Pub Date : 2025-09-11DOI: 10.1016/j.meegid.2025.105822
Fernando Augusto Bertazzo-Silva , Alice Lemos Costa , Jorge Renato Pinheiro Velloso , Flavia Helena Aires Sousa , Carlos Ernesto Gonçalves Reynaud Schaefer , Jair Putzke
We report a rare behavioral observation involving an individual of Chionis alba (snowy sheathbill) attempting to consume a basidiome of the toxic mushroom Galerina marginata on Livingston Island, Antarctica. The bird briefly picked up the basidiome before rejecting it. This event, to our knowledge, represents the first recorded interaction between an Antarctic bird and this deadly fungus, suggesting possible chemical or gustatory deterrence mechanisms. Such interactions, though anecdotal, contribute to the understanding of trophic dynamics and fungal ecology in polar environments.
{"title":"Exploratory interaction of Chionis alba (snowy sheathbill) with the amatoxin-producing mushroom Galerina marginata in Antarctica","authors":"Fernando Augusto Bertazzo-Silva , Alice Lemos Costa , Jorge Renato Pinheiro Velloso , Flavia Helena Aires Sousa , Carlos Ernesto Gonçalves Reynaud Schaefer , Jair Putzke","doi":"10.1016/j.meegid.2025.105822","DOIUrl":"10.1016/j.meegid.2025.105822","url":null,"abstract":"<div><div>We report a rare behavioral observation involving an individual of <em>Chionis alba</em> (snowy sheathbill) attempting to consume a basidiome of the toxic mushroom <em>Galerina marginata</em> on Livingston Island, Antarctica. The bird briefly picked up the basidiome before rejecting it. This event, to our knowledge, represents the first recorded interaction between an Antarctic bird and this deadly fungus, suggesting possible chemical or gustatory deterrence mechanisms. Such interactions, though anecdotal, contribute to the understanding of trophic dynamics and fungal ecology in polar environments.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105822"},"PeriodicalIF":2.6,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-11DOI: 10.1016/j.meegid.2025.105824
Yuanrun Zhu , Zhaodi Liao , Jianan Su , Feng Zhang , Jin Huang , Ping He , Zhifeng Wu , Kangli Xu , Xiaofeng Yang , Chen Jiang , Yadong Wang
Ventilator-associated pneumonia (VAP) is a major infectious complication in the neurologic intensive care unit (NICU). VAP caused by multi-drug resistant (MDR) pathogens is related to poor clinical outcomes. This study investigates the relationship between early plasma cytokine profiles and the development of MDR VAP following neurosurgery. We retrospectively analyzed neurosurgical patients admitted to the NICU who developed VAP between January 2021 and January 2024. A receiver operating characteristic (ROC) curve was used to determine the predictive value of the cytokines. Among 67 VAP patients, MDR VAP cases exhibited lower Glasgow Coma Scale (GCS) scores on admission and a higher incidence of prolonged hospitalization (>5 days) before infection. Significantly elevated levels of IL-2, IL-6, IL-10 and IL-17a were observed in MDR VAP patients, while IL-4, TNFα and IFNγ presented no statistical difference. ROC curves revealed that IL-2 (AUC: 0.722, 95 % CI: 0.599–0.845) and IL-10 (AUC: 0.798, 95 % CI: 0.687–0.909) had the strongest predictive value, with optimal cut-off values of 2.635 pg/mL (IL-2, sensitivity 57.1 %, specificity 84.4 %) and 8.495 pg/mL (IL-10, sensitivity 77.1 %, specificity 84.4 %), respectively. A combined IL-2 + IL-10 model further improved predictive performance (AUC: 0.827, 95 % CI: 0.726–0.927). This was confirmed by a multivariate analysis (OR: 23.1, p = 0.007). In conclusion, early elevations in plasma IL-2, IL-6, IL-10 and IL-17a (at 24 h of admission to the NICU) are associated with MDR VAP in NICU patients. The combined measurement of IL-2 and IL-10 may serve as a useful adjunctive tool for predicting post-neurosurgery MDR VAP risk, aiding in early clinical intervention.
