cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2jk12
title: Data from: Water availability as an agent of selection in introduced populations of Arabidopsis thaliana: impacts on flowering time evolution

description: Flowering is one of the most influential events in the life history of a
 plant and one of the main determinants of reproductive investment and
 lifetime fitness. It is also a highly complex trait controlled by dozens
 of genes. Understanding the selective pressures influencing time to
 flowering, and being able to reliably predict how it will evolve in novel
 environments, are unsolved challenges for plant evolutionary geneticists.
 Using the model plant species, Arabidopsis thaliana, we examined the
 impact of simulated high and low winter precipitation levels on the
 flowering time of naturalized lines from across the eastern portion of the
 introduced North American range, and the fitness consequences of early
 versus late flowering. Flowering time order was significantly correlated
 across two environments—in a previous common garden experiment and in
 environmental chambers set to mimic mid-range photoperiod and temperature
 conditions. Plants in low water flowered earlier, had fewer basal branches
 and produced fewer fruits. Selection in both treatments favored earlier
 flowering and more basal branches. Our analyses revealed an interaction
 between flowering time and water treatment for fitness, where flowering
 later was more deleterious for fitness in the low water treatment. Our
 results are consistent with the hypothesis that differences in winter
 precipitation levels are one of the selective agents underlying a
 flowering time cline in introduced A. thaliana populations.
description: Data from: Water
 availability as an agent of selection in introduced populations of
 Arabidopsis thaliana: impacts on flowering time
 evolutionraw_data_dryad.txtLine means from Stock et al.line_means_dryad.txt
DOI: 10.6084/m9.figshare.24442865
title: Low level of tonic interferon signalling is associated with enhanced susceptibility to SARS-CoV-2 variants of concern in human lung organoids

description: There is tremendous heterogeneity in the severity of COVID-19 disease in the human population, and the mechanisms governing the development of severe disease remain incompletely understood. The emergence of SARS-CoV-2 variants of concern (VOC) Delta (B.1.617.2) and Omicron (B.1.1.529) further compounded this heterogeneity. Virus replication and host cell damage in the distal lung is often associated with severe clinical disease, making this an important site to consider when evaluating pathogenicity of SARS-CoV-2 VOCs. Using distal human lung organoids (hLOs) derived from multiple human donors, we compared the fitness and pathogenicity of SARS-CoV-2 VOC Delta and Omicron, along with an ancestral clade B variant D614G, and evaluated donor-dependent differences in susceptibility to infection. We observed substantial attenuation of Omicron in hLOs and demonstrated enhanced susceptibility to Omicron and D614G replication in hLOs from one donor. Transcriptomic analysis revealed that increased susceptibility to SARS-CoV-2 infection in these hLOs was associated with reduced tonic interferon signaling activity at baseline. We show that hLOs can be used to model heterogeneity of SARS-CoV-2 pathogenesis in humans, and propose that variability in tonic interferon signaling set point may impact susceptibility to SARS-CoV-2 VOCs and subsequent COVID-19 disease progression.
DOI: 10.6084/m9.figshare.24442865.v2
title: Low level of tonic interferon signalling is associated with enhanced susceptibility to SARS-CoV-2 variants of concern in human lung organoids

description: There is tremendous heterogeneity in the severity of COVID-19 disease in the human population, and the mechanisms governing the development of severe disease remain incompletely understood. The emergence of SARS-CoV-2 variants of concern (VOC) Delta (B.1.617.2) and Omicron (B.1.1.529) further compounded this heterogeneity. Virus replication and host cell damage in the distal lung is often associated with severe clinical disease, making this an important site to consider when evaluating pathogenicity of SARS-CoV-2 VOCs. Using distal human lung organoids (hLOs) derived from multiple human donors, we compared the fitness and pathogenicity of SARS-CoV-2 VOC Delta and Omicron, along with an ancestral clade B variant D614G, and evaluated donor-dependent differences in susceptibility to infection. We observed substantial attenuation of Omicron in hLOs and demonstrated enhanced susceptibility to Omicron and D614G replication in hLOs from one donor. Transcriptomic analysis revealed that increased susceptibility to SARS-CoV-2 infection in these hLOs was associated with reduced tonic interferon signaling activity at baseline. We show that hLOs can be used to model heterogeneity of SARS-CoV-2 pathogenesis in humans, and propose that variability in tonic interferon signaling set point may impact susceptibility to SARS-CoV-2 VOCs and subsequent COVID-19 disease progression.
DOI: 10.5061/dryad.b8d4519
title: Data from: Analyses of phenotypic differentiations among South Georgian Diving Petrel (Pelecanoides georgicus) populations reveal an undescribed and highly endangered species from New Zealand

