Pub Date : 2024-11-01DOI: 10.1016/j.meegid.2024.105685
Siat Yee Fong , Yuki Akari , Lia Natasha Amit , Jecelyn Leaslie John , Abraham Zefong Chin , Satoshi Komoto , Kamruddin Ahmed
G9P[8] has been the predominant rotavirus A (RVA) genotype in Malaysia since the 2000s. However, the overall genetic makeup and evolution of Malaysian G9P[8] strains are still unknown. Therefore, this study aimed to evaluate and characterize the complete genomes of three G9P[8] RVA strains isolated from diarrheic children under five years old in Sabah. Contrary to the classical Wa-like constellation, these strains contained a DS-1-like genotype. Two strains, namely L202 and L234, were genotype G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1, while one (KN102) was genotype G9-P[8]-I1-R1-C1-M1-A2-N1-T1-E1-H1. Phylogenetic analysis revealed that the NSP4 genes of L202 and L234 strains were closer to that of G9P[8]-E2 strains from Japan, suggesting they might share a common ancestor. The findings from this study provide new insights into the genetic characteristics of circulating G9P[8] strains in Sabah, which are important for rotavirus surveillance and potential vaccine development in the region.
{"title":"Emergence of non-classical genotype constellations of G9P[8] rotavirus strains in diarrheic children in Sabah, Malaysia","authors":"Siat Yee Fong , Yuki Akari , Lia Natasha Amit , Jecelyn Leaslie John , Abraham Zefong Chin , Satoshi Komoto , Kamruddin Ahmed","doi":"10.1016/j.meegid.2024.105685","DOIUrl":"10.1016/j.meegid.2024.105685","url":null,"abstract":"<div><div>G9P[8] has been the predominant rotavirus A (RVA) genotype in Malaysia since the 2000s. However, the overall genetic makeup and evolution of Malaysian G9P[8] strains are still unknown. Therefore, this study aimed to evaluate and characterize the complete genomes of three G9P[8] RVA strains isolated from diarrheic children under five years old in Sabah. Contrary to the classical Wa-like constellation, these strains contained a DS-1-like genotype. Two strains, namely L202 and L234, were genotype G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1, while one (KN102) was genotype G9-P[8]-I1-R1-C1-M1-A2-N1-T1-E1-H1. Phylogenetic analysis revealed that the NSP4 genes of L202 and L234 strains were closer to that of G9P[8]-E2 strains from Japan, suggesting they might share a common ancestor. The findings from this study provide new insights into the genetic characteristics of circulating G9P[8] strains in Sabah, which are important for rotavirus surveillance and potential vaccine development in the region.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105685"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513264","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}
Pub Date : 2024-11-01DOI: 10.1016/j.meegid.2024.105683
Arnauld Efon-Ekangouo , Hugues C. Nana-Djeunga , Philippe B. Nwane , Narcisse Nzune-Toche , Jeanne C. Sondi-Dissake , Guilhem Sempere , André Domche , Flobert Njiokou , Joseph Kamgno , Paul Moundipa-Fewou , Anne Geiger
Arthropod microbiota plays an important role in host physiology, and there is growing interest in using vector symbionts to modify vector competence and control parasite transmission. This study aims to characterise the blackfly Simulium damnosum s.l. gut microbiota and to explore possible associations with various bio-ecological determinants of the Onchocerca volvulus establishment and the transmission in blackfly. Adult female blackflies were caught in three Cameroonian health districts belonging to different bioecological zones endemic for onchocerciasis. Flies were dissected and qPCR screened for Onchocerca volvulus infection. The diversity of the blackflies gut microbiota was assessed by high-throughput sequencing of the V3-V4 hypervariable region of the bacterial 16S ribosomal RNA. Subsequent metataxo-genomic, multivariate, and association analysis were used to investigate the variables that influence the microbiota diversity.