{"title":"Early plasma cytokines associated with multi-drug resistant ventilator-associated pneumonia after neurosurgery: A retrospective cohort study","authors":"Yuanrun Zhu , Zhaodi Liao , Jianan Su , Feng Zhang , Jin Huang , Ping He , Zhifeng Wu , Kangli Xu , Xiaofeng Yang , Chen Jiang , Yadong Wang","doi":"10.1016/j.meegid.2025.105824","DOIUrl":"10.1016/j.meegid.2025.105824","url":null,"abstract":"<div><div>Ventilator-associated pneumonia (VAP) is a major infectious complication in the neurologic intensive care unit (NICU). VAP caused by multi-drug resistant (MDR) pathogens is related to poor clinical outcomes. This study investigates the relationship between early plasma cytokine profiles and the development of MDR VAP following neurosurgery. We retrospectively analyzed neurosurgical patients admitted to the NICU who developed VAP between January 2021 and January 2024. A receiver operating characteristic (ROC) curve was used to determine the predictive value of the cytokines. Among 67 VAP patients, MDR VAP cases exhibited lower Glasgow Coma Scale (GCS) scores on admission and a higher incidence of prolonged hospitalization (>5 days) before infection. Significantly elevated levels of IL-2, IL-6, IL-10 and IL-17a were observed in MDR VAP patients, while IL-4, TNFα and IFNγ presented no statistical difference. ROC curves revealed that IL-2 (AUC: 0.722, 95 % CI: 0.599–0.845) and IL-10 (AUC: 0.798, 95 % CI: 0.687–0.909) had the strongest predictive value, with optimal cut-off values of 2.635 pg/mL (IL-2, sensitivity 57.1 %, specificity 84.4 %) and 8.495 pg/mL (IL-10, sensitivity 77.1 %, specificity 84.4 %), respectively. A combined IL-2 + IL-10 model further improved predictive performance (AUC: 0.827, 95 % CI: 0.726–0.927). This was confirmed by a multivariate analysis (OR: 23.1, <em>p</em> = 0.007). In conclusion, early elevations in plasma IL-2, IL-6, IL-10 and IL-17a (at 24 h of admission to the NICU) are associated with MDR VAP in NICU patients. The combined measurement of IL-2 and IL-10 may serve as a useful adjunctive tool for predicting post-neurosurgery MDR VAP risk, aiding in early clinical intervention.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105824"},"PeriodicalIF":2.6,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-05DOI: 10.1016/j.meegid.2025.105818
Nkosazana D. Shange , Milton T. Mogotsi , Ayodeji E. Ogunbayo , Nicola Page , Hlengiwe Sondlane , Matthew D. Esona , Benjamin Kumwenda , Chimwemwe Mhango , Flywell Kawonga , Ernest Matambo , Samuel N.K. Mingle , Francis E. Dennis , Jere C. Khuzwayo , Nigel A. Makoah , Celeste M. Donato , Martin M. Nyaga
The sub-Saharan African region bears the highest burden of rotavirus-associated morbidity and mortality, with substantial genetic diversity observed in circulating strains despite vaccine introduction. The G8 genotype, originally predominant in bovine strains, has increasingly become prevalent in humans, suggesting a possible interface of animal-to-human transmission and highlighting its role in African strain diversity. In this study, we performed whole genome sequencing and evolutionary analysis of 21 archival G8P[4] strains collected through gastroenteritis surveillance in South Africa between 2009 and 2021 from children under five years of age. All strains exhibited DS-1-like genome constellations and phylogenetically clustered closely with sub-Saharan African G8P[4] strains across all 11 genome segments. A time-resolved phylogeny indicated the co-circulation of multiple G8 sub-lineages, with specific variants persisting for nearly a decade. The mean evolutionary rate for the G8 lineage V sequences was estimated at 1.49 × 10−3 substitutions per site per year, with a time to most common recent ancestor of 1981.8, suggesting long-term endemic divergence. Radical amino acid substitutions were identified in neutralising epitopes of VP4 (11 variations) and VP7 (18 variations) relative to the Rotarix® vaccine strain. These changes may impact antigenicity and immune recognition. These findings within the key antigenic sites of G8P[4] strains may reflect ongoing viral adaptation with potential implications for infectivity and sustained circulation in African regions. Taken together, the findings underscore the significance of continued genomic surveillance to monitor evolution and guide the reassessment, optimisation of current vaccines and the development of future vaccines with broader protective efficacy.
