cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25845835
title: Biomarkers and genotypes in patients with Central nervous system infection caused by enterovirus

description: Enteroviruses (EV) comprises many different types and are the most common cause of aseptic meningitis. How the virus affects the brain including potential differences between types are largely unknown. Measuring biomarkers in CSF is a tool to estimate brain damage caused by CNS infections. A retrospective study was performed in samples from 38 patients with acute neurological manifestations and positive CSF-EV RNA (<i>n</i> = 37) or serum-IgM (<i>n</i> = 1). The EV in 17 samples were typed by sequencing. The biomarkers neurofilament light (NFL), glial fibrillary acidic protein (GFAP), S-100B protein, amyloid-β (Aβ) 40 and Aβ42, total-tau (T-tau) and phosphorylated tau (P-tau) were measured and compared with data derived from a control group (<i>n</i> = 19). There were no increased levels of GFAP (<i>p</i> ≤ 0.1) nor NFL (<i>p</i> ≤ 0.1) in the CSF of patients with EV meningitis (<i>n</i> = 38) compared with controls. However, we found decreased levels of Aβ42 (<i>p</i> &lt; 0.001), Aβ40 (<i>p</i> &lt; 0.001), T-tau (<i>p</i> ≥ 0.01), P-tau (<i>p</i> ≤ 0.001) and S-100B (<i>p</i> ≤ 0.001). E30 (<i>n</i> = 9) and CVB5 (<i>n</i> = 6) were the most frequent EV-types identified, but no differences in biomarker levels or other clinical parameters were found between the infecting virus type. Seven patients who were followed for longer than one month reported remaining cognitive impairment, although no correlations with biomarker concentrations were observed. There are no indication of neuronal or astrocyte damage in patients with EV meningitis. Yet, decreased concentrations of Aβ40, Aβ42, P-tau and T-tau were shown, a finding of unknown importance. Cognitive impairment after acute disease occurs, but with only a limited number of patients analysed, no conclusion can be drawn concerning any association with biomarker levels or EV types.
DOI: 10.6084/m9.figshare.25845835.v1
title: Biomarkers and genotypes in patients with Central nervous system infection caused by enterovirus

description: Enteroviruses (EV) comprises many different types and are the most common cause of aseptic meningitis. How the virus affects the brain including potential differences between types are largely unknown. Measuring biomarkers in CSF is a tool to estimate brain damage caused by CNS infections. A retrospective study was performed in samples from 38 patients with acute neurological manifestations and positive CSF-EV RNA (<i>n</i> = 37) or serum-IgM (<i>n</i> = 1). The EV in 17 samples were typed by sequencing. The biomarkers neurofilament light (NFL), glial fibrillary acidic protein (GFAP), S-100B protein, amyloid-β (Aβ) 40 and Aβ42, total-tau (T-tau) and phosphorylated tau (P-tau) were measured and compared with data derived from a control group (<i>n</i> = 19). There were no increased levels of GFAP (<i>p</i> ≤ 0.1) nor NFL (<i>p</i> ≤ 0.1) in the CSF of patients with EV meningitis (<i>n</i> = 38) compared with controls. However, we found decreased levels of Aβ42 (<i>p</i> &lt; 0.001), Aβ40 (<i>p</i> &lt; 0.001), T-tau (<i>p</i> ≥ 0.01), P-tau (<i>p</i> ≤ 0.001) and S-100B (<i>p</i> ≤ 0.001). E30 (<i>n</i> = 9) and CVB5 (<i>n</i> = 6) were the most frequent EV-types identified, but no differences in biomarker levels or other clinical parameters were found between the infecting virus type. Seven patients who were followed for longer than one month reported remaining cognitive impairment, although no correlations with biomarker concentrations were observed. There are no indication of neuronal or astrocyte damage in patients with EV meningitis. Yet, decreased concentrations of Aβ40, Aβ42, P-tau and T-tau were shown, a finding of unknown importance. Cognitive impairment after acute disease occurs, but with only a limited number of patients analysed, no conclusion can be drawn concerning any association with biomarker levels or EV types.
DOI: 10.6084/m9.figshare.26090906
title: Serologic evidence of human exposure to the severe fever with thrombocytopenia syndrome virus and associated viruses in Kenya

description: Although the diverse communities of tick-borne viruses (TBVs) have recently been proposed, the threat of infection and exposure to TBVs among humans across Kenya has been poorly understood. Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne viral agent associated with the epidemic of severe fever with thrombocytopenia syndrome (SFTS) disease in East Asian countries. This study investigated the seroprevalence of SFTSV among humans in Kenya. Serum samples were collected from 459 healthy people in Kenya and tested for anti-SFTSV antibodies, which were further confirmed by immunofluorescence assays. Micro neutralization assays were performed to identify neutralising antibodies against SFTSV and SFTSV-related viruses. A high seroprevalence (162/459, 35.3%) of SFTSV was found in the samples from nine of the ten surveyed counties in Kenya, with higher rates in the eastern plateau forelands, semiarid and arid areas, and coastal areas than in the area aside Rift valley. The seropositive rate was slightly higher in women than in men and was significantly higher in the 55-64 age group. Neutralising activity against SFTSV was detected in four samples, resulting in a rate of 0.9%. No cross-neutralising activity against the SFTSV-related Guertu virus and Heartland virus was detected in the anti-SFTSV positive serum samples. The results provide serologic evidence of human exposure to SFTSV in Kenya and extend our understanding of SFTSV prevalence from Asia to Africa. The findings suggest an increasing threat of exposure to emerging TBVs and the need to investigate tick viromes in Kenya.
DOI: 10.15156/bio/sh0896868.10fu
title: SH0896868.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.25903327
title: Mosquito species identity matters: unraveling the complex interplay in vector-borne diseases

