cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20509183
title: A variant NS1 protein from H5N2 avian influenza virus suppresses PKR activation and promotes replication and virulence in mammals

description: Highly pathogenic avian influenza viruses (HPAIVs) frequently receive global attention as threats to public health. The NS1 protein is a key virulence factor known to impair host antiviral responses. The study herein revealed HPAIV H5N2 NS gene encoded additional protein; a truncated NS1 variant, designated NS3, produced by alternative splicing of the NS transcript. To examine the function of NS3 during infection, we generated recombinant viruses expressing either full-length NS1 (RG-AIV-T375G) or NS3 (RG-AIV-NS3). Interestingly, RG-AIV-NS3 virus produced higher titres than RG-AIV-T375G in multiple mammalian cell lines. However, RG-AIV-T375G exhibited a replication advantage over RG-AIV-NS3 in chicken DF-1 cells, indicating that host cell identity dictates the effect of NS3 on viral replication. In mice and mammalian cells, RG-AIV-NS3 infection elicited higher level of cytokines, including IFN-β, MX and TNF-α, potentially due to its higher replication activity. Based on mini-genome assay, NS3 had pronounced effects on viral replication machinery. Surprisingly, NS3 retained an interaction with PKR and suppressed PKR activation despite its lack of amino-acid residues 126-167. The poor replication ability of RG-AIV-T375G was partially restored in cells deficient in PKR suggesting that full-length NS1 may be insufficient to suppress PKR function. Notably, virulence of the full-length NS1-expressing RG-AIV-T375G virus was highly attenuated in mice when compared to RG-AIV-NS3. In summary, our study reveals the existence and function of a previously unidentified H5N2 viral protein, NS3. We found that NS3 is functionally distinct from NS1 protein, as it enhances viral replication and pathogenicity in mammalian systems, potentially via suppression of PKR activity.
DOI: 10.6084/m9.figshare.20509183.v2
title: A variant NS1 protein from H5N2 avian influenza virus suppresses PKR activation and promotes replication and virulence in mammals

description: Highly pathogenic avian influenza viruses (HPAIVs) frequently receive global attention as threats to public health. The NS1 protein is a key virulence factor known to impair host antiviral responses. The study herein revealed HPAIV H5N2 NS gene encoded additional protein; a truncated NS1 variant, designated NS3, produced by alternative splicing of the NS transcript. To examine the function of NS3 during infection, we generated recombinant viruses expressing either full-length NS1 (RG-AIV-T375G) or NS3 (RG-AIV-NS3). Interestingly, RG-AIV-NS3 virus produced higher titres than RG-AIV-T375G in multiple mammalian cell lines. However, RG-AIV-T375G exhibited a replication advantage over RG-AIV-NS3 in chicken DF-1 cells, indicating that host cell identity dictates the effect of NS3 on viral replication. In mice and mammalian cells, RG-AIV-NS3 infection elicited higher level of cytokines, including IFN-β, MX and TNF-α, potentially due to its higher replication activity. Based on mini-genome assay, NS3 had pronounced effects on viral replication machinery. Surprisingly, NS3 retained an interaction with PKR and suppressed PKR activation despite its lack of amino-acid residues 126-167. The poor replication ability of RG-AIV-T375G was partially restored in cells deficient in PKR suggesting that full-length NS1 may be insufficient to suppress PKR function. Notably, virulence of the full-length NS1-expressing RG-AIV-T375G virus was highly attenuated in mice when compared to RG-AIV-NS3. In summary, our study reveals the existence and function of a previously unidentified H5N2 viral protein, NS3. We found that NS3 is functionally distinct from NS1 protein, as it enhances viral replication and pathogenicity in mammalian systems, potentially via suppression of PKR activity.
DOI: 10.15468/dl.yv96r9
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Doryteuthis gahi",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 10",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 35 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001189-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rk7n8
title: Data from: Rust disease of eucalypts, caused by Puccinia psidii, did not originate via host jump from guava in Brazil