description: Unresolved taxonomy of threatened species is problematic for conservation
 as the field relies on species being distinct taxonomic units. Differences
 in breeding habitat and results from a preliminary molecular analysis
 indicated that the New Zealand population of the South Georgian Diving
 Petrel (Pelecanoides georgicus) was a distinct, yet undescribed, species.
 We measured 11 biometric characters and scored eight plumage characters in
 143 live birds and 64 study skins originating from most populations of P.
 georgicus, to assess their taxonomic relationships. We analysed
 differences with principal component analyses (PCA), factorial ANOVAs, and
 Kruskal-Wallis rank sum tests. Results show that individuals from New
 Zealand differ significantly from P. georgicus from all other populations
 as following: 1) longer wings, 2) longer outer tail feathers, 3) deeper
 bills, 4) longer heads, 5) longer tarsi, 6) limited collar extent, 7)
 greater extent of contrasting scapulars, 8) larger contrasting markings on
 the secondaries, 9) paler ear coverts, 10) paler collars, and 11) paler
 flanks. Furthermore, we used a species delimitation test with quantitative
 phenotypic criteria; results reveal that the New Zealand population of P.
 georgicus indeed merits species status. We hereby name this new species
 Pelecanoides whenuahouensis sp. nov. Due to severe reductions in its range
 and the very low number of remaining birds (~150 individuals limited to a
 single breeding colony on Codfish Island/Whenua Hou) the species warrants
 listing as ‘Critically Endangered’.
description: Fischeretal.2018.dataRaw data on biometric measurements and plumage scores of 207 Pelecanoides georgicus individuals.
DOI: 10.6084/m9.figshare.24001738
title: Genomic and epidemiological perspectives on the first local sporadic cases of Mpox in China

description: From June 7th to 11th, 2023, eight cases of Mpox were identified in Guangzhou, China. This is the first report of multiple local sporadic cases after the imported case in Chongqing, China. Epidemiological investigation revealed that these cases had no history of international travel and no connections with each other. Haplotype network and phylogenetic analyses indicated that the possible origin is likely from Japan, although the direct origin may remain uncertain due to limited genomic sequences and sampling bias in GISAID. The three Guangzhou sequences have accumulated several novel mutations, suggesting the local transmission of Mpox may have been ongoing for some time. Based on the daily cases during the early stage of Mpox outbreak in four other countries, the number of possible infected cases in Guangzhou is inferred to be more than 300, suggesting that swift and efficient control measures must be implemented to mitigate the risk of a potential epidemic.
DOI: 10.6084/m9.figshare.24014767.v1
title: Immunization with a heat-killed prm1 deletion strain protects the host from <i>Cryptococcus neoformans</i> infection

description: Systemic infection with <i>Cryptococcus neoformans</i>, a dangerous and contagious pathogen found throughout the world, frequently results in lethal cryptococcal pneumonia and meningoencephalitis, and no effective treatments and vaccination of cryptococcosis are available. Here, we describe Prm1, a novel regulator of <i>C. neoformans</i> virulence<i>. C. neoformans prm1Δ</i> cells exhibit extreme sensitivity to various environmental stress conditions. Furthermore, <i>prm1Δ</i> cells show deficiencies in the biosynthesis of chitosan and mannoprotein, which in turn result in impairment of cell wall integrity. Treatment of mice with heat-killed <i>prm1Δ</i> cells was found to facilitate the host immunological defence against infection with wild-type <i>C. neoformans</i>. Further investigation demonstrated that <i>prm1Δ</i> cells strongly promote pulmonary production of interferon-γ, leading to activation of macrophage M1 differentiation and inhibition of M2 polarization. Therefore, our findings suggest that <i>C. neoformans</i> Prm1 may be a viable target for the development of anti-cryptococcosis medications and, cells lacking Prm1 represent a promising candidate for a vaccine.
DOI: 10.6084/m9.figshare.24093751
title: Genomic epidemiology sheds light on the emergence and spread of <i>Mycobacterium bovis</i> Eu2 Clonal Complex in Portugal

