Infection Genetics and Evolution最新文献

{"title":"Genomic surveillance of dengue virus in Benin","authors":"Anges Yadouleton ,&nbsp;Odilon Nouatin ,&nbsp;Islamiath Kissira ,&nbsp;Parfait Houngbegnon ,&nbsp;Gilles Cottrell ,&nbsp;Nadine Fievet ,&nbsp;Stephane Sohou ,&nbsp;Christelle Butel ,&nbsp;Laetitia Serrano ,&nbsp;Emilande Guichet ,&nbsp;Nicole Vidal ,&nbsp;Eric Delaporte ,&nbsp;Ahidjo Ayouba ,&nbsp;Martine Peeters ,&nbsp;Achille Massougbodji","doi":"10.1016/j.meegid.2024.105674","DOIUrl":"10.1016/j.meegid.2024.105674","url":null,"abstract":"<div><h3>Objective</h3><div>Dengue is a widespread viral infection transmitted from mosquitoes to humans, mainly in tropical and subtropical climates. In Benin, only dengue virus (DENV) serotype 2 infection has been previously described in humans. This study aimed to investigate DENV infection and serotypes in suspected patients.</div></div><div><h3>Methods</h3><div>Plasma samples from 464 patients attending health centers in February 2023 with clinical symptoms and suspected for dengue infection were included, and analyzed for DENV by real time quantitative Polymerase Chain Reaction (Dengue Altona 3.0 kit). PCR positives samples were further characterized by whole genome sequencing and phylogenetic analysis to identify the circulating DENV serotype.</div></div><div><h3>Results</h3><div>The RT-qPCR results showed that four patients (D6, D23, D28, D44) were positive with the cycle threshold values less than 40 (31.3, 34.7, 14.7 and 14.3) respectively. Full-length DENV sequences were obtained for D6, D28 and D44. One patient (D6) was infected with DENV-1 serotype, and the two others (D28 and D44) were positive for DENV-3. Phylogenetic analysis shows that the new DENV-1 sequence is close to those obtained in Burkina Faso in 2022 and Nigeria in 2023, and the two DENV-3 sequences form a separate cluster with sequences obtained in Burkina Faso in 2022.</div></div><div><h3>Conclusion</h3><div>We showed for the first time, the presence of dengue serotype 1 and serotype 3 infection in Benin. These results send a strong signal to health authorities and show that arbovirus surveillance efforts must be integrated into pathogen monitoring programs.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105674"},"PeriodicalIF":2.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Feline bocaviruses found in Thailand have undergone genetic recombination for their evolutions","authors":"Pattiya Lohavicharn ,&nbsp;Tanit Kasantikul ,&nbsp;Chutchai Piewbang ,&nbsp;Somporn Techangamsuwan","doi":"10.1016/j.meegid.2024.105675","DOIUrl":"10.1016/j.meegid.2024.105675","url":null,"abstract":"<div><div>Feline bocaviruses (FBoVs) have been discovered for a decade and are often detected in feces, possibly associated with diarrhea in cats. Studies on FBoV evolution remain limited and have mainly focused on prevalence and genetic characterization. Although genetic recombination serves as a potential mechanism in bocavirus evolution, research on this process for FBoVs has been scarce. In this study, we characterized 19 complete coding sequences of FBoVs obtained from Thai cats, revealing that FBoV-1, -2, and -3 were endemic in Thailand. Genetic characterizations showed that most Thai FBoVs were closely related to previously detected strains in Thailand and China. Recombination analyses indicated intragenic, intraspecies recombination in all FBoV species, with recombination breakpoints commonly found in the NP1 and VP1/2 genes, highlighting these genes may be hotspots for FBoV recombination. However, no interspecies recombination was detected. Selective pressure analysis of various FBoV genes revealed that these viruses underwent purifying selection. Although the VP1/2 gene of all FBoV species was under the strongest negative selection pressure, positive selection sites were only found in FBoV-1 and FBoV-3. This study is the first to identify natural recombination in FBoV-2 and FBoV-3 and provides evidence that genetic recombination is a potential driver of FBoV evolutions. Additionally, this study offers up-to-date information on the genetic characteristics, evolutionary dynamics, and selective pressure status of FBoVs, which should be continuously monitored.