Transmission index rates ranging from 20.7 to 6.0 % and 6.2to 2.0 % for infection and infectivity rates, respectively, indicate ongoing transmission of onchocerciasis across all surveyed health districts. The identified bacterial taxa were clustered into four phyla, five classes, and 23 genera. The S. damnosum s.l. gut microbiota was dominated by Wolbachia and by Rosenbergiella in Wolbachia-free Simulium. Significant differences were observed in the diversity of S. damnosum s.l. microbiota concerning parity status (P = 0.007), health district of origin (P = 0.001), and the presence of the Onchocerca volvulus. Simulium from the Bafia health district also showed increased bacterial diversity between two consecutive years (P = 0.001). Four bacterial taxa, including Serratia, were associated with the absence of the O. volvulus infection.
These results indicate that S. damnosum s.l. from different onchocerciasis foci in Cameroon, exhibit distinguishable gut microbial compositions which are dynamic over time. Some bacterial species are associated with the O. volvulus infection and could be further investigated as biological target/tool for vector modified-based onchocerciasis control.
{"title":"Spatial and temporal diversity of Simulium damnosum s.l. gut microbiota and association with Onchocerca volvulus infection in Cameroon","authors":"Arnauld Efon-Ekangouo , Hugues C. Nana-Djeunga , Philippe B. Nwane , Narcisse Nzune-Toche , Jeanne C. Sondi-Dissake , Guilhem Sempere , André Domche , Flobert Njiokou , Joseph Kamgno , Paul Moundipa-Fewou , Anne Geiger","doi":"10.1016/j.meegid.2024.105683","DOIUrl":"10.1016/j.meegid.2024.105683","url":null,"abstract":"<div><div>Arthropod microbiota plays an important role in host physiology, and there is growing interest in using vector symbionts to modify vector competence and control parasite transmission. This study aims to characterise the blackfly <em>Simulium damnosum</em> s.l. gut microbiota and to explore possible associations with various bio-ecological determinants of the <em>Onchocerca volvulus</em> establishment and the transmission in blackfly. Adult female blackflies were caught in three Cameroonian health districts belonging to different bioecological zones endemic for onchocerciasis. Flies were dissected and qPCR screened for <em>Onchocerca volvulus</em> infection. The diversity of the blackflies gut microbiota was assessed by high-throughput sequencing of the V3-V4 hypervariable region of the bacterial 16S ribosomal RNA. Subsequent metataxo-genomic, multivariate, and association analysis were used to investigate the variables that influence the microbiota diversity.</div><div>Transmission index rates ranging from 20.7 to 6.0 % and 6.2to 2.0 % for infection and infectivity rates, respectively, indicate ongoing transmission of onchocerciasis across all surveyed health districts. The identified bacterial taxa were clustered into four phyla, five classes, and 23 genera. The <em>S. damnosum</em> s.l. gut microbiota was dominated by <em>Wolbachia</em> and by <em>Rosenbergiella</em> in <em>Wolbachia</em>-free <em>Simulium</em>. Significant differences were observed in the diversity of <em>S. damnosum</em> s.l<em>.</em> microbiota concerning parity status (<em>P</em> = 0.007), health district of origin (<em>P</em> = 0.001), and the presence of the <em>Onchocerca volvulus</em>. <em>Simulium</em> from the Bafia health district also showed increased bacterial diversity between two consecutive years (P = 0.001). Four bacterial taxa, including <em>Serratia</em>, were associated with the absence of the <em>O. volvulus</em> infection.</div><div>These results indicate that <em>S. damnosum</em> s.l<em>.</em> from different onchocerciasis foci in Cameroon, exhibit distinguishable gut microbial compositions which are dynamic over time. Some bacterial species are associated with the <em>O. volvulus</em> infection and could be further investigated as biological target/tool for vector modified-based onchocerciasis control.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105683"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513265","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}