description: Animal tuberculosis (TB) remains a serious concern for animal and human health. <i>Mycobacterium bovis</i> circulates in multi-host systems, dominated by the European 2 clonal complex (Eu2) in Iberia. In this work, we use genomic epidemiology to infer the emergence, spread, and spatiotemporal patterns of Eu2 in the official epidemiological risk area of animal TB in Portugal. Phylogenetic analysis of 144 <i>M. bovis</i> whole-genome sequences from cattle, wild boar, and red deer, representing the 2002–2021 period, distinguished three Eu2 clades that evolved independently. The major Eu2 clade underwent phylodynamic inferences to estimate the time and location of outbreaks, host transitions, and spatial diffusion as well. The origin of this Eu2 clade was attributed to the red deer population in the Castelo Branco district, near the border with Spain. Most host transitions were intraspecific (80%), while interspecific transmissions between wildlife species (wild boar-red deer), and between wild boar and cattle, were highly supported. Phylogeographic reconstruction evidenced that most transitions (82%) occur within municipalities, highlighting local transmission corridors. Our study indicates that <i>M. bovis</i> continues to spread at the cattle-wildlife interface within the animal TB hotspot area, possibly driven by the foraging behaviour of wild boar near agricultural lands. Red deer seems to be an important driver of TB within wildlife hosts, while the wild boar links the multi-host wildlife community and livestock. This work highlights the value of combining genomic epidemiology with phylodynamic inference to resolve host jumps and spatial patterns of <i>M. bovis</i>, providing real-time clues about points of intervention.
DOI: 10.5061/dryad.7bp771n4
title: Data from: Patterns of male fitness conform to predictions of evolutionary models of late-life

description: We studied lifetime male virility, a male fitness component, in five
 populations of Drosophila melanogaster. Virility was measured as the
 number of females, out of eight total, that a male could fertilize in 24
 hours. Individual males were measured at weekly intervals until they died.
 Virility declined in an approximately linear fashion for the first three
 weeks of adult life. It then stayed low but relatively constant for
 another three weeks, exhibiting a clear plateau. These observations are
 consistent with the evolutionary theories of late-life.The results were
 not consistent with a simple heterogeneity theory of late-life. This is
 the first demonstration of a late-life plateau for a male fitness
 component. We also found that the virility of males that were within seven
 days of death was significantly lower than similarly aged males that were
 not about to die. This rapid deterioration of virility prior to death, or
 death spiral, is similar to a decline in fecundity that we had previously
 documented.
description: all B
 virilityThe file contains male
 virility for 1000 fruitflies as a function of age. An "NA" in
 the age-at-death field (death) indicates the fly was accidently killed or
 escaped. These flies were not used in the anlaysis.
DOI: 10.6084/m9.figshare.24047073.v1
title: Emergence of a new designated clade 16 with significant antigenic drift in hemagglutinin gene of H9N2 subtype avian influenza virus in eastern China

description: H9N2 avian influenza viruses (AIVs) pose an increasing threat to the poultry industry worldwide and have pandemic potential. Vaccination has been principal prevention strategy to control H9N2 in China since 1998, but vaccine effectiveness is persistently challenged by the emergence of the genetic and/or antigenic variants. Here, we analysed the genetic and antigenic characteristics of H9N2 viruses in China, including 70 HA sequences of H9N2 isolates from poultry, 7358 from online databases during 2010–2020, and 15 from the early reference strains. Bayesian analyses based on hemagglutinin (HA) gene revealed that a new designated clade16 emerged in April 2012, and was prevalent and co-circulated with clade 15 since 2013 in China. Clade 16 viruses exhibited decreased cross-reactivity with those from clade 15. Antigenic Cartography analyses showed represent strains were classified into three antigenic groups named as Group1, Group2 and Group3, and most of the strains in Group 3 (15/17, 88.2%) were from Clade 16 while most of the strains in Group2 (26/29, 89.7%) were from Clade 15. The mean distance between Group 3 and Group 2 was 4.079 (95%CI 3.605–4.554), revealing that major switches to antigenic properties were observed over the emergence of clade 16. Genetic analysis indicated that 11 coevolving amino acid substitutions primarily at antigenic sites were associated with the antigenic differences between clade 15 and clade 16. These data highlight complexities of the genetic evolution and provide a framework for the genetic basis and antigenic characterization of emerging clade 16 of H9N2 subtype avian influenza virus.
DOI: 10.6084/m9.figshare.24420590
title: Previous exposure to Spike-providing parental strains confers neutralizing immunity to XBB lineage and other SARS-CoV-2 recombinants in the context of vaccination