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105675"},"PeriodicalIF":2.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variation and population structure of Taenia multiceps (Coenurus cerebralis) based on mitochondrial cox1 gene: A comprehensive global analysis","authors":"Shahbaz Ul Haq ,&nbsp;Muhammad Abdullah Malik ,&nbsp;Ayed Alshammari ,&nbsp;Abu Bakar Yameen ,&nbsp;Majed H. Wakid ,&nbsp;Mughees Aizaz Alvi ,&nbsp;Abdulbaset Mohammad Kabli ,&nbsp;Muhammad Saqib ,&nbsp;Warda Qamar ,&nbsp;Muhammad Sohail Sajid ,&nbsp;Fenfei Gao ,&nbsp;Li Li ,&nbsp;Bao-Quan Fu ,&nbsp;Hong-Bin Yan ,&nbsp;Wan-Zhong Jia","doi":"10.1016/j.meegid.2024.105676","DOIUrl":"10.1016/j.meegid.2024.105676","url":null,"abstract":"<div><div><em>Taenia multiceps</em> is a neglected parasite having veterinary and public health importance. The predilection sites of the parasite larva (<em>Coenurus cerebralis</em>) are brain (cerebral coenurosis) and subcutaneous (non-cerebral coenurosis). There is a dearth of data regarding molecular characterization of <em>T</em>. <em>multiceps</em> and even fewer population structure-based studies on <em>T</em>. <em>multiceps</em>. The current study was conducted to provide epidemiological information regarding the global population structure of the parasite. The NCBI GenBank database was accessed to download the sequences of <em>cox</em>1 gene, which were further subjected to PopArt software to construct median-joining networks. The DnaSp software was used to compute neutrality and diversity indices. Host and region-wise indices of neutrality and diversity were also computed. There were 166 gene sequences found in the NCBI database. Followed by removal of short gene sequences, 143 were considered to perform bioinformatic analyses. A total of 30 haplotypes with 46 mutations and 23 parsimony informative sites were found. High diversity (Hd = 0.889, π = 0.01186) and negative but statistically insignificant neutrality indices (Tajima's D = −1.57659, Fu's Fs = −10.552) were found. Region-wise results revealed highest haplotype diversities in isolates from KSA (Hd = 1.00) followed by Greece and Italy (Hd = 0.962), and China (Hd = 0.931). Host-wise data analysis showed an overall negative Tajima's D value and there exists highest haplotype diversity in cattle (Hd = 1.00) followed by dogs (Hd = 0.833), sheep (Hd = 0.795) and goats (Hd = 0.788). The findings of the study indicate that the population diversity of <em>T</em>. <em>multiceps</em> will increase worldwide as shown by high diversity and negative neutrality indices. The findings of the study significantly add-in to the existing bank of knowledge about population structure of <em>T</em>. <em>multiceps</em>. We recommend conducting more studies employing different genetic markers to better comprehend the epidemiology of the parasite.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105676"},"PeriodicalIF":2.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondrial genome analysis across different populations reveals the intraspecific variation and phylogeography of the Caucasian soft tick relapsing fever vector, Ornithodoros (Pavlovskyella) verrucosus (Ixodida: Argasidae)","authors":"Serhii Filatov ,&nbsp;Alexander R. Kneubehl ,&nbsp;Aparna Krishnavajhala ,&nbsp;Giorgi Melashvili ,&nbsp;Ana Tsitsishvili ,&nbsp;Küşver Mamedova ,&nbsp;Perot Saelao ,&nbsp;Adalberto Á. Pérez de León ,&nbsp;Job E. Lopez","doi":"10.1016/j.meegid.2024.105673","DOIUrl":"10.1016/j.meegid.2024.105673","url":null,"abstract":"<div><div>Territories in southern parts of Eastern Europe and in the Caucasus are endemic for tick-borne relapsing fever (TBRF), caused by <em>Borrelia caucasica</em>. This spirochete is transmitted exclusively by the bites of <em>Ornithodoros verrucosus</em>; however, the distribution and genetic diversity of the tick vector have not been explored. To address this, we performed a phylogeographic study of <em>O. verrucosus</em> specimens collected across a large geographic distribution. We sequenced and analyzed complete mitochondrial genomes of 