Pub Date : 2024-11-01DOI: 10.1016/j.meegid.2024.105686
Ansu Kumari , Divya Agnihotri , Anil Kumar Nehra , Aman Dev Moudgil , Yudhbir Singh , Devendra Prasad Pateer , Rajat Garg
<div><div>Canine babesiosis, a severe haemoparasitic disease caused by <em>Babesia</em> species, has a significant global presence and can be fatal if left untreated. The current study was aimed to perform the population genetic characterization of <em>B. vogeli</em> on the basis of the internal transcribed spacer regions (ITS1–5.8S–ITS2). A maximum likelihood tree constructed with the Hasegawa-Kishino-Yano model grouped all sequences into a single major clade (BvG1), with the exception of a Taiwanese isolate (EF186914), which branched separately. This Taiwanese isolate represented a novel genotype (BvG2) identified in the present study. Nucleotide sequences (<em>n</em> = 62) exhibited 92.5–100 % nucleotide identity among themselves. However, the BvG1 and BvG2 genotypes shared a lower identity of 92.5–93.8 % between them. Notably, the newly generated Indian sequences (<em>n</em> = 21) demonstrated a high degree of homology, with 98.3–100 % identity. Alignment of the nucleotide sequences revealed 58 variations across the dataset. Additionally, 32 sites exhibited variation within the BvG1 genotype, while 56 sites differed between BvG1 and BvG2 genotypes. Within different <em>B. vogeli</em> populations, the nucleotide diversity (π) was low, but the haplotype diversity (Hd) was high. The haplotype diversity of the Indian population, BvG1 genotype, and the combined dataset was ∼0.8 suggesting a high haplotype diversity. The median-joining haplotype network displayed a total of 21 haplotypes, out of which six haplotypes consisted of more than one sequence (2–25 sequences). Haplotype distribution showed significant geographical structuring, with most haplotypes confined to a single country. Only two haplotypes (9.52 %; Hap_1 and Hap_4) were shared between countries, whereas 19 haplotypes (90.48 %) were country-specific. Hap_1, Hap_6, and Hap_4 were the most representative haplotypes, comprising 25, 10, and four sequences, respectively. India exhibited the highest number of haplotypes (h = 13) followed by China (h = 4), the United States of America (h = 3), Taiwan and Tunisia (h = 2), and Thailand (h = 1). Both location-wise and genotype-wise median joining haplotype networks clustered the haplotypes in two groups, representing two distinct genotypes (BvG1 and BvG2). The <em>B. vogeli</em> populations between Thailand and Tunisia exhibited the highest genetic differentiation (F<sub>ST</sub> = 0.80) with a low gene flow (Nm = 0.125) between them. Results of AMOVA revealed a higher genetic variation within populations (69.43 %) as compared to the variation between them (30.57 %). Neutrality indices and the mismatch distributions of the Indian population and the overall dataset of <em>B. vogeli</em> indicated a constant population size to population expansion and population expansion, respectively, with the presence of two distinct genotypes. These data provide information about parasite population genetics and highlight the importance of starting a long-te
{"title":"Genetic diversity and molecular evolution of the internal transcribed spacer regions (ITS1–5.8S–ITS2) of Babesia vogeli","authors":"Ansu Kumari , Divya Agnihotri , Anil Kumar Nehra , Aman Dev Moudgil , Yudhbir Singh , Devendra Prasad Pateer , Rajat Garg","doi":"10.1016/j.meegid.2024.105686","DOIUrl":"10.1016/j.meegid.2024.105686","url":null,"abstract":"<div><div>Canine babesiosis, a severe haemoparasitic disease caused by <em>Babesia</em> species, has a significant global presence and can be fatal if left untreated. The current study was aimed to perform the population genetic characterization of <em>B. vogeli</em> on the basis of the internal transcribed spacer