description: The emergence of SARS-CoV-2 recombinants is of particular concern as they can result in a sudden increase in immune evasion due to antigenic shift. Recent recombinants XBB and XBB.1.5 have higher transmissibility than previous recombinants such as “Deltacron.” We hypothesized that immunity to a SARS-CoV-2 recombinant depends on prior exposure to its parental strains. To test this hypothesis, we examined whether Delta or Omicron (BA.1 or BA.2) immunity conferred through infection, vaccination, or breakthrough infection could neutralize Deltacron and XBB/XBB.1.5 recombinants. We found that Delta, BA.1, or BA.2 breakthrough infections provided better immune protection against Deltacron and its parental strains than did the vaccine booster. None of the sera were effective at neutralizing the XBB lineage or its parent BA.2.75.2, except for the sera from the BA.2 breakthrough group. These results support our hypothesis. In turn, our findings underscore the importance of multivalent vaccines that correspond to the antigenic profile of circulating variants of concern and of variant-specific diagnostics that may guide public health and individual decisions in response to emerging SARS-CoV-2 recombinants.
DOI: 10.6084/m9.figshare.24420590.v2
title: Previous exposure to Spike-providing parental strains confers neutralizing immunity to XBB lineage and other SARS-CoV-2 recombinants in the context of vaccination

description: The emergence of SARS-CoV-2 recombinants is of particular concern as they can result in a sudden increase in immune evasion due to antigenic shift. Recent recombinants XBB and XBB.1.5 have higher transmissibility than previous recombinants such as “Deltacron.” We hypothesized that immunity to a SARS-CoV-2 recombinant depends on prior exposure to its parental strains. To test this hypothesis, we examined whether Delta or Omicron (BA.1 or BA.2) immunity conferred through infection, vaccination, or breakthrough infection could neutralize Deltacron and XBB/XBB.1.5 recombinants. We found that Delta, BA.1, or BA.2 breakthrough infections provided better immune protection against Deltacron and its parental strains than did the vaccine booster. None of the sera were effective at neutralizing the XBB lineage or its parent BA.2.75.2, except for the sera from the BA.2 breakthrough group. These results support our hypothesis. In turn, our findings underscore the importance of multivalent vaccines that correspond to the antigenic profile of circulating variants of concern and of variant-specific diagnostics that may guide public health and individual decisions in response to emerging SARS-CoV-2 recombinants.
DOI: 10.6084/m9.figshare.24314841
title: High number of HPAI H5 virus infections and antibodies in wild carnivores in the Netherlands, 2020–2022

description: In October 2020, a new lineage of a clade 2.3.4.4b HPAI virus of the H5 subtype emerged in Europe, resulting in the largest global outbreak of HPAI to date, with unprecedented mortality in wild birds and poultry. The virus appears to have become enzootic in birds, continuously yielding novel HPAI virus variants. The recently increased abundance of infected birds worldwide increases the probability of bird–mammal contact, particularly in wild carnivores. Here, we performed molecular and serological screening of over 500 dead wild carnivores and sequencing of RNA positive materials. We show virological evidence for HPAI H5 virus infection in 0.8%, 1.4%, and 9.9% of animals tested in 2020, 2021, and 2022 respectively, with the highest proportion of positives in foxes, polecats and stone martens. We obtained near full genomes of 7 viruses and detected PB2 amino acid substitutions known to play a role in mammalian adaptation in three sequences. Infections were also found in without neurological signs or mortality. Serological evidence for infection was detected in 20% of the study population. These findings suggests that a high proportion of wild carnivores is infected but undetected in current surveillance programmes. We recommend increased surveillance in susceptible mammals, irrespective of neurological signs or encephalitis.
DOI: 10.6084/m9.figshare.24314841.v2
title: High number of HPAI H5 virus infections and antibodies in wild carnivores in the Netherlands, 2020–2022