54 individual <em>O. verrucosus</em> ticks representing 23 geographically diverse populations from Ukraine, Georgia, and Azerbaijan. We detected 47 unique haplotypes, with every collection site exhibiting distinct polymorphisms. This, along with other population genetic indices, suggests little evidence of gene flow between populations. The Bayesian coalescent analysis revealed the presence of four lineages that diverged in the Middle Pleistocene (770–126 kya). Two lineages were widespread and present in all study regions, while the other two were restricted to the southern foothills of the Lesser Caucasus mountain range. The sympatry of these ancient lineages suggests that isolation by environment, in addition to geographic distance, may play a role in the intraspecific divergence of tick populations. Using a phylogeographic approach, we provide a snapshot of genetic diversity in <em>O. verrucosus</em> and discuss the evolutionary history of the tick vector.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105673"},"PeriodicalIF":2.6,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pneumococcal transposon profiling associated with macrolide, tetracycline, and chloramphenicol resistance from carriage isolates of serotype 19F in Indonesia","authors":"Yustinus Maladan ,&nbsp;Endah Retnaningrum ,&nbsp;Budi Setiadi Daryono ,&nbsp;Korrie Salsabila ,&nbsp;Rosantia Sarassari ,&nbsp;Miftahuddin Majid Khoeri ,&nbsp;Ratna Fathma Sari ,&nbsp;Sarah Azhari Balqis ,&nbsp;Ghina Athyah Wahid ,&nbsp;Dodi Safari","doi":"10.1016/j.meegid.2024.105672","DOIUrl":"10.1016/j.meegid.2024.105672","url":null,"abstract":"<div><div>Genetic evolution of resistance due to mutations and transposon insertions is the primary cause of antimicrobial resistance in <em>Streptococcus pneumoniae</em>. Resistance to macrolide, tetracycline, and chloramphenicol is caused by the insertion of specific genes that carried by transposon (Tn). This study aims to analyze transposon profiling associated with macrolide, tetracycline, and chloramphenicol resistance from carriage isolates of <em>S. pneumoniae</em> serotype 19F in Indonesia. <em>S. pneumoniae</em> serotype 19F isolates were collected from nasopharyngeal swab specimens from different regions in Indonesia. Genomic DNA was extracted from sixteen isolates and whole genome sequencing was performed on Illumina platform. Raw sequence data were analyzed using de novo assembly by ASA³P and Microscope server. The presence of transposons was identified with detection of <em>int</em> and <em>xis</em> genes and visualized by pyGenomeViz. The genome size of <em>S. pneumoniae</em> ranges from 2,040,117 bp to 2,437,939 bp, with a GC content of around 39 %. ST1464 (4/16) and ST271 (3/16) were found as the predominant sequence type among isolates. Tn2010 was the most common transposon among <em>S. pneumoniae</em> serotype 19F isolates (7/16) followed by Tn2009 (4/16), and Tn5253 (3/16). We identified two deletion sites within the <em>tetM</em> gene (2 bp and 58 bp) that confer tetracycline susceptibility from one isolate. This study suggests that genomic analysis can be employed for the detection and surveillance of antimicrobial resistance genes among <em>S. pneumoniae</em> strains isolated from various regions in Indonesia.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105672"},"PeriodicalIF":2.6,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001230/pdfft?md5=4a0e1d5404153d8316fb369293de5676&pid=1-s2.0-S1567134824001230-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial resistance profiling of bacteria isolated from wastewater and samples of pharmaceutical industries in South India","authors":"Sravani Kamatham ,&nbsp;Manoharan Seeralan ,&nbsp;Uma Sekar ,&nbsp;Sujatha Kuppusamy","doi":"10.1016/j.meegid.2024.105670","DOIUrl":"10.1016/j.meegid.2024.105670","url":null,"abstract":"<div><div>The study was aimed to determine the phenotypic and genotypic antimicrobial resistance in the isolated bacteria from the influent (25), effluent (15), surface and ground water samples (15) surrounding the pharmaceutical industries located in south India. From 55 samples, 48 isolates of 10 different bacteria were obtained. The identified bacterial isolates were viz. <em>Klebsiella pneumoniae</em>, <em>Pseudomonas aeruginosa</em>, <em>Enterobacter aerogenes</em>, <em>Corynebacterium</em> sp., <em>Acinetobacter</em> sp., <em>Aeromonas punctata</em>, <em>Ralstonia picketti</em>, <em>Staphylococcus aureus, Stenotrophomonas maltophillia</em>, <em>and Citrobacter freundii.