regions (ITS1–5.8S–ITS2). A maximum likelihood tree constructed with the Hasegawa-Kishino-Yano model grouped all sequences into a single major clade (BvG1), with the exception of a Taiwanese isolate (EF186914), which branched separately. This Taiwanese isolate represented a novel genotype (BvG2) identified in the present study. Nucleotide sequences (<em>n</em> = 62) exhibited 92.5–100 % nucleotide identity among themselves. However, the BvG1 and BvG2 genotypes shared a lower identity of 92.5–93.8 % between them. Notably, the newly generated Indian sequences (<em>n</em> = 21) demonstrated a high degree of homology, with 98.3–100 % identity. Alignment of the nucleotide sequences revealed 58 variations across the dataset. Additionally, 32 sites exhibited variation within the BvG1 genotype, while 56 sites differed between BvG1 and BvG2 genotypes. Within different <em>B. vogeli</em> populations, the nucleotide diversity (π) was low, but the haplotype diversity (Hd) was high. The haplotype diversity of the Indian population, BvG1 genotype, and the combined dataset was ∼0.8 suggesting a high haplotype diversity. The median-joining haplotype network displayed a total of 21 haplotypes, out of which six haplotypes consisted of more than one sequence (2–25 sequences). Haplotype distribution showed significant geographical structuring, with most haplotypes confined to a single country. Only two haplotypes (9.52 %; Hap_1 and Hap_4) were shared between countries, whereas 19 haplotypes (90.48 %) were country-specific. Hap_1, Hap_6, and Hap_4 were the most representative haplotypes, comprising 25, 10, and four sequences, respectively. India exhibited the highest number of haplotypes (h = 13) followed by China (h = 4), the United States of America (h = 3), Taiwan and Tunisia (h = 2), and Thailand (h = 1). Both location-wise and genotype-wise median joining haplotype networks clustered the haplotypes in two groups, representing two distinct genotypes (BvG1 and BvG2). The <em>B. vogeli</em> populations between Thailand and Tunisia exhibited the highest genetic differentiation (F<sub>ST</sub> = 0.80) with a low gene flow (Nm = 0.125) between them. Results of AMOVA revealed a higher genetic variation within populations (69.43 %) as compared to the variation between them (30.57 %). Neutrality indices and the mismatch distributions of the Indian population and the overall dataset of <em>B. vogeli</em> indicated a constant population size to population expansion and population expansion, respectively, with the presence of two distinct genotypes. These data provide information about parasite population genetics and highlight the importance of starting a long-te","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105686"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142570490","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}
Pub Date : 2024-11-01DOI: 10.1016/j.meegid.2024.105678
Endrya do Socorro Foro Ramos , Mikaela Renata Funada Barbosa , Fabiola Villanova , Renan Lourenço Oliveira Silva , Suzi Cristina Garcia , Maria Cassiá Mendes-Correa , Ramendra Pati Pandey , Adriana Luchs , Maria Inês Zanoli Sato , Antonio Charlys da Costa , Elcio Leal
{"title":"Corrigendum to: Novel members of the order Picornavirales identified in freshwater from Guarapiranga reservoir in São Paulo (infection, Genetics and Evolution Volume 124, October 2024, 105668)","authors":"Endrya do Socorro Foro Ramos , Mikaela Renata Funada Barbosa , Fabiola Villanova , Renan Lourenço Oliveira Silva , Suzi Cristina Garcia , Maria Cassiá Mendes-Correa , Ramendra Pati Pandey , Adriana Luchs , Maria Inês Zanoli Sato , Antonio Charlys da Costa , Elcio Leal","doi":"10.1016/j.meegid.2024.105678","DOIUrl":"10.1016/j.meegid.2024.105678","url":null,"abstract":"","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105678"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481321","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}
Pub Date : 2024-10-23DOI: 10.1016/j.meegid.2024.105684