description: Research on vector-borne diseases has traditionally centred on a limited number of vertebrate hosts and their associated pathogens, often neglecting the broader array of vectors within communities. Mosquitoes, with their vast species diversity, hold a central role in disease transmission, yet their capacity to transmit specific pathogens varies considerably among species. Quantitative modelling of mosquito-borne diseases is essential for understanding transmission dynamics and requires the necessity of incorporating the identity of vector species into these models. Consequently, understanding the role of different species of mosquitoes in modelling vector-borne diseases is crucial for comprehending pathogen amplification and spill-over into humans. This comprehensive overview highlights the importance of considering mosquito identity and emphasises the essential need for targeted research efforts to gain a complete understanding of vector-pathogen specificity. Leveraging the recently published book, ‘Mosquitoes of the World’, I identified 19 target mosquito species in Europe, highlighting the diverse transmission patterns exhibited by different vector species and the presence of 135 medically important pathogens. The review delves into the complexities of vector-pathogen interactions, with a focus on specialist and generalist strategies. Furthermore, I discuss the importance of using appropriate diversity indices and the challenges associated with the identification of correct indices. Given that the diversity and relative abundance of key species within a community significantly impact disease risk, comprehending the implications of mosquito diversity in pathogen transmission at a fine scale is crucial for advancing the management and surveillance of mosquito-borne diseases.
DOI: 10.6084/m9.figshare.25903327.v1
title: Mosquito species identity matters: unraveling the complex interplay in vector-borne diseases

description: Research on vector-borne diseases has traditionally centred on a limited number of vertebrate hosts and their associated pathogens, often neglecting the broader array of vectors within communities. Mosquitoes, with their vast species diversity, hold a central role in disease transmission, yet their capacity to transmit specific pathogens varies considerably among species. Quantitative modelling of mosquito-borne diseases is essential for understanding transmission dynamics and requires the necessity of incorporating the identity of vector species into these models. Consequently, understanding the role of different species of mosquitoes in modelling vector-borne diseases is crucial for comprehending pathogen amplification and spill-over into humans. This comprehensive overview highlights the importance of considering mosquito identity and emphasises the essential need for targeted research efforts to gain a complete understanding of vector-pathogen specificity. Leveraging the recently published book, ‘Mosquitoes of the World’, I identified 19 target mosquito species in Europe, highlighting the diverse transmission patterns exhibited by different vector species and the presence of 135 medically important pathogens. The review delves into the complexities of vector-pathogen interactions, with a focus on specialist and generalist strategies. Furthermore, I discuss the importance of using appropriate diversity indices and the challenges associated with the identification of correct indices. Given that the diversity and relative abundance of key species within a community significantly impact disease risk, comprehending the implications of mosquito diversity in pathogen transmission at a fine scale is crucial for advancing the management and surveillance of mosquito-borne diseases.
DOI: 10.6084/m9.figshare.25974714
title: The key role of Spain in the traffic of West Nile virus lineage 1 strains between Europe and Africa

description: West Nile Virus (WNV) is a zoonotic arbovirus worldwide spread. Seasonal WNV outbreaks occur in the Mediterranean basin since the late 1990’s with ever-increasing incidence. In Southern Spain WNV is endemic, as disease foci - caused by WNV lineage 1 (WNV-L1) strains - occur every year. On the contrary, WNV-L2 is the dominant lineage in Europe, so most European WNV sequences available belong to this lineage, WNV-L1 sequences being still scarce. To fill this gap, this study reports the genetic characterisation of 27 newly described WNV-L1 strains, involved in outbreaks affecting wild birds and horses during the last decade in South-Western Spain. All strains except one belong to the Western Mediterranean-1 sub-cluster (WMed-1), related phylogenetically to Italian, French, Portuguese, Moroccan and, remarkably, Senegalese strains. This sub-cluster persisted, spread and evolved into three distinguishable WMed-1 phylogenetic groups that co-circulated, notably, in the same province (Cádiz). They displayed different behaviours: from long-term persistence and rapid spread to neighbouring regions within Spain, to long-distance spread to different countries, including transcontinental spread to Africa. Among the different introductions of WNV in Spain revealed in this study, some of them succeeded to get established, some extinguished from the territory shortly afterwards. Furthermore, Spain’s southernmost province, Cádiz, constitutes a hotspot for virus incursion. Southern Spain seems a likely scenario for emergence of exotic pathogens of African origin. Therefore, circulation of diverse WNV-L1 variants in Spain prompts for an extensive surveillance under a One Health approach.
DOI: 10.6084/m9.figshare.26090906.v2
title: Serologic evidence of human exposure to the severe fever with thrombocytopenia syndrome virus and associated viruses in Kenya