description: The rust fungus, Puccinia psidii, is a devastating pathogen of introduced
 eucalypts (Eucalyptus spp.) in Brazil where it was first observed in 1912.
 This pathogen is hypothesized to be endemic to South and Central America
 and to have first infected eucalypts via a host jump from native guava
 (Psidium guajava). Ten microsatellite markers were used to genotype 148 P.
 psidii samples from eucalypts and guava plus five additional myrtaceous
 hosts across a wide geographic range of southeastern Brazil and Uruguay.
 Principal coordinates analysis, a Bayesian clustering analysis, and a
 minimum spanning network revealed two major genetic clusters among the
 sampled isolates, one associated with guava and another associated with
 eucalypts and three additional hosts. Multilocus genotypes infecting guava
 differed by multiple mutational steps at eight loci compared to those
 infecting eucalypts. Approximate Bayesian computation revealed that
 evolutionary scenarios involving a coalescence event between guava- and
 eucalypt-associated pathogen populations within the past 1000 years to be
 highly unlikely. Divergence time estimates conducted over a wide range of
 demographic scenarios indicated that the population split between
 eucalypt- and guava-infecting pathogens occurred approximately 15,000 to
 150,000 years ago. None of the analyses supported the hypothesis that
 eucalypt-infecting P. psidii in Brazil originated via host jump from guava
 since the introduction of eucalypts to Brazil approximately 185 years ago.
 The existence of host-associated biotypes of P. psidii in Brazil indicates
 that this diversity must be considered when assessing the invasive threat
 posed by this pathogen to myrtaceous hosts worldwide.
description: Geographic coordinates
 and allele scores of Puccinia psidii samples from Brazil and
 UruguayData include geographic
 coordinates of single uredinial pustules of Puccinia psidii ca. 6 mm
 diameter collected between March 2008 and August 2009 from 148 individual
 plants representing seven myrtaceous taxa (eucalypts, guava, rose apple,
 Brazilian guava, Java plum, jabuticaba, and pitanga) in nine Brazilian
 states and one location in Uruguay. Samples were genotyped at 10
 microsatellite loci (PpSSR012, PpSSR014, PpSSR018, PpSSR022, PpSSR087,
 PpSSR102, PpSSR146, PpSSR161, PpSSR178, and PpSSR195) using genomic DNA
 extracted directly from each pustule following a modified CTAB-based
 protocol. Fragment analysis was via capillary electrophoresis using an ABI
 3700 DNA automated sequencer. Positive and negative controls were included
 for each locus scored and scoring was repeated for representative alleles
 for each locus to ensure the accuracy of genotyping. Allele sizes were
 estimated using marker standards (ROX Geneflo 625, CHIMERx, Milwaukee, WI,
 USA) and scored using ABI PeakScanner Analysis Software
 v1.0.DRYAD.xlsx
DOI: 10.6084/m9.figshare.21252603
title: Outbreak of occupational <i>Brucella</i> infection caused by live attenuated <i>Brucella</i> vaccine in a biological products company in Chongqing, China, 2020

description: The northern areas of China are traditional endemic regions for brucellosis in both animals and humans, while occasional outbreaks of brucellosis have been observed in neglected southern provinces. On 16 December 2020, Chongqing Center for Disease Control and Prevention (CQCDC) received a report of 15 <i>Brucella</i> seropositive employees in a biological products company. The CQCDC and the local health administrative department launched an investigation that included identification of cases, laboratory testing of samples, and employees’ interview to identify the cause of this incident. A case-control study was implemented to compare high-risk factors between cases and serology-negative personals. Human and animal serum samples and environmental swabs were collected for testing. A total of 61 recessive infectors were found with an infection rate of 43.57% (61/140). Fisher’s exact test showed that there were significant differences in <i>Brucella</i> infection rates among different post classifications (<i>p </i>= 0.02), working places (<i>p </i>= 0.007), and buildings (<i>p</i> &lt; 0.0001). Case-control study showed that working in vaccine production workshop was independently associated with an increased risk of infection (odds ratio (<i>OR</i>): 2.60; 95% confidence interval (<i>CI</i>): 1.31–5.19). The positive detection rate was 88.06% (59/67) for production environment and 16.67% (2/12) for external environment. The investigation indicated that close contact with biological products and aerosol were the potential transmission routes of this outbreak under the condition of insufficient personal protection and disinfection. Our study provides new epidemiological evidence for a more detailed understanding of occupational infections with live attenuated <i>Brucella</i> vaccine.
DOI: 10.6084/m9.figshare.21252603.v2
title: Outbreak of occupational <i>Brucella</i> infection caused by live attenuated <i>Brucella</i> vaccine in a biological products company in Chongqing, China, 2020

