Infection Genetics and Evolution最新文献

{"title":"Rapid confirmation of autochthonous origin in suspected cases of melioidosis from French overseas departments in the Caribbean and the Indian Ocean by PCR-high resolution melting (HRM) analysis","authors":"Mégane Gasqué ,&nbsp;Vanina Guernier-Cambert ,&nbsp;Guillaume Girault ,&nbsp;Jules Terret ,&nbsp;Fabienne Neulat-Ripoll ,&nbsp;Emma Rochelle-Newall ,&nbsp;Karine Laroucau","doi":"10.1016/j.meegid.2024.105711","DOIUrl":"10.1016/j.meegid.2024.105711","url":null,"abstract":"<div><div><em>Burkholderia pseudomallei</em>, a soil-borne bacterium that causes melioidosis, endemic in South and Southeast Asia and northern Australia, is now emerging in new regions. Since the 1990s, cases have been reported in French overseas departments, including Martinique and Guadeloupe in the Caribbean, and Reunion Island and Mayotte in the Indian Ocean, suggesting a local presence of the bacterium. Our phylogenetic analysis of 111 <em>B. pseudomallei</em> genomes isolated worldwide, including three strains from Martinique, revealed distinct geography-specific clades for Africa, the Americas, Asia and Australasia. Single nucleotide polymorphisms (SNP) that define clade branches in the phylogeny were identified; we selected those specific to three regions relevant to the French overseas departments: the Indian Ocean, the Americas and a unique subset specific to Martinique. Three SNP markers (one per region) were used to develop a PCR-high resolution melting tool to discriminate between local and imported strains in each region. Blind tests on <em>B. pseudomallei</em> strains from French patients, from overseas departments and mainland France, were used for validation. Our method accurately predicted the geographic origin of the patient as recorded from the patient travel history and/or from the multilocus sequence typing data. This rapid typing method, which allows timely identification of local cases and targeted public health interventions, is particularly valuable in the French overseas departments where melioidosis is emerging and regulatory constraints limit the handling of <em>B. pseudomallei</em>. Although initially tailored to specific regions, this tool can be adapted for use in other areas to support local epidemiological surveillance of melioidosis.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"127 ","pages":"Article 105711"},"PeriodicalIF":2.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900536","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":"Identifying the unknown: Application of molecular epidemiology tools to identify clustering and HIV transmission routes in Poland.","authors":"Marcin Horecki, Karol Serwin, Iwona Cielniak, Ewa Siwak, Monika Bociąga Jasik, Anna Kalinowska-Nowak, Błażej Rozpłochowski, Bogusz Aksak-Wąs, Magdalena Witak-Jędra, Aleksandra Szymczak, Bartosz Szetela, Elżbieta Mularska, Adam Witor, Paweł Jakubowski, Maria Hlebowicz, Anita Olczak, Władysław Łojewski, Elżbieta Jabłonowska, Kaja Mielczak, Piotr Ząbek, Miłosz Parczewski","doi":"10.1016/j.meegid.2024.105699","DOIUrl":"https://doi.org/10.1016/j.meegid.2024.105699","url":null,"abstract":"<p><strong>Background: </strong>Understanding the dynamics of HIV-1 transmission is essential for developing effective screening and intervention strategies. Viral genetic sequences provide valuable information that can be used to infer the history and patterns of viral transmission.</p><p><strong>Purpose: </strong>Our study explores the structure and dynamics of HIV transmissions in Poland from 1999 to 2022 to elucidate key patterns related with national epidemics.</p><p><strong>Methods: </strong>To understand the temporal dynamics of transmission routes we examined HIV pol sequence data from 5705 Polish PWH. The HIV-TRAnsmission Cluster Engine (HIV-TRACE) was utilized to identify potential links between different risk groups and putative links to individuals with unreported transmission risk.