</em> The phenotypic profile of resistance through antibiotic susceptibility test was carried out against sixteen different antibiotics. Standard PCR technique was used for the detection of 12 resistance genes encoding carbapenems, quinoline, aminoglycoside, β-lactam belonging <em>blaOXA-58</em>_<em>,</em> <em>blaOXA-22</em>_<em>,</em> <em>qnrA, qnrB, aac(6)-Ib-cr, aac (3)-XI, mec A, qepA,</em> aadB, <em>blaVIM</em>, <em>blaOXA-48</em> and <em>blaNDM</em>. <em>Pseudomonas aeruginosa</em> (1: TN/I/2020) showed presence of 3 resistance genes. <em>qnrB</em> (489 bp) gene was present in maximum of 7 isolates while <em>blaVIM</em> (196 bp) gene was present in 6 isolates. The resistance genes <em>blaNDM</em> (621 bp) was present in three different isolates; <em>aac (X):6)-lb-cr</em> (482 bp), <em>qepA</em> (495 bp), <em>aadB</em> (500 bp), <em>blaOXA-58</em> (843 bp) resistant genes were present in two different isolates each among the bacterial isolates obtained in this study. In phenotypic resistance profiling by AST method, out of 16 antibiotics tested, 14 showed resistance. Similarly, in genotypic resistance profiling, among 12 resistance genes tested, a maximum of three resistance genes were noticed in <em>Pseudomonas aeruginosa.</em> There were positive and negative correlations observed between phenotypic and genotypic resistance among different antibiotics and their resistance genes indicating the variations in the resistance gene expression.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105670"},"PeriodicalIF":2.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The presence of genes encoding carbapenem-hydrolyzing oxacillinase and lack of carbapenem resistance in non-baumannii Acinetobacter misidentified as Acinetobacter baumannii causing bloodstream infections in a tertiary hospital over a 3-year period","authors":"Jie Zheng ,&nbsp;Jingru Ji ,&nbsp;Wei Chen ,&nbsp;Danwei Wang ,&nbsp;Chang Liu ,&nbsp;Yan Zhang ,&nbsp;Han Shen ,&nbsp;Xiaoli Cao ,&nbsp;Chao Wu","doi":"10.1016/j.meegid.2024.105669","DOIUrl":"10.1016/j.meegid.2024.105669","url":null,"abstract":"<div><h3>Objective</h3><div>This study aims to analyze the genomic and clinical characteristics of Non-baumannii <em>Acinetobacter</em> strains misidentified as <em>A. baumannii</em>, causing bloodstream infections (BSIs) in our hospital.</div></div><div><h3>Materials and methods</h3><div>Whole genome sequencing was performed and average nucleotide identity (ANI) was analyzed. Susceptibility testing was conducted using micro-broth methods. The distribution of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) was examined using online software tools. The prevalence of virulence factors (VFs) was investigated through nucleotide coding sequence comparisons. Genetic structures of <em>bla</em>OXA genes were analyzed by Gcluster software. Clinical information was collected from electronic medical records for patient characterization.</div></div><div><h3>Results</h3><div>ANI analysis identified five strains as <em>Acinetobacter pittii</em>, with the remaining four identified as <em>A. geminorum</em>, <em>A. nosocomialis</em>, <em>A. soli</em> and <em>A. bereziniae</em>. The GC content of all isolates was less than 38.9 % except for <em>A. soli</em> 16,294. All Non-baumannii <em>Acinetobacter</em> strains were relatively susceptible to antibiotics, except for one <em>A. pittii</em> isolate. Nine <em>bla</em>OXA variants were identified in seven isolates, with two isolates co-carrying 2 different types of <em>bla</em>OXA. Twenty-four insertion sequences (ISs) were identified, with ISAba and IS17 being the primary ISs. Five <em>A. pittii</em> isolates shared the same genetic structures around <em>bla</em>OXA. Genes related to adherence, immune modulation, and nutritional/metabolic factors were the most frequent. Few VFs were detected in <em>A. soli</em> 16,294 and <em>A.bereziniae</em> 14,325.