{"title":"Whole genome characterisation of DS-1-like G8P[4] rotavirus A strains circulating in South Africa between 2009 and 2021 reveals endemic sub-lineages and evidence of radical epitope changes","authors":"Nkosazana D. Shange , Milton T. Mogotsi , Ayodeji E. Ogunbayo , Nicola Page , Hlengiwe Sondlane , Matthew D. Esona , Benjamin Kumwenda , Chimwemwe Mhango , Flywell Kawonga , Ernest Matambo , Samuel N.K. Mingle , Francis E. Dennis , Jere C. Khuzwayo , Nigel A. Makoah , Celeste M. Donato , Martin M. Nyaga","doi":"10.1016/j.meegid.2025.105818","DOIUrl":"10.1016/j.meegid.2025.105818","url":null,"abstract":"<div><div>The sub-Saharan African region bears the highest burden of rotavirus-associated morbidity and mortality, with substantial genetic diversity observed in circulating strains despite vaccine introduction. The G8 genotype, originally predominant in bovine strains, has increasingly become prevalent in humans, suggesting a possible interface of animal-to-human transmission and highlighting its role in African strain diversity. In this study, we performed whole genome sequencing and evolutionary analysis of 21 archival G8P[4] strains collected through gastroenteritis surveillance in South Africa between 2009 and 2021 from children under five years of age. All strains exhibited DS-1-like genome constellations and phylogenetically clustered closely with sub-Saharan African G8P[4] strains across all 11 genome segments. A time-resolved phylogeny indicated the co-circulation of multiple G8 sub-lineages, with specific variants persisting for nearly a decade. The mean evolutionary rate for the G8 lineage V sequences was estimated at 1.49 × 10<sup>−3</sup> substitutions per site per year, with a time to most common recent ancestor of 1981.8, suggesting long-term endemic divergence. Radical amino acid substitutions were identified in neutralising epitopes of VP4 (11 variations) and VP7 (18 variations) relative to the Rotarix® vaccine strain. These changes may impact antigenicity and immune recognition. These findings within the key antigenic sites of G8P[4] strains may reflect ongoing viral adaptation with potential implications for infectivity and sustained circulation in African regions. Taken together, the findings underscore the significance of continued genomic surveillance to monitor evolution and guide the reassessment, optimisation of current vaccines and the development of future vaccines with broader protective efficacy.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105818"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145010089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-02DOI: 10.1016/j.meegid.2025.105819
Molly Kroeger , Christopher James Stott , Huigang Shen , Ganwu Li , Rodger Main , Eric Bush , Margaret Parker , Dachrit Nilubo , Jean Paul Cano , Jack Creel , Pablo Piñeyro
Porcine circovirus type 3 (PCV3) was identified in 2016 and has since been associated with reproductive failure, multisystemic inflammation, and subclinical infection in swine. Numerous countries have retrospectively detected the presence of PCV3 before its first clinical description in 2016. The reported detection rate of PCV3 has varied from 6.5 to 84 % in pigs with various coinfections. Today, PCV3/PCV2 coinfection is commonly observed. However, the PCV3 prevalence and coinfection rate with PCV2 in the US swine industry had not been reported before 2016. The present study used serum samples from US grower finisher farms from 2000, 2006, and 2012 to determine the PCV3 and PCV3/PCV2 farm prevalence and geographical distribution, to evaluate the PCV3 evolutionary rate and selection pressure forces, and to identify structural and morphological changes in the Cap protein. Our findings revealed that PCV3 was endemic in the US swine industry before its first description in 2016. The PCV3 farm prevalence decreased from 47 % in 2000 to 22 % in 2012. The PCV3/PCV2 coinfection rate at the farm level was 47 % in 2000 and 39 % in 2006. After the introduction of PCV2 vaccines in 2006, the PCV3/PCV2 coinfection rate drastically declined to 3 % and 59 % of farms were negative for both PCV3 and PCV2 in 2012. From 13 PCV3 whole genome sequences, 12 sequences were clustered with PCV3a reference strain and one with the PCV3c subtype. From 28 PCV3 ORF2 sequences, PCV3a1 (1/28), PCV3a2 (4/28), PCV3a3 (19/28), PCV3b (2/28), and PCV3c (2/28) subtypes were obtained. ORF2 nucleotide identity ranged from 97.8 to 100 %. Diversifying selection occurred at amino acids 24 and 150 in 2006 and at amino acids 24 and 27 in 2012. Mutations A24V and R27K were common among all PCV3 subtypes in sequences identified in the present study and in reference sequences. Both the S77T and I150L mutation was common among sequences within the PCV3a2 subtype. The F104Y mutation lies within a predicted T-cell epitope and was present in sequences of the PCV3c, PCV3b, and PCV3a3 subtypes. Cap molecular modeling revealed that the structural folding of amino acids 24 and 27 changed from alpha helix to coiled in 2012 sequences. Thus, this study broadens current knowledge of PCV3's prevalence and molecular evolution in the US swine herd from 2000 to 2012.