</p><p><strong>Results: </strong>Our analyses generated 503 clusters, containing 3942 individuals, and identified 13,917 putative links. Approximately 69.1 % of the sequences formed clusters. In the dataset 32.2 % of individuals were reported MSM transmission route, 7.9 % by heterosexual, and 5.6 % by PWID transmissions. The transmission route was unknown for 54.2 % of patients. Putative transmissions from MSM to all other groups revealed that 45.1 % of links lead to people with unregistered transmission mode. For heterosexual patients, 40.2 % of connections were directed to patients lacking information on infection routes and 30.5 % to MSM individuals. Our analysis unveiled that 45.1 % of cases with unreported transmission routes may be identified as MSM, while 3.5 % might be potential non-disclosed MSM.</p><p><strong>Conclusions: </strong>Genetic linkages can provide valuable insights into the transmission dynamics among individuals, even in cases where transmission risk information is missing or unreported. The observed association between MSM and unreported cases highlights the potential of molecular epidemiology to complete missing patient data.</p>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":" ","pages":"105699"},"PeriodicalIF":2.6,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792830","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}

{"title":"Genomic analysis of blaNDM-1-carrying-Pseudomonas aeruginosa ST2407 in the chromosome from Brazil","authors":"Ivson Cassiano de Oliveira Santos ,&nbsp;Melise Chaves Silveira ,&nbsp;Daiana Cristina Silva Rodrigues ,&nbsp;Bruna Ribeiro Sued-Karam ,&nbsp;Bruno Rocha Pribul ,&nbsp;Giovanna de Oliveira Santos ,&nbsp;Jônathas Dias Nunes ,&nbsp;Marcos Dornelas-Ribeiro ,&nbsp;Gabriela Bergiante Kraychete ,&nbsp;Renata Cristina Picão ,&nbsp;Elizabeth Andrade Marques ,&nbsp;Robson Souza Leão ,&nbsp;Cláudio Marcos Rocha-de-Souza ,&nbsp;Ana Paula D'Alincourt Carvalho-Assef","doi":"10.1016/j.meegid.2024.105702","DOIUrl":"10.1016/j.meegid.2024.105702","url":null,"abstract":"<div><div><em>Pseudomonas aeruginosa</em>, an opportunistic pathogen often found in Healthcare-associated infections (HAI), has shown increased resistance to carbapenems (imipenem, meropenem, doripenem), the primary treatment options. We've seen a rise in carbapenemase-producing <em>P. aeruginosa</em> in Brazil, including NDM-producers. This study characterises an isolate carrying <em>bla</em>_NDM-1 from a patient's skin fragment in a Brazilian hospital. The whole genomic sequence (WGS) of <em>P. aeruginosa</em> CCBH26428 was extracted and sequenced using Illumina and minION platforms. The assembly used MinION results mapped with Illumina reads, and annotation was performed by the RAST server. Resistance genes and clonality were identified using the CABGen platform. Additional information was carried out by manual annotation using Geneious software and BLAST tool. The genomic analysis revealed a genome of 6.995.008 bp and G+C 65.9 %. <em>P. aeruginosa</em> CCBH26428 belongs to ST2407. The <em>bla</em>_NDM gene, associated with ISA<em>ba</em>125, was found in a 63.862 pb genomic region flanked by IS26 insertion sequences. This region also contained the repA of the plasmid incompatibility group IncC2 and other resistance genes, suggesting it is a possible “translocation unit”. Additionally, 17 resistance genes, mutations in OprD and GyrA, and several virulence genes were detected, potentially exacerbating the infection. This study is report a WGS analysis of <em>P. aeruginosa</em> carrying <em>bla</em>_NDM-1 in Brazil, highlighting the role of IS26 in the acquisition and spread of resistance genes between plasmids and chromosomes.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105702"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808683","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":"Phylogenetic and phylodynamic analysis of respiratory syncytial virus strains circulating in children less than five years of age in Karachi-Pakistan","authors":"Fatima Aziz ,&nbsp;Nida Farooqui ,&nbsp;Tanveer Abbas ,&nbsp;Mahnoor Javaid ,&nbsp;Wardah Rafaqat ,&nbsp;Alnara Zhamalbekova ,&nbsp;Syed Asad Ali ,&nbsp;Syed Ali ,&nbsp;Syed Hani Abid","doi":"10.1016/j.meegid.2024.105694","DOIUrl":"10.1016/j.meegid.2024.105694","url":null,"abstract":"<div><h3>Background</h3><div>Respiratory syncytial virus (RSV) is one of the leading causes of infant morbidity and mortality worldwide, especially in Pakistan. To date, few studies have explored RSV epidemiology in different areas of Pakistan. However, none have performed comprehensive phylogenetic and phylodynamic analyses of RSV strains. This study presents a comprehensive genetic and phylodynamic analysis of RSV strains in children less than five years old in Karachi, Pakistan.