Xiaoying Shan , Shuang Chen , Aiying Bai , Yuwen Shi , Xuanli Song , Xiaoyu Yin , Chunhong Duan , Jinglei Tang , Xian Xia , Lanzheng Liu , Bingqing Zhu
Considering the significant role of commensal Neisseria carried in the pharynx on the variation of N.meningitidis and the acquisition of its resistance genes, understanding the true Neisseria population colonizing the human pharynx is of great significance. In this study, we carried out a five-month continuous survey of oropharyngeal carriage in a certain healthy population to reveal the long-term carriage status of different Neisseria species. Totally, 419 Neisseria strains were isolated from 203 out of 205 pharyngeal swabs of 49 participants. Using combined methods (MALDI-TOF-MS, rplF sequencing and genome sequencing), the isolates were identified as N.subflava (n = 290), N.mucosa (n = 52), N.oralis (n = 8), N.elongata group (n = 6) and non-species-confirmed (n = 63). N.subflava was isolated from all individuals and 168 swabs (81.95 %). N.mucosa, N.oralis, N.elongata and non-species-confirmed were isolated from 25 (45), 6 (7), 4 (5) and 20 (53) individuals (swabs) respectively. It was common that multiple Neisseria spp. or multiple clones of one species were isolated from a single sample. An identical strain could be isolated frequently from a single person within five months. These results indicate that Neisseria spp. and N.subflava are ubiquitous in human pharynx and both have diverse population; we should pay more attention to them when studying N.meningitidis or other respiratory pathogens; robust and handy method for identifying Neisseria species remains to be developed.
{"title":"Dynamic pharyngeal carriage of Neisseria species in healthy population","authors":"Xiaoying Shan , Shuang Chen , Aiying Bai , Yuwen Shi , Xuanli Song , Xiaoyu Yin , Chunhong Duan , Jinglei Tang , Xian Xia , Lanzheng Liu , Bingqing Zhu","doi":"10.1016/j.meegid.2024.105684","DOIUrl":"10.1016/j.meegid.2024.105684","url":null,"abstract":"<div><div>Considering the significant role of commensal <em>Neisseria</em> carried in the pharynx on the variation of <em>N.meningitidis</em> and the acquisition of its resistance genes, understanding the true <em>Neisseria</em> population colonizing the human pharynx is of great significance. In this study, we carried out a five-month continuous survey of oropharyngeal carriage in a certain healthy population to reveal the long-term carriage status of different <em>Neisseria</em> species. Totally, 419 <em>Neisseria</em> strains were isolated from 203 out of 205 pharyngeal swabs of 49 participants. Using combined methods (MALDI-TOF-MS, <em>rplF</em> sequencing and genome sequencing), the isolates were identified as <em>N.subflava</em> (<em>n</em> = 290), <em>N.mucosa</em> (<em>n</em> = 52), <em>N.oralis</em> (<em>n</em> = 8), <em>N.elongata</em> group (<em>n</em> = 6) and non-species-confirmed (<em>n</em> = 63). <em>N.subflava</em> was isolated from all individuals and 168 swabs (81.95 %). <em>N.mucosa</em>, <em>N.oralis, N.elongata</em> and non-species-confirmed were isolated from 25 (45), 6 (7), 4 (5) and 20 (53) individuals (swabs) respectively. It was common that multiple <em>Neisseria</em> spp. or multiple clones of one species were isolated from a single sample. An identical strain could be isolated frequently from a single person within five months. These results indicate that <em>Neisseria</em> spp. and <em>N.subflava</em> are ubiquitous in human pharynx and both have diverse population; we should pay more attention to them when studying <em>N.meningitidis</em> or other respiratory pathogens; robust and handy method for identifying <em>Neisseria</em> species remains to be developed.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105684"},"PeriodicalIF":2.6,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513263","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}
Pub Date : 2024-10-20DOI: 10.1016/j.meegid.2024.105682
Sofia Carneiro , Miguel Pinto , Joana Rodrigues , João Paulo Gomes , Rita Macedo