</div></div><div><h3>Conclusions</h3><div>The presence of carbapenem hydrolyzing oxacillinase encoding genes did not confer carbapenem resistance, possibly due to the lack of ISs in the <em>bla</em>OXA flanking sequences. Different <em>bla</em>OXA variants within distinct strains shared the same genetic structures, suggesting potential for multidrug resistance development, which warrants our attention.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105669"},"PeriodicalIF":2.6,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001205/pdfft?md5=3457782c0565ca872d7f4c3ed085bf49&pid=1-s2.0-S1567134824001205-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring genetic diversity of hepatitis D virus full-length genome in Brazil: Discovery of a novel HDV-8 subgenotype beyond African borders","authors":"Giovana P. Angelice,&nbsp;Tairine M. Barros,&nbsp;Vanessa A. Marques,&nbsp;Livia M. Villar,&nbsp;Barbara V. Lago,&nbsp;Francisco C.A. Mello","doi":"10.1016/j.meegid.2024.105671","DOIUrl":"10.1016/j.meegid.2024.105671","url":null,"abstract":"<div><div>Hepatitis D virus (HDV) is currently classified into 8 genotypes (1 to 8) and several subgenotypes, with distinct distribution worldwide. However, due to the scarcity of complete genome sequences in databases, this classification is constantly being updated and tends to be regularly revisited in upcoming years as more sequence data becomes available. Aiming to increase knowledge about the genetic variability of HDV, this study presents the full-length genomes of 11 HDV samples collected in Brazil in endemic and non-endemic regions, including the first complete genomes of the genotypes 5 and 8 obtained outside Africa. We also determined the co-infecting HBV genotypes to investigate their prevalence among the HDV-infected individuals throughout the country. Whole genome sequencing confirmed our previous findings based on a partial fragment of the HDV genome, in which HDV subgenoypes 3c (9/11; 81.8 %), 5b (1/11; 9.1 %) and one HDV-8 sequence (1/11; 9.1 %) were detected. As previously observed, HDV-8 formed a distinct branch apart from subgenotypes 8a and 8b, a monophyletic clade representing a novel HDV-8 subgenotype, designated as 8c. Among HDV-3 samples, the main co-infecting HBV genotype found was HBV-F (4/8; 50 %), reflecting the higher incidence of this native South American genotype in the endemic Amazon Basin. Both samples infected with HDV-5 and HDV-8 were coinfected with HBV genotype E, also a genotype with African origin. Our findings based on complete genome sequence of HDV corroborated our results based on a partial region of the HDV genome of a novel HDV-8 subgenotype and reinforced the need to use full-length genomes to properly subdivide genotypes with very low intragroup genetic variability, such as HDV-3. The provision of these complete genomes is expected to contribute to the enrichment of sequence databases for future molecular and evolutionary investigations of HDV.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105671"},"PeriodicalIF":2.6,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel members of the order Picornavirales identified in freshwater from Guarapiranga reservoir in São Paulo","authors":"Endrya do Socorro Foro Ramos ,&nbsp;Mikaela Renata Funada Barbosa ,&nbsp;Fabiola Villanova ,&nbsp;Renan Lourenço Oliveira Silva ,&nbsp;Suzi Cristina Garcia ,&nbsp;Maria Cássia Mendes-Correa ,&nbsp;Ramendra Pati Pandey ,&nbsp;Adriana Luchs ,&nbsp;Maria Inês Zanoli Sato ,&nbsp;Antonio Charlys da Costa ,&nbsp;Elcio Leal","doi":"10.1016/j.meegid.2024.105668","DOIUrl":"10.1016/j.meegid.2024.105668","url":null,"abstract":"<div><p>The global challenge of water resource availability is exacerbated by anthropogenic influences that promote the emergence of pollutants. Among these pollutants are microbiological agents, including viruses, which are ubiquitous in the biosphere and play a pivotal role in both ecological balance and the occurrence of diseases in animals and