</div></div><div><h3>Methods</h3><div>This study used retrospectively collected nasopharyngeal (swab) samples from 155 children with qPCR-confirmed RSV infection. The samples were used to perform RSV genotyping using PCR employing RSV glycoprotein gene-specific primers. The RSVA and RSVB genotyping was performed using BLAST and Maximum-likelihood (ML) phylogenetic methods. Similarly, the relationship with other RSV strains was analyzed using ML phylogenetic cluster analysis. The RSVA and RSVB mean genetic diversity and coefficient of differentiation were calculated using MEGA7 software. Furthermore, the time to the most common recent ancestor (tMRCA) and effective population size of RSV genotypes A and B were estimated using a Bayesian MCMC analysis. Finally, site selection pressure and glycosylation analyses were performed using FUBAR and NetNGlyc/NetOGlyc tools.</div></div><div><h3>Results</h3><div>Out of 155, 98 and 57 sequences were RSVA and RSVB, respectively. The tMRCA was estimated to be around 2002 and 2005 for RSVA and RSVB, respectively. RSVA sequences formed two NA1 genotype clusters, comprising 95 and three sequences, respectively. RSVB formed three clusters, where 24 and two sequences clustered with BA9 and BA12 genotypes, respectively, while 31 sequences formed a unique cluster. The RSVA and RSVB glycoprotein gene sequences exhibited N- and O- glycosylation and selection pressure at several sites. RSV B exhibited slightly higher (0.042) nucleotide diversity per site (π) as compared to RSVA (0.019).</div></div><div><h3>Conclusions</h3><div>Our results suggest that RSVA and RSVB strains in Pakistan exhibit distinct genotypic clusters and differ in their estimated tMRCA. Additionally, both genotypes showed glycosylation and selection pressure at specific sites, with RSVB exhibiting higher nucleotide divergence per site (π), indicating its potential to undergo further evolutionary changes and adaptation. Overall, this study provides unique insights into RSV molecular epidemiology. The study may also help improve our understanding of RSV evolutionary changes and the emergence of new genotypes in different regions worldwide and within Pakistan.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105694"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142746233","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":"Corrigendum to “Epidemiological and phylogenetic characteristics of emerging Anaplasma capra: A systematic review with modeling analysis” [Infection, Genetics and Evolution, volume 115, article 105510]","authors":"Zhe-Tao Lin ,&nbsp;Run-Ze Ye ,&nbsp;Jin-Yue Liu ,&nbsp;Xiao-Yang Wang ,&nbsp;Wen-Jie Zhu ,&nbsp;Yu-Yu Li ,&nbsp;Xiao-Ming Cui ,&nbsp;Wu-Chun Cao","doi":"10.1016/j.meegid.2024.105696","DOIUrl":"10.1016/j.meegid.2024.105696","url":null,"abstract":"","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105696"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787913","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 characteristics and diversity of PDC variants of Pseudomonas aeruginosa and its clinical relevance","authors":"Maruthan Karthik ,&nbsp;Srujal Kacha ,&nbsp;Subbulakshmi Rajendran ,&nbsp;Yamuna Devi Bakthavatchalam ,&nbsp;Binesh Lal ,&nbsp;Kamini Walia ,&nbsp;Balaji Veeraraghavan","doi":"10.1016/j.meegid.2024.105701","DOIUrl":"10.1016/j.meegid.2024.105701","url":null,"abstract":"<div><div><em>Pseudomonas aeruginosa</em> exhibits significant antibiotic resistance facilitated by both intrinsic and acquired mechanisms, prominently through Pseudomonas-derived cephalosporinase (PDC), serine Ambler class C β-lactamases encoded by the AmpC. AmpC, involved