{"title":"Epidemiological and molecular retrospective analysis of porcine circovirus 3 in the US grower-finisher herd","authors":"Molly Kroeger , Christopher James Stott , Huigang Shen , Ganwu Li , Rodger Main , Eric Bush , Margaret Parker , Dachrit Nilubo , Jean Paul Cano , Jack Creel , Pablo Piñeyro","doi":"10.1016/j.meegid.2025.105819","DOIUrl":"10.1016/j.meegid.2025.105819","url":null,"abstract":"<div><div>Porcine circovirus type 3 (PCV3) was identified in 2016 and has since been associated with reproductive failure, multisystemic inflammation, and subclinical infection in swine. Numerous countries have retrospectively detected the presence of PCV3 before its first clinical description in 2016. The reported detection rate of PCV3 has varied from 6.5 to 84 % in pigs with various coinfections. Today, PCV3/PCV2 coinfection is commonly observed. However, the PCV3 prevalence and coinfection rate with PCV2 in the US swine industry had not been reported before 2016. The present study used serum samples from US grower finisher farms from 2000, 2006, and 2012 to determine the PCV3 and PCV3/PCV2 farm prevalence and geographical distribution, to evaluate the PCV3 evolutionary rate and selection pressure forces, and to identify structural and morphological changes in the Cap protein. Our findings revealed that PCV3 was endemic in the US swine industry before its first description in 2016. The PCV3 farm prevalence decreased from 47 % in 2000 to 22 % in 2012. The PCV3/PCV2 coinfection rate at the farm level was 47 % in 2000 and 39 % in 2006. After the introduction of PCV2 vaccines in 2006, the PCV3/PCV2 coinfection rate drastically declined to 3 % and 59 % of farms were negative for both PCV3 and PCV2 in 2012. From 13 PCV3 whole genome sequences, 12 sequences were clustered with PCV3a reference strain and one with the PCV3c subtype. From 28 PCV3 ORF2 sequences, PCV3a1 (1/28), PCV3a2 (4/28), PCV3a3 (19/28), PCV3b (2/28), and PCV3c (2/28) subtypes were obtained. ORF2 nucleotide identity ranged from 97.8 to 100 %. Diversifying selection occurred at amino acids 24 and 150 in 2006 and at amino acids 24 and 27 in 2012. Mutations A24V and R27K were common among all PCV3 subtypes in sequences identified in the present study and in reference sequences. Both the S77T and I150L mutation was common among sequences within the PCV3a2 subtype. The F104Y mutation lies within a predicted T-cell epitope and was present in sequences of the PCV3c, PCV3b, and PCV3a3 subtypes. Cap molecular modeling revealed that the structural folding of amino acids 24 and 27 changed from alpha helix to coiled in 2012 sequences. Thus, this study broadens current knowledge of PCV3's prevalence and molecular evolution in the US swine herd from 2000 to 2012.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105819"},"PeriodicalIF":2.6,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144996763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gastrointestinal strongyle nematodes pose significant health risks to captive megaherbivores, including Asian elephants (Elephas maximus) and white rhinoceroses (Ceratotherium simum). Traditional diagnostic methods often fail to accurately identify species due to morphological similarities, limiting understanding of parasite diversity and host-specificity. This study is among the first in Southeast Asia to apply high-throughput internal transcribed spacer-2 (ITS-2) rDNA metabarcoding to characterize strongyle nematode communities in these endangered hosts. Fecal samples from six rhinoceroses and four elephants housed in a private zoo in Thailand were processed using flotation, larval culture, and DNA extraction protocols. Amplicon sequencing was conducted on the Illumina MiSeq platform, and taxonomic assignments were performed using the DADA2 pipeline and NCBI/GenBank databases. Our results revealed the presence of strongyle infections. Murshidia spp. were detected in both host species, while Kiluluma ceratotherii was found exclusively in rhinoceroses. Phylogenetic analysis based on ITS-2 rDNA sequences demonstrated clear host-associated clades and suggested potential cryptic species within Kiluluma and Murshidia lineages. These findings provide new genetic evidence of host specificity and evolutionary divergence among strongylid nematodes in captive wildlife. The study underscores the utility of DNA metabarcoding for non-invasive parasite surveillance and highlights the urgent need to expand molecular databases for better taxonomic resolution in wildlife parasitology.
