000006, -83.6721005100000070 43.0293214000000006, -83.6726634300000001 43.0293214000000006, -83.6731012599999957 43.0293214000000006, -83.6736329200000029 43.0293214000000006, -83.6742271199999976 43.0293214000000006, -83.6750715099999951 43.0293214000000006, -83.6757908000000015 43.0293214000000006))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098547-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.7936988
title: Wild ducks excrete highly pathogenic avian influenza virus H5N8 (2014–2015) without clinical or pathological evidence of disease

description: Highly pathogenic avian influenza (HPAI) is essentially a poultry disease. Wild birds have traditionally not been involved in its spread, but the epidemiology of HPAI has changed in recent years. After its emergence in southeastern Asia in 1996, H5 HPAI virus of the Goose/Guangdong lineage has evolved into several sub-lineages, some of which have spread over thousands of kilometers via long-distance migration of wild waterbirds. In order to determine whether the virus is adapting to wild waterbirds, we experimentally inoculated the HPAI H5N8 virus clade 2.3.4.4 group A from 2014 into four key waterbird species—Eurasian wigeon (<i>Anas penelope</i>), common teal (<i>Anas crecca</i>), mallard (<i>Anas platyrhynchos</i>), and common pochard (<i>Aythya ferina</i>)—and compared virus excretion and disease severity with historical data of the HPAI H5N1 virus infection from 2005 in the same four species. Our results showed that excretion was highest in Eurasian wigeons for the 2014 virus, whereas excretion was highest in common pochards and mallards for the 2005 virus. The 2014 virus infection was subclinical in all four waterbird species, while the 2005 virus caused clinical disease and pathological changes in over 50% of the common pochards. In chickens, the 2014 virus infection caused systemic disease and high mortality, similar to the 2005 virus. In conclusion, the evidence was strongest for Eurasian wigeons as long-distance vectors for HPAI H5N8 virus from 2014. The implications of the switch in species-specific virus excretion and decreased disease severity may be that the HPAI H5 virus more easily spreads in the wild-waterbird population.
DOI: 10.6084/m9.figshare.7936988.v2
title: Wild ducks excrete highly pathogenic avian influenza virus H5N8 (2014–2015) without clinical or pathological evidence of disease

description: Highly pathogenic avian influenza (HPAI) is essentially a poultry disease. Wild birds have traditionally not been involved in its spread, but the epidemiology of HPAI has changed in recent years. After its emergence in southeastern Asia in 1996, H5 HPAI virus of the Goose/Guangdong lineage has evolved into several sub-lineages, some of which have spread over thousands of kilometers via long-distance migration of wild waterbirds. In order to determine whether the virus is adapting to wild waterbirds, we experimentally inoculated the HPAI H5N8 virus clade 2.3.4.4 group A from 2014 into four key waterbird species—Eurasian wigeon (<i>Anas penelope</i>), common teal (<i>Anas crecca</i>), mallard (<i>Anas platyrhynchos</i>), and common pochard (<i>Aythya ferina</i>)—and compared virus excretion and disease severity with historical data of the HPAI H5N1 virus infection from 2005 in the same four species. Our results showed that excretion was highest in Eurasian wigeons for the 2014 virus, whereas excretion was highest in common pochards and mallards for the 2005 virus. The 2014 virus infection was subclinical in all four waterbird species, while the 2005 virus caused clinical disease and pathological changes in over 50% of the common pochards. In chickens, the 2014 virus infection caused systemic disease and high mortality, similar to the 2005 virus. In conclusion, the evidence was strongest for Eurasian wigeons as long-distance vectors for HPAI H5N8 virus from 2014. The implications of the switch in species-specific virus excretion and decreased disease severity may be that the HPAI H5 virus more easily spreads in the wild-waterbird population.
DOI: 10.6084/m9.figshare.7937132.v1
title: Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium <i>Treponema pallidum</i> subsp. <i>pertenue</i>

description: Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium <i>Treponema pallidum</i> subsp. <i>pertenue</i>
DOI: 10.6084/m9.figshare.7937795
title: Avian hepatitis E virus infection of duck, goose, and rabbit in northwest China

description: Avian hepatitis E virus infection of duck, goose, and rabbit in northwest China
DOI: 10.6084/m9.figshare.7937795.v1
title: Avian hepatitis E virus infection of duck, goose, and rabbit in northwest China

description: Avian hepatitis E virus infection of duck, goose, and rabbit in northwest China
DOI: 10.25549/pcra-c14-64240
title: Redemption tidings, vol. 44, nos. 1-52, 4 Jan. - 26 Dec. 1968

description: [description english/roman)] Issued weekly.
DOI: 10.6084/m9.figshare.7936988.v1
title: Wild ducks excrete highly pathogenic avian influenza virus H5N8 (2014–2015) without clinical or pathological evidence of disease