in the peptidoglycan recycling pathway, is regulated by genes such as ampD, ampR, and ampG, leading to increased expression and resistance to various beta-lactams. PDCs are classified into three main types: classical class C β-lactamases, extended-spectrum class C β-lactamases (ESAC β-lactamases), and inhibitor-resistant class C β-lactamases. This study aimed to identify prevalent PDC variants and its genetic characteristics in Indian and global <em>P. aeruginosa</em> isolates, focusing on their role in β-lactam resistance. Analyzing PDC sequences from 111 <em>P. aeruginosa</em> isolates collected at Christian Medical College (CMC), Vellore, we found the ESAC allele PDC-447 to be the most widespread among Indian isolates, present in 18 % of carbapenem-resistant and 11 % of carbapenem-susceptible strains. Global and Indian isolates PDC variants were validated using the NCBI PathogenWatch database, and the sequenced PDC region compared to PDC-1. PDC-398 and PDC-397 followed in prevalence among carbapenem-resistant isolates, while PDC-5 (ESAC) and PDC-1 (classical class C) were common in carbapenem-susceptible strains. A global analysis of 19,478 genomes revealed significant prevalence of ESAC variants such as PDC-3 (17.28 %) and PDC-5 (12.91 %), alongside classical class C beta-lactamases like PDC-8 (10.65 %). Indian isolates exhibited distinct patterns with PDC-3 and PDC-5 prevailing at 19.84 % and 10 %, respectively. Mutations in the omega loop, H-helix, and R2 region of PDCs were linked to enhanced antibiotic resistance, particularly the T105A mutation in the H-helix region. These findings underscore the complexity of antimicrobial resistance mechanisms in <em>P. aeruginosa</em> and highlight the need for novel therapeutic strategies and continuous surveillance to manage infections by this versatile pathogen. Understanding the prevalence and genetic characteristics of PDC variants is crucial for effective treatment strategies against <em>P. aeruginosa</em> and combating antibiotic resistance.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105701"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142803473","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":"Phenotypic and genotypic characteristics of Trueperella abortisuis recovered from the feline reproductive tract","authors":"Siti Gusti Ningrum ,&nbsp;Antonia Kreitlow ,&nbsp;Christoph Lämmler ,&nbsp;Martin Metzner ,&nbsp;Madeleine Plötz ,&nbsp;Amir Abdulmawjood","doi":"10.1016/j.meegid.2024.105697","DOIUrl":"10.1016/j.meegid.2024.105697","url":null,"abstract":"<div><div>Large numbers of infections and effective treatment or control depend on the ability to identify the causative agents of animal infections. Here we describe a study of an isolate DG22/1209/12 obtained from vaginal pus exudate collected from a Siamese cat. The isolate was believed to be a member of <em>Trueperella abortisuis</em>, which is related to problems with reproduction. The most important was to identify this isolate by applying different techniques of diagnosis. It included phenotypic testing, Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS), and molecular techniques such as amplification and sequencing of the 16S rRNA gene, intergenic spacer region (ISR), and the <em>gap</em> and <em>tuf</em> genes. Phenotypic tests confirmed the identification of DG22/1209/12 as <em>T. abortisuis</em>. Finally, the identification was confirmed with MALDI-TOF MS analysis which demonstrated log (score) value of 2.09 indicating a secure genus identification, probable species identification on <em>T. abortisuis</em>. Molecular analysis revealed a high sequence identity of 99.9 %, 99.5 %, 99.4 %, and 99.5 % for the 16S rRNA gene, ISR, <em>gap</em>, and <em>tuf</em> genes, respectively, for both the isolate DG22/1209/12 and the reference isolate <em>T. abortisuis</em> DSM 19515^T. The study highlights the effectiveness of combining phenotypic and genomic methods to accurately identify bacterial pathogens in veterinary medicine, leading towards focused intervention strategies.