Opportunist infections caused by nontuberculous mycobacteria (NTM) have emerged as a significant public health problem. Among these, species of the Mycobacterium avium complex (MAC) are the main responsible for the increase in the number of human disease cases. In order to address the current needs in the detection and surveillance of MAC disease cases, we evaluated different species classification methodologies (BLASTn-based marker-gene approach, Kraken v2, rMLST and MLST databases) and their congruence with a core-SNP phylogenetic approach, based on whole genome sequencing (WGS) data. For this purpose, we used a collection of 142 MAC isolates from Portuguese patients diagnosed between 2014 and 2022. The marker-gene approach (based on the rpoB, hsp65 and groEL genes), showed the best results, allowing the identification of the 142 MAC isolates to the species/subspecies level (M. avium subsp. hominissuis, M. intracellulare, M. intracellulare subsp. chimaera, M. intracellulare subsp. yongonense, M. marseillence and M. colombiense). Additionally, we performed drug susceptibility testing that confirmed clarithromycin efficacy as a first-line treatment for MAC disease, as 93 % of the Portuguese isolates were susceptible. Using a core-SNP approach we also performed an in-depth phylogenetic analysis within each identified species group, and despite the high genetic diversity within the MAC species, we were able to clearly distinguish all the species/subspecies and identify genetic clusters with epidemiological potential.
We highlight not only the need for the standardization of an appropriate genotyping approach for species identification and management of MAC disease, but also a more robust large-scale WGS data analysis, in a One Health perspective, in order to identify potential routes of transmission.
由非结核分枝杆菌（NTM）引起的机会性感染已成为一个重要的公共卫生问题。其中，非结核分枝杆菌复合体（MAC）是导致人类疾病病例增加的主要原因。为了满足当前检测和监控 MAC 疾病病例的需要，我们评估了不同的物种分类方法（基于 BLASTn 的标记基因方法、Kraken v2、rMLST 和 MLST 数据库）及其与基于全基因组测序（WGS）数据的核心-SNP 系统发生学方法的一致性。为此，我们从 2014 年至 2022 年期间确诊的葡萄牙患者中收集了 142 个 MAC 分离物。标记基因方法（基于 rpoB、hsp65 和 groEL 基因）显示出最佳结果，可将 142 个 MAC 分离物鉴定为种/亚种水平（M. avium subsp. hominissuis、M. intracellulare、M. intracellulare subsp.）此外，我们还进行了药物敏感性测试，证实克拉霉素可作为治疗 MAC 疾病的一线药物，因为 93% 的葡萄牙分离株对克拉霉素敏感。尽管 MAC 物种的遗传多样性很高，但我们仍能清楚地区分所有物种/亚种，并识别出具有流行病学潜力的基因群。我们强调，不仅需要标准化适当的基因分型方法来识别和管理 MAC 疾病，还需要从 "一体健康 "的角度进行更强大的大规模 WGS 数据分析，以确定潜在的传播途径。
{"title":"Genome-scale analysis of Mycobacterium avium complex isolates from Portugal reveals extensive genetic diversity","authors":"Sofia Carneiro , Miguel Pinto , Joana Rodrigues , João Paulo Gomes , Rita Macedo","doi":"10.1016/j.meegid.2024.105682","DOIUrl":"10.1016/j.meegid.2024.105682","url":null,"abstract":"<div><div>Opportunist infections caused by nontuberculous mycobacteria (NTM) have emerged as a significant public health problem. Among these, species of the <em>Mycobacterium avium</em> complex (MAC) are the main responsible for the increase in the number of human disease cases. In order to address the current needs in the detection and surveillance of MAC disease cases, we evaluated different species classification methodologies (BLASTn-based marker-gene approach, Kraken v2, rMLST and MLST databases) and their congruence with a core-SNP phylogenetic approach, based on whole genome sequencing (WGS) data. For this purpose, we used a collection of 142 MAC isolates from Portuguese patients diagnosed between 2014 and 2022. The marker-gene approach (based on the <em>rpoB</em>, <em>hsp65</em> and <em>groEL</em> genes), showed the best results, allowing the identification of the 142 MAC isolates to the species/subspecies level (<em>M. avium</em> subsp. <em>hominissuis, M. intracellulare, M. intracellulare</em> subsp. <em>chimaera, M. intracellulare</em> subsp. <em>yongonense, M. marseillence</em> and <em>M. colombiense</em>). Additionally, we performed drug susceptibility testing that confirmed clarithromycin efficacy as a first-line treatment for MAC disease, as 93 % of the Portuguese isolates were susceptible. Using a core-SNP approach we also performed an in-depth phylogenetic analysis within each identified species group, and despite the high genetic diversity within the MAC species, we were able to clearly distinguish all the species/subspecies and identify genetic clusters with epidemiological potential.