description: The northern areas of China are traditional endemic regions for brucellosis in both animals and humans, while occasional outbreaks of brucellosis have been observed in neglected southern provinces. On 16 December 2020, Chongqing Center for Disease Control and Prevention (CQCDC) received a report of 15 <i>Brucella</i> seropositive employees in a biological products company. The CQCDC and the local health administrative department launched an investigation that included identification of cases, laboratory testing of samples, and employees’ interview to identify the cause of this incident. A case-control study was implemented to compare high-risk factors between cases and serology-negative personals. Human and animal serum samples and environmental swabs were collected for testing. A total of 61 recessive infectors were found with an infection rate of 43.57% (61/140). Fisher’s exact test showed that there were significant differences in <i>Brucella</i> infection rates among different post classifications (<i>p </i>= 0.02), working places (<i>p </i>= 0.007), and buildings (<i>p</i> &lt; 0.0001). Case-control study showed that working in vaccine production workshop was independently associated with an increased risk of infection (odds ratio (<i>OR</i>): 2.60; 95% confidence interval (<i>CI</i>): 1.31–5.19). The positive detection rate was 88.06% (59/67) for production environment and 16.67% (2/12) for external environment. The investigation indicated that close contact with biological products and aerosol were the potential transmission routes of this outbreak under the condition of insufficient personal protection and disinfection. Our study provides new epidemiological evidence for a more detailed understanding of occupational infections with live attenuated <i>Brucella</i> vaccine.
DOI: 10.6084/m9.figshare.20440567
title: Total RNA sequencing of <i>Phlebotomus chinensis</i> sandflies in China revealed viral, bacterial, and eukaryotic microbes potentially pathogenic to humans

description: <i>Phlebotomus chinensis</i> sandfly is a neglected insect vector in China that is well-known for carrying <i>Leishmania</i>. Recent studies have expanded its pathogen repertoire with two novel arthropod-borne phleboviruses capable of infecting humans and animals. Despite these discoveries, our knowledge of the general pathogen diversity and overall microbiome composition of this vector species is still very limited. Here we carried out a meta-transcriptomics analysis that revealed the actively replicating/transcribing RNA viruses, DNA viruses, bacteria, and eukaryotic microbes, namely, the “total microbiome”, of several sandfly populations in China. Strikingly, “microbiome” made up 1.8% of total non-ribosomal RNA and comprised more than 87 species, among which 70 were novel, including divergent members of the genera <i>Flavivirus</i> and of the family Trypanosomatidae. Importantly, among these microbes we were able to reveal four distinguished types of human and/or mammalian pathogens, including two phleboviruses (hedi and wuxiang viruses), one novel Spotted fever group rickettsia, as well as a member of <i>Leishmania donovani</i> complex, among which hedi virus and <i>Leishmania</i> each had &gt; 50% pool prevalence rate and relatively high abundance levels. Our study also showed the ubiquitous presence of an endosymbiont, namely <i>Wolbachia</i>, although no anti-viral or anti-pathogen effects were detected based on our data. In summary, our results uncovered the much un-explored diversity of microbes harboured by sandflies in China and demonstrated that high pathogen diversity and abundance are currently present in multiple populations, implying disease potential for exposed local human population or domestic animals.
DOI: 10.6084/m9.figshare.20440567.v2
title: Total RNA sequencing of <i>Phlebotomus chinensis</i> sandflies in China revealed viral, bacterial, and eukaryotic microbes potentially pathogenic to humans