{"title":"Metabarcoding characterization of gastrointestinal strongyle nematodes in captive Asian elephants (Elephas maximus) and white rhinoceroses (Ceratotherium simum) in a private zoo, Thailand","authors":"Mohamed H. Hamad , Witchuta Junsiri , Tanagrit Sumpanpae , Duriyang Narapakdeesakul , Piyanan Taweethavonsawat","doi":"10.1016/j.meegid.2025.105817","DOIUrl":"10.1016/j.meegid.2025.105817","url":null,"abstract":"<div><div>Gastrointestinal strongyle nematodes pose significant health risks to captive megaherbivores, including Asian elephants (<em>Elephas maximus</em>) and white rhinoceroses (<em>Ceratotherium simum</em>). Traditional diagnostic methods often fail to accurately identify species due to morphological similarities, limiting understanding of parasite diversity and host-specificity. This study is among the first in Southeast Asia to apply high-throughput internal transcribed spacer-2 (ITS-2) rDNA metabarcoding to characterize strongyle nematode communities in these endangered hosts. Fecal samples from six rhinoceroses and four elephants housed in a private zoo in Thailand were processed using flotation, larval culture, and DNA extraction protocols. Amplicon sequencing was conducted on the Illumina MiSeq platform, and taxonomic assignments were performed using the DADA2 pipeline and NCBI/GenBank databases. Our results revealed the presence of strongyle infections. <em>Murshidia</em> spp. were detected in both host species, while <em>Kiluluma ceratotherii</em> was found exclusively in rhinoceroses. Phylogenetic analysis based on ITS-2 rDNA sequences demonstrated clear host-associated clades and suggested potential cryptic species within <em>Kiluluma</em> and <em>Murshidia</em> lineages. These findings provide new genetic evidence of host specificity and evolutionary divergence among strongylid nematodes in captive wildlife. The study underscores the utility of DNA metabarcoding for non-invasive parasite surveillance and highlights the urgent need to expand molecular databases for better taxonomic resolution in wildlife parasitology.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105817"},"PeriodicalIF":2.6,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144921659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Porcine astrovirus (PAstV) is an enteropathogen that belongs to the family Astroviridae and the genus Mamastrovirus, and is divided into five distinct genotypes (PAstV1-PAstV5). PAstV has been reported in pigs from several countries worldwide. In India, there are limited reports of genetic characterization of PAstV. The present study aimed to characterize the whole genome of PAstV from Haryana, a state in Northern India. Initially, 70 porcine fecal samples were screened for the presence of PAstV using RT-PCR that targeted the partial RdRp region. Three PAstV-positive samples were selected and their complete genomes successfully amplified by RT-PCR in two overlapping segments: segment A (∼3.6 kb) and segment B (∼3.1 kb). The phylogenetic analysis of PAstV, based on complete nucleotide sequences, revealed that PV247173 and PV247174 clustered within the PAstV1 group, whereas PV455027 clustered within the PAstV4 group. In contrast, analysis of the ORF2 amino acid sequence revealed that only PV247173 was classified in PAstV1, while PV455027 and PV247174 were classified in PAstV4. This study reports the first whole-genome molecular characterization of PAstV from Northern India.