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105697"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774926","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":"Prevalence and molecular epidemiology of methicillin-resistant Staphylococcus aureus in livestock farmers, livestock, and livestock products in southern Sri Lanka: A one health approach","authors":"M.R.P. Kurukulasooriya ,&nbsp;L.G. Tillekeratne ,&nbsp;W.M.D.G.B. Wijayaratne ,&nbsp;C.K. Bodinayake ,&nbsp;U.H.B.Y. Dilshan ,&nbsp;A.D. De Silva ,&nbsp;B.P. Nicholson ,&nbsp;T. Østbye ,&nbsp;C.W. Woods ,&nbsp;A. De S. Nagahawatte","doi":"10.1016/j.meegid.2024.105693","DOIUrl":"10.1016/j.meegid.2024.105693","url":null,"abstract":"<div><div>Methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) colonization can lead to subsequent severe infections. Unlike community and hospital-associated types, Livestock-associated MRSA (LA-MRSA) transmits to humans through direct contact with livestock and contaminated livestock products. This study aimed to investigate MRSA prevalence and molecular epidemiology in livestock farmers, livestock, and livestock products, including LA-MRSA presence and MRSA abundance in human and animal nasal microbiome, in southern Sri Lanka using a One Health approach.</div><div>Nasal swabs from farmers and livestock on 50 farms (Nov 2020 - Dec 2021) and livestock products were collected. MRSA was isolated and confirmed using standard microbiological techniques. Staphylococcal chromosomal cassette <em>mec</em> typing, <em>spa</em> typing, and multilocus sequence typing were performed. Identified clones were compared with hospital isolates. Metagenomics analysis was performed on selected samples.</div><div>MRSA prevalence was 24.0 % (12/50) in farms, 7.9 % (12/152) in farmers, 2.1 % (5/240) in livestock, and 1.9 % (3/157) in products. Of 372 <em>S. aureus</em> collected from clinical cultures, 59.4 % were MRSA. MRSA clones were identified in farm personnel (CC5/ST5/t002, CC1/ST1/t127, and ST45/CC45/t026), livestock (CC5/ST5/t002), and clinical cultures (CC5/ST5/t002 and CC5/ST6/t304), with ST45/CC45/t026 and CC5/ST6/t304 reported for the first time in Sri Lanka. LA-MRSA clones (ST389/ST9) were not detected. Animals had more diverse nasal microbiomes and lower MRSA abundance (&lt;1.4 %) compared to humans (&gt;82.3 %).</div><div>MRSA colonization prevalence in southern Sri Lanka was relatively low. Two new clones and no LA-MRSA clones were identified. This study highlights the importance of continuing MRSA surveillance under the One Health framework to identify MRSA transmission between humans, animals, and the environment.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105693"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774927","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":"A potential bimodal interplay between heme and complement factor H 402H in the deregulation of the complement alternative pathway by SARS-CoV-2","authors":"Stefanos A. Tsiftsoglou ,&nbsp;Eleni Gavriilaki","doi":"10.1016/j.meegid.2024.105698","DOIUrl":"10.1016/j.meegid.2024.105698","url":null,"abstract":"<div><div>The recent discovery that the trimeric SARS-CoV-2 spike S glycoprotein carries heme within an NTD domain pocket of the S1 subunits, suggested that this virus may be cleverly utilizing heme, in addition to the S1 RBD domains, for invading target cells carrying a specific entry receptor like ACE2, TMEM106B and others. Studies during the COVID-19 pandemic revealed that the infectivity of this virus depends on cell surface heparan sulfate and that the infection induces non-canonical activation of the Complement Alternative pathway (AP) on the surface of infected cells.</div><div>In our recent COVID-19 genomic studies, among the coding SNPs of interest we also detected the presence of the CFH rs1061170, rs800292 and rs1065489 within all the infected patient subgroups examined. The minor C allele of rs1061170 encodes CFH 402H that over the years has been associated with diseases characterized by complement dysregulation namely the age-related macular degeneration (AMD) and the atypical haemolytic uremic syndrome (aHUS). Also, more recently with the diminishment of CD4⁺ T cell responses with ageing. The rs800292 minor allele A encodes CFH 62I that supports enhanced cofactor activity for Complement factor I (CFI). Also, the rs1065489 minor allele T encodes CFH 936D and is located within the CCP16 domain that influences the affinity of CFH with extracellular laminins.