description: Highly pathogenic avian influenza (HPAI) is essentially a poultry disease. Wild birds have traditionally not been involved in its spread, but the epidemiology of HPAI has changed in recent years. After its emergence in southeastern Asia in 1996, H5 HPAI virus of the Goose/Guangdong lineage has evolved into several sub-lineages, some of which have spread over thousands of kilometers via long-distance migration of wild waterbirds. In order to determine whether the virus is adapting to wild waterbirds, we experimentally inoculated the HPAI H5N8 virus clade 2.3.4.4 group A from 2014 into four key waterbird species—Eurasian wigeon (<i>Anas penelope</i>), common teal (<i>Anas crecca</i>), mallard (<i>Anas platyrhynchos</i>), and common pochard (<i>Aythya ferina</i>)—and compared virus excretion and disease severity with historical data of the HPAI H5N1 virus infection from 2005 in the same four species. Our results showed that excretion was highest in Eurasian wigeons for the 2014 virus, whereas excretion was highest in common pochards and mallards for the 2005 virus. The 2014 virus infection was subclinical in all four waterbird species, while the 2005 virus caused clinical disease and pathological changes in over 50% of the common pochards. In chickens, the 2014 virus infection caused systemic disease and high mortality, similar to the 2005 virus. In conclusion, the evidence was strongest for Eurasian wigeons as long-distance vectors for HPAI H5N8 virus from 2014. The implications of the switch in species-specific virus excretion and decreased disease severity may be that the HPAI H5 virus more easily spreads in the wild-waterbird population.
DOI: 10.15468/dl.8zwma5
title: Occurrence Download

description: A dataset containing 163 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phlomoides tatsienensis (Bureau & Franch.) Kamelin & Makhm."
 ]
}

 The dataset includes 163 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075139-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.7936928
title: Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings

description: Astroviruses are recognized as a leading cause of gastroenteritis in humans and animals. They are also associated with extra-intestinal diseases, such as hepatitis in ducklings, nephritis in chickens, and encephalitis in cattle. In February 2017, a fatal infection of goslings characterized by visceral urate deposition was reported in the Shandong province, China. Our systematic investigation led to the isolation of an astrovirus, designated AAstV/Goose/CHN/2017/SD01, and similar disease was reproduced by experimental infection of healthy goslings, fulfilling Koch’s postulates. The isolated astrovirus replicated well and resulted in 100% mortality of goose embryos. Complete genome sequence analysis revealed that the isolate was genetically distinct from known astroviruses and closely related to members of the avastrovirus genogroup II. Experimental infection showed that the isolate was highly pathogenic in goslings, causing clinical signs, growth repression and in many cases mortality. Histopathological examination indicated that lesions occurred mainly in the kidneys of infected birds. However, virus-specific genomic RNA was detected in all representative tissues, and virus shedding was detected up to 12 days after inoculation, suggesting that the isolate was able to spread systemically and replicate efficiently in vivo. Collectively, our study demonstrates, for the first time, the etiological role of a genetically distinct astrovirus in the fatal infection of goslings.
DOI: 10.6084/m9.figshare.7936928.v1
title: Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings

description: Astroviruses are recognized as a leading cause of gastroenteritis in humans and animals. They are also associated with extra-intestinal diseases, such as hepatitis in ducklings, nephritis in chickens, and encephalitis in cattle. In February 2017, a fatal infection of goslings characterized by visceral urate deposition was reported in the Shandong province, China. Our systematic investigation led to the isolation of an astrovirus, designated AAstV/Goose/CHN/2017/SD01, and similar disease was reproduced by experimental infection of healthy goslings, fulfilling Koch’s postulates. The isolated astrovirus replicated well and resulted in 100% mortality of goose embryos. Complete genome sequence analysis revealed that the isolate was genetically distinct from known astroviruses and closely related to members of the avastrovirus genogroup II. Experimental infection showed that the isolate was highly pathogenic in goslings, causing clinical signs, growth repression and in many cases mortality. Histopathological examination indicated that lesions occurred mainly in the kidneys of infected birds. However, virus-specific genomic RNA was detected in all representative tissues, and virus shedding was detected up to 12 days after inoculation, suggesting that the isolate was able to spread systemically and replicate efficiently in vivo. Collectively, our study demonstrates, for the first time, the etiological role of a genetically distinct astrovirus in the fatal infection of goslings.
DOI: 10.6084/m9.figshare.7937048
title: Replication and pathogenic potential of influenza A virus subtypes H3, H7, and H15 from free-range ducks in Bangladesh in mammals

description: Surveillance of wild aquatic birds and free-range domestic ducks in the Tanguar Haor wetlands in Bangladesh has identified influenza virus subtypes H3N6, H7N1, H7N5, H7N9, and H15N9. Molecular characterization of these viruses indicates their contribution to the genesis of new genotypes of H5N1 influenza viruses from clade 2.3.2.1a that are dominant in poultry markets in Bangladesh as well as to the genesis of the highly pathogenic H5N8 virus currently causing disease outbreaks in domestic poultry in Europe and the Middle East. Therefore, we studied the antigenicity, replication, and pathogenicity of influenza viruses isolated from Tanguar Haor in the DBA/2J mouse model. All viruses replicated in the lung without prior mammalian adaptation, and H7N1 and H7N9 viruses caused 100% and 60% mortality, respectively. H7N5 viruses replicated only in the lungs, whereas H7N1 and H7N9 viruses also replicated in the heart, liver, and brain. Replication and transmission studies in mallard ducks showed that H7N1 and H7N9 viruses replicated in ducks without clinical signs of disease and shed at high titers from the cloaca of infected and contact ducks, which could facilitate virus transmission and spread. Our results indicate that H7 avian influenza viruses from free-range ducks can replicate in mammals, cause severe disease, and be efficiently transmitted to contact ducks. Our study highlights the role of free-range ducks in the spread of influenza viruses to other species in live poultry markets and the potential for these viruses to infect and cause disease in mammals.