{"title":"Whole genome sequencing and molecular characterization of porcine astrovirus from Haryana, India","authors":"Ritu Panghal , Parveen Kumar , Sanjeevna K. Minhas , Raman Mehtani , Sweety Kalonia , Deepika Sheoran , Pawan Kumar , Akhil K. Gupta , Rajesh Chhabra , Naresh Jindal","doi":"10.1016/j.meegid.2025.105816","DOIUrl":"10.1016/j.meegid.2025.105816","url":null,"abstract":"<div><div>Porcine astrovirus (PAstV) is an enteropathogen that belongs to the family <em>Astroviridae</em> and the genus <em>Mamastrovirus,</em> and is divided into five distinct genotypes (PAstV1-PAstV5). PAstV has been reported in pigs from several countries worldwide. In India, there are limited reports of genetic characterization of PAstV. The present study aimed to characterize the whole genome of PAstV from Haryana, a state in Northern India. Initially, 70 porcine fecal samples were screened for the presence of PAstV using RT-PCR that targeted the partial RdRp region. Three PAstV-positive samples were selected and their complete genomes successfully amplified by RT-PCR in two overlapping segments: segment A (∼3.6 kb) and segment B (∼3.1 kb). The phylogenetic analysis of PAstV, based on complete nucleotide sequences, revealed that PV247173 and PV247174 clustered within the PAstV1 group, whereas PV455027 clustered within the PAstV4 group. In contrast, analysis of the ORF2 amino acid sequence revealed that only PV247173 was classified in PAstV1, while PV455027 and PV247174 were classified in PAstV4. This study reports the first whole-genome molecular characterization of PAstV from Northern India.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105816"},"PeriodicalIF":2.6,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144913554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-26DOI: 10.1016/j.meegid.2025.105815
Zunera Jamal , Fahad Humayun , Syed Adnan Haider , Rabia Hakim , Verity Hill , Syed Yawar Saeed , Guy Baele , Muhammad Ishaq , Mansur Ayub , Amjad Ullah , Nasir Hussain , Muhammad Salman , Massab Umair
Dengue virus (DENV) remains a significant public health concern in Pakistan, with recurrent outbreaks necessitating continuous genomic surveillance. The 2024 dengue outbreak prompted an investigation into circulating serotypes and genomic diversity. The National Institute of Health (NIH), Pakistan, received 524 NS-1 confirmed dengue samples across multiple districts in 2024. Serotyping via real-time PCR confirmed DENV-2 in 93 % (n = 361) and DENV-1 in 7 % (n = 27) of 388 positive samples, with no co-infections detected. Males accounted for 65 % of cases, with a mean age of 30.78 ± 15.03 years. Metagenomic sequencing using Illumina MiSeq yielded 33 successful DENV genomes (DENV-2: 23; DENV-1: 10), including the first reports from Chilas and Kech. Phylogenetic analysis showed 2024 DENV-1 (genotype III) and DENV-2 (Cosmopolitan genotype, clade IV-A/2II_F.1.1) closely resembling 2022–2023 Pakistani strains (∼99 % homology). Time-scaled analysis estimated 22 of 23 DENV-2 sequences shared a most recent common ancestor (MRCA) in 2018, while a divergent strain (NIHPAK-246) traced back to 2005. DENV-2 strains from Kech exhibited >99.8 % similarity with Rawalpindi strains, suggesting transmission links. DENV-1 sequences shared an MRCA in 2016, indicating sustained circulation. Mutation analysis identified NS4B: G240S in DENV-1 from Chilas, suggesting localized adaptation. These findings highlight the need for sustained genomic surveillance, monitoring transmission dynamics, and targeted public health interventions in Pakistan.
{"title":"Genomic characterization and serotype distribution of dengue virus circulating in Pakistan during 2024","authors":"Zunera Jamal , Fahad Humayun , Syed Adnan Haider , Rabia Hakim , Verity Hill , Syed Yawar Saeed , Guy Baele , Muhammad Ishaq , Mansur Ayub , Amjad Ullah , Nasir Hussain , Muhammad Salman , Massab Umair","doi":"10.1016/j.meegid.2025.105815","DOIUrl":"10.1016/j.meegid.2025.105815","url":null,"abstract":"<div><div>Dengue virus (DENV) remains a significant public health concern in Pakistan, with recurrent outbreaks necessitating continuous genomic surveillance. The 2024 dengue outbreak prompted an investigation into circulating serotypes and genomic diversity. The National Institute of Health (NIH), Pakistan, received 524 NS-1 confirmed dengue samples across multiple districts in 2024. Serotyping via real-time PCR confirmed DENV-2 in 93 % (<em>n</em> = 361) and DENV-1 in 7 % (<em>n</em> = 27) of 388 positive samples, with no co-infections detected. Males accounted for 65 % of cases, with a mean age of 30.78 ± 15.03 years. Metagenomic sequencing using Illumina MiSeq yielded 33 successful DENV genomes (DENV-2: 23; DENV-1: 10), including the first reports from Chilas and Kech. Phylogenetic analysis showed 2024 DENV-1 (genotype III) and DENV-2 (Cosmopolitan genotype, clade IV-A/2II_F.1.1) closely resembling 2022–2023 Pakistani strains (∼99 % homology). Time-scaled analysis estimated 22 of 23 DENV-2 sequences shared a most recent common ancestor (MRCA) in 2018, while a divergent strain (NIHPAK-246) traced back to 2005. DENV-2 strains from Kech exhibited >99.8 % similarity with Rawalpindi strains, suggesting transmission links. DENV-1 sequences shared an MRCA in 2016, indicating sustained circulation. Mutation analysis identified NS4B: G240S in DENV-1 from Chilas, suggesting localized adaptation. These findings highlight the need for sustained genomic surveillance, monitoring transmission dynamics, and targeted public health interventions in Pakistan.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105815"},"PeriodicalIF":2.6,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144916286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-22DOI: 10.1016/j.meegid.2025.105814
Hamadou Oumarou Hama , Mahmoud Boualam , Jean Armengaud , Michel Drancourt , Gérard Aboudharam , Adrian Bălășescu , Valentin Radu
Six camels exhumed from a 17th-century Silk Route site in Romania, along with negative controls, were blindly investigated via dental pulp paleometagenomics and paleoproteomics for traces of Yersinia pseudotuberculosis complex including the plague agent Yersinia pestis. Specific reads were detected in sample R04 (one read) and R05 (two reads) which also yielded a 16S rRNA guanine transferase specific for Y. pestis and one other Y. pseudotuberculosis complex peptide. Taken together, these validated data diagnosed plague in these ancient camels which likely participated in plague dissemination along ancient Silk Routes during the large Medieval and Modern Times pandemic in Europe.