description: <i>Phlebotomus chinensis</i> sandfly is a neglected insect vector in China that is well-known for carrying <i>Leishmania</i>. Recent studies have expanded its pathogen repertoire with two novel arthropod-borne phleboviruses capable of infecting humans and animals. Despite these discoveries, our knowledge of the general pathogen diversity and overall microbiome composition of this vector species is still very limited. Here we carried out a meta-transcriptomics analysis that revealed the actively replicating/transcribing RNA viruses, DNA viruses, bacteria, and eukaryotic microbes, namely, the “total microbiome”, of several sandfly populations in China. Strikingly, “microbiome” made up 1.8% of total non-ribosomal RNA and comprised more than 87 species, among which 70 were novel, including divergent members of the genera <i>Flavivirus</i> and of the family Trypanosomatidae. Importantly, among these microbes we were able to reveal four distinguished types of human and/or mammalian pathogens, including two phleboviruses (hedi and wuxiang viruses), one novel Spotted fever group rickettsia, as well as a member of <i>Leishmania donovani</i> complex, among which hedi virus and <i>Leishmania</i> each had &gt; 50% pool prevalence rate and relatively high abundance levels. Our study also showed the ubiquitous presence of an endosymbiont, namely <i>Wolbachia</i>, although no anti-viral or anti-pathogen effects were detected based on our data. In summary, our results uncovered the much un-explored diversity of microbes harboured by sandflies in China and demonstrated that high pathogen diversity and abundance are currently present in multiple populations, implying disease potential for exposed local human population or domestic animals.
DOI: 10.6084/m9.figshare.21080953
title: Clinical features of the first critical case of acute encephalitis caused by the avian influenza A (H5N6) virus

description: Highly pathogenic avian influenza viruses (HPAIV), such as H5N1, H5N6, and H7N9, have been reported to frequently infect humans, but acute encephalitis caused by HPAIV in humans has been rarely reported. We report the first critical case of acute encephalitis with mild pneumonia caused by the H5N6 virus. On January 25 of 2022, a 6-year-old girl with severe neurological symptoms was admitted to our hospital and rapidly developed into seizures and coma. Brain imaging showed abnormalities. Electroencephalogram (EEG) presented abnormal slow waves. Cerebrospinal fluid (CSF) contained elevated protein (1.64 g/L) and white cells (546 × 10<sup>6</sup>/L). Laboratory investigations revealed abnormally elevated transaminases, lactate dehydrogenase, and cytokines in serum. A novel reassortant H5N6 virus was identified from the patient’s serum, CSF, and tracheal aspirate specimens. Phylogenic analysis indicated that this virus was a novel reassortant avian-origin influenza A (H5N6) virus that belonged to clade 2.3.4.4b. This patient was diagnosed with acute encephalitis and discharged from the hospital accompanied by a language barrier. An epidemiological investigation confirmed that wild waterfowls were the direct source of infection in this case. Our study highlights the urgent need to pay attention to acute encephalitis caused by HPAIV.
DOI: 10.6084/m9.figshare.21080953.v2
title: Clinical features of the first critical case of acute encephalitis caused by the avian influenza A (H5N6) virus

description: Highly pathogenic avian influenza viruses (HPAIV), such as H5N1, H5N6, and H7N9, have been reported to frequently infect humans, but acute encephalitis caused by HPAIV in humans has been rarely reported. We report the first critical case of acute encephalitis with mild pneumonia caused by the H5N6 virus. On January 25 of 2022, a 6-year-old girl with severe neurological symptoms was admitted to our hospital and rapidly developed into seizures and coma. Brain imaging showed abnormalities. Electroencephalogram (EEG) presented abnormal slow waves. Cerebrospinal fluid (CSF) contained elevated protein (1.64 g/L) and white cells (546 × 10<sup>6</sup>/L). Laboratory investigations revealed abnormally elevated transaminases, lactate dehydrogenase, and cytokines in serum. A novel reassortant H5N6 virus was identified from the patient’s serum, CSF, and tracheal aspirate specimens. Phylogenic analysis indicated that this virus was a novel reassortant avian-origin influenza A (H5N6) virus that belonged to clade 2.3.4.4b. This patient was diagnosed with acute encephalitis and discharged from the hospital accompanied by a language barrier. An epidemiological investigation confirmed that wild waterfowls were the direct source of infection in this case. Our study highlights the urgent need to pay attention to acute encephalitis caused by HPAIV.
DOI: 10.5061/dryad.rm93865
title: Data from: Matching habitat choice promotes species persistence under climate change