description: In October 2020, a new lineage of a clade 2.3.4.4b HPAI virus of the H5 subtype emerged in Europe, resulting in the largest global outbreak of HPAI to date, with unprecedented mortality in wild birds and poultry. The virus appears to have become enzootic in birds, continuously yielding novel HPAI virus variants. The recently increased abundance of infected birds worldwide increases the probability of bird–mammal contact, particularly in wild carnivores. Here, we performed molecular and serological screening of over 500 dead wild carnivores and sequencing of RNA positive materials. We show virological evidence for HPAI H5 virus infection in 0.8%, 1.4%, and 9.9% of animals tested in 2020, 2021, and 2022 respectively, with the highest proportion of positives in foxes, polecats and stone martens. We obtained near full genomes of 7 viruses and detected PB2 amino acid substitutions known to play a role in mammalian adaptation in three sequences. Infections were also found in without neurological signs or mortality. Serological evidence for infection was detected in 20% of the study population. These findings suggests that a high proportion of wild carnivores is infected but undetected in current surveillance programmes. We recommend increased surveillance in susceptible mammals, irrespective of neurological signs or encephalitis.
DOI: 10.6084/m9.figshare.23540588
title: Assessment and sero-diagnosis for coronaviruses with risk of human spillover

description: Zoonotic coronaviruses (CoVs) caused major human outbreaks in the last two decades. One of the biggest challenges during future CoV disease is ensuring rapid detection and diagnosis at the early phase of a zoonotic event, and active surveillance to the zoonotic high-risk CoVs appears the best way at the present time to provide early warnings. However, there is neither an evaluation of spillover potential nor diagnosis tools for the majority of CoVs. Here, we analyzed the viral traits, including population, genetic diversity, receptor and host species for all 40 alpha- and beta-CoV species, where the human-infecting CoVs are from. Our analysis proposed 20 high-risk CoV species, including 6 of which jumped to human, 3 with evidence of spillover but not to human and 11 without evidence of spillover yet, which prediction were further supported by an analysis of the history of CoV zoonosis. We also found three major zoonotic sources: multiple bat-origin CoV species, the rodent-origin sub-genus <i>Embecovirus</i> and the CoV species AlphaCoV1. Moreover, the <i>Rhinolophidae</i> and <i>Hipposideridae</i> bats harbour a significantly higher proportion of human-threatening CoV species, whereas camel, civet, swine and pangolin could be important intermediate hosts during CoV zoonotic transmission. Finally, we established quick and sensitive serologic tools for a list of proposed high-risk CoVs and validated the methods in serum cross-reaction assays using hyper-immune rabbit sera or clinical samples. By comprehensive risk assessment of the potential human-infecting CoVs, our work provides a theoretical or practical basis for future CoV disease preparedness.
DOI: 10.6084/m9.figshare.23540588.v3
title: Assessment and sero-diagnosis for coronaviruses with risk of human spillover

description: Zoonotic coronaviruses (CoVs) caused major human outbreaks in the last two decades. One of the biggest challenges during future CoV disease is ensuring rapid detection and diagnosis at the early phase of a zoonotic event, and active surveillance to the zoonotic high-risk CoVs appears the best way at the present time to provide early warnings. However, there is neither an evaluation of spillover potential nor diagnosis tools for the majority of CoVs. Here, we analyzed the viral traits, including population, genetic diversity, receptor and host species for all 40 alpha- and beta-CoV species, where the human-infecting CoVs are from. Our analysis proposed 20 high-risk CoV species, including 6 of which jumped to human, 3 with evidence of spillover but not to human and 11 without evidence of spillover yet, which prediction were further supported by an analysis of the history of CoV zoonosis. We also found three major zoonotic sources: multiple bat-origin CoV species, the rodent-origin sub-genus <i>Embecovirus</i> and the CoV species AlphaCoV1. Moreover, the <i>Rhinolophidae</i> and <i>Hipposideridae</i> bats harbour a significantly higher proportion of human-threatening CoV species, whereas camel, civet, swine and pangolin could be important intermediate hosts during CoV zoonotic transmission. Finally, we established quick and sensitive serologic tools for a list of proposed high-risk CoVs and validated the methods in serum cross-reaction assays using hyper-immune rabbit sera or clinical samples. By comprehensive risk assessment of the potential human-infecting CoVs, our work provides a theoretical or practical basis for future CoV disease preparedness.