description: Although the diverse communities of tick-borne viruses (TBVs) have recently been proposed, the threat of infection and exposure to TBVs among humans across Kenya has been poorly understood. Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne viral agent associated with the epidemic of severe fever with thrombocytopenia syndrome (SFTS) disease in East Asian countries. This study investigated the seroprevalence of SFTSV among humans in Kenya. Serum samples were collected from 459 healthy people in Kenya and tested for anti-SFTSV antibodies, which were further confirmed by immunofluorescence assays. Micro neutralization assays were performed to identify neutralising antibodies against SFTSV and SFTSV-related viruses. A high seroprevalence (162/459, 35.3%) of SFTSV was found in the samples from nine of the ten surveyed counties in Kenya, with higher rates in the eastern plateau forelands, semiarid and arid areas, and coastal areas than in the area aside Rift valley. The seropositive rate was slightly higher in women than in men and was significantly higher in the 55-64 age group. Neutralising activity against SFTSV was detected in four samples, resulting in a rate of 0.9%. No cross-neutralising activity against the SFTSV-related Guertu virus and Heartland virus was detected in the anti-SFTSV positive serum samples. The results provide serologic evidence of human exposure to SFTSV in Kenya and extend our understanding of SFTSV prevalence from Asia to Africa. The findings suggest an increasing threat of exposure to emerging TBVs and the need to investigate tick viromes in Kenya.
DOI: 10.15156/bio/sh0896869.10fu
title: SH0896869.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.25974714.v1
title: The key role of Spain in the traffic of West Nile virus lineage 1 strains between Europe and Africa

description: West Nile Virus (WNV) is a zoonotic arbovirus worldwide spread. Seasonal WNV outbreaks occur in the Mediterranean basin since the late 1990’s with ever-increasing incidence. In Southern Spain WNV is endemic, as disease foci - caused by WNV lineage 1 (WNV-L1) strains - occur every year. On the contrary, WNV-L2 is the dominant lineage in Europe, so most European WNV sequences available belong to this lineage, WNV-L1 sequences being still scarce. To fill this gap, this study reports the genetic characterisation of 27 newly described WNV-L1 strains, involved in outbreaks affecting wild birds and horses during the last decade in South-Western Spain. All strains except one belong to the Western Mediterranean-1 sub-cluster (WMed-1), related phylogenetically to Italian, French, Portuguese, Moroccan and, remarkably, Senegalese strains. This sub-cluster persisted, spread and evolved into three distinguishable WMed-1 phylogenetic groups that co-circulated, notably, in the same province (Cádiz). They displayed different behaviours: from long-term persistence and rapid spread to neighbouring regions within Spain, to long-distance spread to different countries, including transcontinental spread to Africa. Among the different introductions of WNV in Spain revealed in this study, some of them succeeded to get established, some extinguished from the territory shortly afterwards. Furthermore, Spain’s southernmost province, Cádiz, constitutes a hotspot for virus incursion. Southern Spain seems a likely scenario for emergence of exotic pathogens of African origin. Therefore, circulation of diverse WNV-L1 variants in Spain prompts for an extensive surveillance under a One Health approach.
DOI: 10.6084/m9.figshare.26090906.v1
title: Serologic evidence of human exposure to the severe fever with thrombocytopenia syndrome virus and associated viruses in Kenya

description: Although the diverse communities of tick-borne viruses (TBVs) have recently been proposed, the threat of infection and exposure to TBVs among humans across Kenya has been poorly understood. Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne viral agent associated with the epidemic of severe fever with thrombocytopenia syndrome (SFTS) disease in East Asian countries. This study investigated the seroprevalence of SFTSV among humans in Kenya. Serum samples were collected from 459 healthy people in Kenya and tested for anti-SFTSV antibodies, which were further confirmed by immunofluorescence assays. Micro neutralization assays were performed to identify neutralising antibodies against SFTSV and SFTSV-related viruses. A high seroprevalence (162/459, 35.3%) of SFTSV was found in the samples from nine of the ten surveyed counties in Kenya, with higher rates in the eastern plateau forelands, semiarid and arid areas, and coastal areas than in the area aside Rift valley. The seropositive rate was slightly higher in women than in men and was significantly higher in the 55-64 age group. Neutralising activity against SFTSV was detected in four samples, resulting in a rate of 0.9%. No cross-neutralising activity against the SFTSV-related Guertu virus and Heartland virus was detected in the anti-SFTSV positive serum samples. The results provide serologic evidence of human exposure to SFTSV in Kenya and extend our understanding of SFTSV prevalence from Asia to Africa. The findings suggest an increasing threat of exposure to emerging TBVs and the need to investigate tick viromes in Kenya.
DOI: 10.15156/bio/sh0896870.10fu
title: SH0896870.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0896871.10fu
title: SH0896871.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0896872.10fu
title: SH0896872.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0896873.10fu
title: SH0896873.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.