</div><div>A subsequent computational analysis revealed that the CFH residue 402 is located centrally within a heme-binding motif (HBM) in domain CCP7 (³⁹⁸YNQN<u>Y</u>GRKF⁴⁰⁶). Heme on the viral spike glycoprotein S1 subunit could recruit CFH 402H for masking free viral particles from opsonisation, and when in proximity to cell surface, act as a bait disrupting CFH 402H from the heparan sulphate coat of the target cells. Publicly available genetic data for European populations indicate that the minor C allele of rs1061170 is present only in haplotypes that carry the major alleles of rs800292 and rs1065489. This combination encodes for CFH 402H that exhibits increased biochemical affinity for heme in proximity, without enhanced cofactor activity for CFI and weaker association with the extracellular matrix. In the theatre of infection, this combination can promote heme-mediated viral infection with weaker complement opsonisation and potential AP deregulation. This strategy may be evolutionary conserved among various classes of infectious agents.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105698"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792839","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":"Discovery of two novel foamy viruses in sea lions and dolphins provides insight into their evolutionary history","authors":"Xiaoyuan Hu ,&nbsp;Youyou Li ,&nbsp;Yun Zhang ,&nbsp;Zihan Li ,&nbsp;Lei Dong ,&nbsp;Shijie Bai ,&nbsp;Gaoyu Wang ,&nbsp;Ruoyan Peng ,&nbsp;Yi Huang ,&nbsp;Xin Li ,&nbsp;Chuanning Tang ,&nbsp;Xiuji Cui ,&nbsp;Lina Niu ,&nbsp;Gang Lu ,&nbsp;Jiang Du ,&nbsp;Feifei Yin","doi":"10.1016/j.meegid.2024.105695","DOIUrl":"10.1016/j.meegid.2024.105695","url":null,"abstract":"<div><div>The prevalence and evolution of foamy viruses (FVs) have become the focus of research because of the risk of new zoonotic diseases. FVs have been isolated from various mammals and exhibit long-term co-speciation with their hosts. They also appear to be mild and nonpathogenic to their hosts. However, they may increase the risk of infection by other pathogens or exacerbate the symptoms of other diseases. Based on the data obtained using next-generation sequencing (NGS), we amplified and obtained the complete genomes of the two new FVs discovered in the bottlenose dolphin (<em>Tursiops truncatus</em>) and the South American sea lion (<em>Otaria byronia</em>) at the Qingdao Polar Haichang Ocean Park. Analysis and prediction of the novel FV's genomic structure revealed that it was consistent with that of the known mammalian FVs. The polmerase (<em>pol</em>) genes of the novel OFVoby_1 and DFVttr_1 showed less than 61.87 % and 61.83 % amino acid identity, respectively, with other known FVs belonging to the <em>Retroviridae</em> family<em>.</em> The host was likely to carry the FV for a considerable amount of time, as evidenced by the different times DFVttr_1 was discovered. The phylogenetic analysis revealed that the <em>pol</em> of OFVoby_1 and DFVttr_1 closely clustered with the FVs of <em>Simiispumavirus</em> and <em>Felispumavirus</em>, respectively. However, they both displayed distinct branches. According to the international committee on taxonomy of viruses (ICTV) FV classification criteria, FVs carried by dolphins and sea lions belong to two new genera within the <em>Spumaretrovirinae</em> subfamily. Using Bayesian analysis to simultaneously determine divergence dates and phylogenetic relationships revealed unique FVs with a divergence date of approximately 60 million years. This study helps us understand the FVs evolution and provides a scientific basis for future investigations into animal-borne infectious diseases.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105695"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792826","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}