description: Species may survive under contemporary climate change by either shifting
 their range or adapting locally to the warmer conditions. Theoretical and
 empirical studies recently underlined that dispersal, the central
 mechanism behind these responses, may depend on the match between an
 individuals’ phenotype and local environment. Such matching habitat choice
 is expected to induce an adaptive gene flow, but it now remains to be
 studied whether this local process could promote species’ responses to
 climate change. Here, we investigate this by developing an
 individual-based model including either random dispersal or
 temperature-dependent matching habitat choice. We monitored population
 composition and distribution through space and time under climate change.
 Relative to random dispersal, matching habitat choice induced an adaptive
 gene flow that lessened spatial range loss during climate warming by
 improving populations' viability within the range (i.e. limiting
 range fragmentation) and by facilitating colonization of new habitats at
 the cold margin. The model even predicted in some cases range contraction
 under random dispersal but range expansion under optimal matching habitat
 choice. These benefits of matching habitat choice for population
 persistence mostly resulted from adaptive immigration decision and were
 greater for populations with larger dispersal distance and higher
 emigration probability. We also found that environmental stochasticity
 resulted in suboptimal matching habitat choice, decreasing the benefits of
 this dispersal mode under climate change. However population persistence
 was still better under suboptimal matching habitat choice than under
 random dispersal. Our results highlight the urgent need to implement more
 realistic mechanisms of dispersal such as matching habitat choice into
 models predicting the impacts of ongoing climate change on biodiversity.
description: source_code
DOI: 10.6084/m9.figshare.19298659
title: Molecular epidemiology of carbapenem-resistant hypervirulent <i>Klebsiella pneumoniae</i> in China

description: The epidemiological features of the newly emerged carbapenem-resistant hypervirulent <i>Klebsiella pneumoniae</i> (CR-HvKP) and its potential threat to human health are currently unknown. In this study, a total of 784 <i>bla</i><sub>KPC-2</sub>-bearing CRKP strains collected from three hospitals located at different geographical locales in China during 2014–2017 were subjected to molecular typing, screening of virulence plasmid, string test and WGS (367/784 strains). The proportion of CRKP among all clinical <i>K. pneumoniae</i> strains increased sharply in China during 2014–2017. A large proportion (58%) of these CRKP strains were found to harbour a virulence-encoding plasmid, while only 13% of such strains exhibited a hypervirulent phenotype by string test and neutrophil assay. The lack of hypervirulent phenotype in virulent plasmid-bearing CRKP strains was found to be due to the mutation’s presence on <i>rmpA</i> and <i>rmpA2</i> genes, which rendered them non-functional, while some strains carrying wild type <i>rmpA</i> did not exhibit hypervirulent phenotype either suggesting that other factors might also contribute to the hypervirulence of CRKP. Phylogenetic and SNP analysis indicated that the transmission of these CRKP strains in China likely involved several major clones of ST11. Carriage of IncFII pSWU01-like, <i>bla</i><sub>KPC-2</sub>-bearing plasmid was found to be the major mechanism of carbapenem resistance in these CRKP strains. In conclusion, our data indicated that the prevalence of CRKP strains carrying the virulence plasmid has rapidly increased in China, while genetic markers were not correlated well with the hypervirulent phenotypes, which call for a better definition and screening for these truly hypervirulent CR-HvKP strains in clinical settings.