{"title":"Diagnosing plague in 17th century camelids from Romania along historical Silk Routes","authors":"Hamadou Oumarou Hama , Mahmoud Boualam , Jean Armengaud , Michel Drancourt , Gérard Aboudharam , Adrian Bălășescu , Valentin Radu","doi":"10.1016/j.meegid.2025.105814","DOIUrl":"10.1016/j.meegid.2025.105814","url":null,"abstract":"<div><div>Six camels exhumed from a 17th-century Silk Route site in Romania, along with negative controls, were blindly investigated via dental pulp paleometagenomics and paleoproteomics for traces of <em>Yersinia pseudotuberculosis</em> complex including the plague agent <em>Yersinia pestis</em>. Specific reads were detected in sample R04 (one read) and R05 (two reads) which also yielded a 16S rRNA guanine transferase specific for <em>Y. pestis</em> and one other <em>Y. pseudotuberculosis</em> complex peptide. Taken together, these validated data diagnosed plague in these ancient camels which likely participated in plague dissemination along ancient Silk Routes during the large Medieval and Modern Times pandemic in Europe.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105814"},"PeriodicalIF":2.6,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144916287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-21DOI: 10.1016/j.meegid.2025.105813
Susanthika Jayachandiran, Roja Suresh, Ramasamy Dhamodharan
Chlamydia pneumoniae is an obligatory intracellular pathogen found in humans and animals. Understanding the genomic diversity is crucial for unravelling its pathogenic mechanisms and transmission dynamics. In this study, 14 complete genomes of C. pneumoniae strains were compared for functional diversity analysis. The koala isolate LPCoLN appears as a phylogenetically distinct, showing the fewest accessory genes and the highest incorporation of unique or absent genes among the strains analyzed. Functional annotation indicates that certain metabolic pathways between the LPCoLN and the human respiratory strain AR39 were the same, which is most likely due to phage-associated elements present in AR39. The presence of the GT5 CAZyme family is significantly associated with strains of respiratory origin, suggesting a potential role in respiratory adaptation and pathogenic strategies, including tissue colonization, immune evasion, and niche-specific persistence. The strong association between GT5 CAZymes and respiratory-origin strains highlights their potential as diagnostic markers and therapeutic targets.
{"title":"Comparative and phylogenomic analysis of Chlamydia pneumoniae reveals unique carbohydrate active enzyme family (GT5) among respiratory isolates","authors":"Susanthika Jayachandiran, Roja Suresh, Ramasamy Dhamodharan","doi":"10.1016/j.meegid.2025.105813","DOIUrl":"10.1016/j.meegid.2025.105813","url":null,"abstract":"<div><div><em>Chlamydia pneumoniae</em> is an obligatory intracellular pathogen found in humans and animals. Understanding the genomic diversity is crucial for unravelling its pathogenic mechanisms and transmission dynamics. In this study, 14 complete genomes of <em>C. pneumoniae</em> strains were compared for functional diversity analysis. The koala isolate LPCoLN appears as a phylogenetically distinct, showing the fewest accessory genes and the highest incorporation of unique or absent genes among the strains analyzed. Functional annotation indicates that certain metabolic pathways between the LPCoLN and the human respiratory strain AR39 were the same, which is most likely due to phage-associated elements present in AR39. The presence of the GT5 CAZyme family is significantly associated with strains of respiratory origin, suggesting a potential role in respiratory adaptation and pathogenic strategies, including tissue colonization, immune evasion, and niche-specific persistence. The strong association between GT5 CAZymes and respiratory-origin strains highlights their potential as diagnostic markers and therapeutic targets.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105813"},"PeriodicalIF":2.6,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144890077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-18DOI: 10.1016/j.meegid.2025.105808
Catherine Dauga , Valentine Gilbart , Azimdine Habib , Laura Tondeur , Rindra Randremanana , Boris Hedible , Alexandre Manirazika , Muriel Vray , Ronan Jambou , the Malinea Clinical Trial Group
In children, the gut microbiota is a dynamic ecosystem derived from breastfeeding, oral microbiota and diet. Diversity can vary from one country to another, and the aim of this study was to compare microbiota of well-nourished children between three African countries using fully standardized protocols from sampling to data analysis.