</div><div>We highlight not only the need for the standardization of an appropriate genotyping approach for species identification and management of MAC disease, but also a more robust large-scale WGS data analysis, in a One Health perspective, in order to identify potential routes of transmission.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105682"},"PeriodicalIF":2.6,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513267","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}
Pub Date : 2024-10-20DOI: 10.1016/j.meegid.2024.105681
Josue Togo , Anou Moise Somboro , Oumar Dolo , Fatoumata Tata Traore , Ibrehima Guindo , Djeneba B. Fofana , Eve Todesco , Anne-Geneviève Marcelin , Vincent Calvez , Jane Holl , Robert Leo Murphy , Christophe Rodriguez , Mamoudou Maiga , Almoustapha Issiaka Maiga
SARS-CoV-2 geno-surveillance has been challenging in West Africa. Despite the multiple challenges encountered, particularly in West Africa during the COVID-19 pandemic, efforts were made to circumscribe the spread of the disease and to provide methods and resources for surveillance. We aim to describe the dynamic of SARS-CoV-2 variants and highlight the efforts made in genomic surveillance in West Africa. Therefore, we proceeded to retrieve West African countries' SARS-CoV-2 data from public repository (GISAID) and then ensued to a descriptive statistical analysis. From the start of the pandemic till December 2023, we found less than a million COVID-19 cases notified within the West African region. Overall, the study population was 50.21 % Males with a median age of 37. Regarding genomic data, only 3.02 % of cases were sequenced and deposited in GISAID. Of the available sequence, we noted that most of the variants have circulated in West Africa before the official notification of the variants. Nigeria, Ghana, and Senegal provided together more than half of West Africa's originating sequences when Omicron and Delta variants were the most sequenced in West Africa.
{"title":"Dynamics of SARS-CoV-2 variants in West Africa: Insights into genomic surveillance in resource-constrained settings","authors":"Josue Togo , Anou Moise Somboro , Oumar Dolo , Fatoumata Tata Traore , Ibrehima Guindo , Djeneba B. Fofana , Eve Todesco , Anne-Geneviève Marcelin , Vincent Calvez , Jane Holl , Robert Leo Murphy , Christophe Rodriguez , Mamoudou Maiga , Almoustapha Issiaka Maiga","doi":"10.1016/j.meegid.2024.105681","DOIUrl":"10.1016/j.meegid.2024.105681","url":null,"abstract":"<div><div>SARS-CoV-2 geno-surveillance has been challenging in West Africa. Despite the multiple challenges encountered, particularly in West Africa during the COVID-19 pandemic, efforts were made to circumscribe the spread of the disease and to provide methods and resources for surveillance. We aim to describe the dynamic of SARS-CoV-2 variants and highlight the efforts made in genomic surveillance in West Africa. Therefore, we proceeded to retrieve West African countries' SARS-CoV-2 data from public repository (GISAID) and then ensued to a descriptive statistical analysis. From the start of the pandemic till December 2023, we found less than a million COVID-19 cases notified within the West African region. Overall, the study population was 50.21 % Males with a median age of 37. Regarding genomic data, only 3.02 % of cases were sequenced and deposited in GISAID. Of the available sequence, we noted that most of the variants have circulated in West Africa before the official notification of the variants. Nigeria, Ghana, and Senegal provided together more than half of West Africa's originating sequences when Omicron and Delta variants were the most sequenced in West Africa.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105681"},"PeriodicalIF":2.6,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513266","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}