plants. Consequently, monitoring viruses in water sources becomes indispensable for the establishment of effective prevention, promotion, and control strategies. Within this context, the study focuses on the identification of novel viruses belonging to the <em>Picornavirales</em> order in freshwater from the Guarapiranga Reservoir in the state of São Paulo, Brazil. The samples were subjected to viral metagenomics. Our analysis led to the characterization of four distinct sequences (GinkV-05, AquaV_10, MarV_14, and MarV_64), which exhibited significant divergence compared to other members of the <em>Picornavirales</em> order. This remarkable diversity prompted the identification of a potential new genus within the <em>Marnaviridae</em> family, tentatively named <em>Ginkgonavirus</em>. Additionally, we characterized four sequences in a very distinct clade and propose the recognition of a novel family (named <em>Aquaviridae</em>) within the <em>Picornavirales</em> order. Our findings contribute valuable insights into the previously uncharted diversity of <em>Picornavirales</em> present in water sources, shedding light on an important facet of viral ecology and evolution in aquatic environments.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"124 ","pages":"Article 105668"},"PeriodicalIF":2.6,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001199/pdfft?md5=4ec0eb4d282f3beeefe9c393f76b15dc&pid=1-s2.0-S1567134824001199-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142230794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The 2023 South Sudanese outbreak of Hepatitis E emphasizes ongoing circulation of genotype 1 in North, Central, and East Africa","authors":"Gregory S. Orf ,&nbsp;Nicholas Bbosa ,&nbsp;Michael G. Berg ,&nbsp;Robert Downing ,&nbsp;Sonja L. Weiss ,&nbsp;Deogratius Ssemwanga ,&nbsp;Alfred Ssekagiri ,&nbsp;Shirin Ashraf ,&nbsp;Ana da Silva Filipe ,&nbsp;Ronald Kiiza ,&nbsp;Joshua Buule ,&nbsp;Hamidah Suubi Namagembe ,&nbsp;Stella Esther Nabirye ,&nbsp;John Kayiwa ,&nbsp;Lul Lojok Deng ,&nbsp;Gregory Wani ,&nbsp;James A. Maror ,&nbsp;Andrew Baguma ,&nbsp;Juma J.H. Mogga ,&nbsp;Saleem Kamili ,&nbsp;Gavin A. Cloherty","doi":"10.1016/j.meegid.2024.105667","DOIUrl":"10.1016/j.meegid.2024.105667","url":null,"abstract":"<div><p>In April 2023, an outbreak of acute hepatitis was reported amongst internally displaced persons in the Nazareth community of South Sudan. IgM serology-based screening suggested the likely etiologic agent to be Hepatitis E virus (HEV). In this study, plasma specimens collected from anti-HEV IgM-positive cases were subjected to additional RT-qPCR testing and sequencing of extracted nucleic acids, resulting in the recovery of five full and eight partial HEV genomes. Maximum likelihood phylogenetic reconstruction confirmed the genomes belong to HEV genotype 1. Using distance-based methods, we show that genotype 1 is best split into three sub-genotypes instead of the previously proposed seven, and that these sub-genotypes are geographically restricted. The South Sudanese sequences confidently cluster within sub-genotype 1e, endemic to northeast, central, and east Africa. Bayesian Inference of phylogeny incorporating sampling dates shows that this new outbreak is not directly descended from other recent local outbreaks for which sequence data is available. However, the analysis suggests that sub-genotype 1e has been consistently and cryptically circulating locally for at least the past half century and that the known outbreaks are often not directly descended from one another. The ongoing presence of HEV, combined with poor sanitation and hygiene in the conflict-affected areas in the region, place vulnerable populations at risk for infection and its more serious effects, including progression to fulminant hepatitis.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"124 ","pages":"Article 105667"},"PeriodicalIF":2.6,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001187/pdfft?md5=6c323f9c6380c1ba150f88c1c01aedf4&pid=1-s2.0-S1567134824001187-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142232296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}