Well-nourished (WHZ weight for height z-score ≥ −1.5) children aged 18–24 months were enrolled. Libraries were constructed using Illumina 16S protocol. Sequences were aligned to the Silva.nr and clustered into OTUs (organism taxonomic unit) using greedy clustering (dgc). Consensus determination was done using classify.otu and the OTU table, taxonomy and metadata were assembled using Phyloseq. Alpha diversity was assessed using Chao1, Shannon and Simpson's index using Mothur.
106 well-nourished children were selected (31 in Madagascar, 40 in Senegal and 35 in Centrafrican Republic CAR). Richness was higher in Senegal than in CAR or Madagascar, but diversity was lowest in Senegal and highest in CAR. As the quality of drinking water increased, richness increased and diversity decreased. Microbiota shared five dominant phyla in different proportions: Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Verrucomicrobia. The composition of the microbiota in Madagascar and Centrafrica republic (CAR) was more similar, with more Prevotella 9 in Madagascar and more Bifidobacterium in CAR. Only two taxa were markers from CAR (Prevotella 9 and Ruminococcus 2).
Apart from a pool of common species, a large proportion of rare species may characterize each geographical context. Therefore, the microbiota of children in Africa cannot be considered comparable between countries. Each biotope harbors specific species on a common background.
{"title":"Intestinal microbiota diversity in children from three African countries","authors":"Catherine Dauga , Valentine Gilbart , Azimdine Habib , Laura Tondeur , Rindra Randremanana , Boris Hedible , Alexandre Manirazika , Muriel Vray , Ronan Jambou , the Malinea Clinical Trial Group","doi":"10.1016/j.meegid.2025.105808","DOIUrl":"10.1016/j.meegid.2025.105808","url":null,"abstract":"<div><div>In children, the gut microbiota is a dynamic ecosystem derived from breastfeeding, oral microbiota and diet. Diversity can vary from one country to another, and the aim of this study was to compare microbiota of well-nourished children between three African countries using fully standardized protocols from sampling to data analysis.</div><div>Well-nourished (WHZ weight for height z-score ≥ −1.5) children aged 18–24 months were enrolled. Libraries were constructed using Illumina 16S protocol. Sequences were aligned to the Silva.nr and clustered into OTUs (organism taxonomic unit) using greedy clustering (dgc). Consensus determination was done using classify.otu and the OTU table, taxonomy and metadata were assembled using Phyloseq. Alpha diversity was assessed using Chao1, Shannon and Simpson's index using Mothur.</div><div>106 well-nourished children were selected (31 in Madagascar, 40 in Senegal and 35 in Centrafrican Republic CAR). Richness was higher in Senegal than in CAR or Madagascar, but diversity was lowest in Senegal and highest in CAR. As the quality of drinking water increased, richness increased and diversity decreased. Microbiota shared five dominant phyla in different proportions: <em>Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Verrucomicrobia</em>. The composition of the microbiota in Madagascar and Centrafrica republic (CAR) was more similar, with more <em>Prevotella 9</em> in Madagascar and more <em>Bifidobacterium</em> in CAR. Only two taxa were markers from CAR (<em>Prevotella 9</em> and <em>Ruminococcus 2</em>).</div><div>Apart from a pool of common species, a large proportion of rare species may characterize each geographical context. Therefore, the microbiota of children in Africa cannot be considered comparable between countries. Each biotope harbors specific species on a common background.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105808"},"PeriodicalIF":2.6,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144913422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号