Pub Date : 2024-10-05DOI: 10.1016/j.meegid.2024.105680
Alejandro Barrios-Navas , Thanh Long Nguyen , Juan Esteban Gallo , Leonardo Mariño-Ramírez , José María Satizabal Soto , Adalberto Sánchez , I. King Jordan , Augusto Valderrama-Aguirre
AIDS remains a significant global health challenge since its emergence in 1981, with millions of deaths and new cases every year. The CCR5 ∆32 genetic deletion confers immunity to HIV infection by altering a cell membrane protein crucial for viral entry. Stem cell transplants from homozygous carriers of this mutation to HIV-infected individuals have resulted in viral load reduction and disease remission, suggesting a potential therapeutic avenue. This study aims to investigate the relationship between genetic ancestry and the frequency of the CCR5 ∆32 mutation in Colombian populations, exploring the feasibility of targeted donor searches based on ancestry composition. Utilizing genomic data from the CÓDIGO-Colombia consortium, comprising 532 individuals, the study assessed the presence of the CCR5 ∆32 mutation and examined if the population was on Hardy-Weinberg equilibrium. Individuals were stratified into clusters based on African, American, and European ancestry percentages, with logistic regression analysis performed to evaluate the association between ancestry and mutation frequency. Additionally, global genomic databases were utilized to visualize the worldwide distribution of the mutation. The findings revealed a significant positive association between European ancestry and the CCR5 ∆32 mutation frequency, underscoring its relevance in donor selection. African and American ancestry showed negative but non-significant associations with CCR5 ∆32 frequency, which may be attributed to the study's limitations. These results emphasize the potential importance of considering ancestry in donor selection strategies, reveal the scarcity of potential donors in Colombia, and underscore the need to consider donors from other populations with mainly European ancestry if the CCR5 ∆32 stem cell transplant becomes a routine treatment for HIV/AIDS in Colombia.
{"title":"Unveiling ancestral threads: Exploring CCR5 ∆32 mutation frequencies in Colombian populations for HIV/AIDS therapeutics","authors":"Alejandro Barrios-Navas , Thanh Long Nguyen , Juan Esteban Gallo , Leonardo Mariño-Ramírez , José María Satizabal Soto , Adalberto Sánchez , I. King Jordan , Augusto Valderrama-Aguirre","doi":"10.1016/j.meegid.2024.105680","DOIUrl":"10.1016/j.meegid.2024.105680","url":null,"abstract":"<div><div>AIDS remains a significant global health challenge since its emergence in 1981, with millions of deaths and new cases every year. The CCR5 ∆32 genetic deletion confers immunity to HIV infection by altering a cell membrane protein crucial for viral entry. Stem cell transplants from homozygous carriers of this mutation to HIV-infected individuals have resulted in viral load reduction and disease remission, suggesting a potential therapeutic avenue. This study aims to investigate the relationship between genetic ancestry and the frequency of the CCR5 ∆32 mutation in Colombian populations, exploring the feasibility of targeted donor searches based on ancestry composition. Utilizing genomic data from the CÓDIGO-Colombia consortium, comprising 532 individuals, the study assessed the presence of the CCR5 ∆32 mutation and examined if the population was on Hardy-Weinberg equilibrium. Individuals were stratified into clusters based on African, American, and European ancestry percentages, with logistic regression analysis performed to evaluate the association between ancestry and mutation frequency. Additionally, global genomic databases were utilized to visualize the worldwide distribution of the mutation. The findings revealed a significant positive association between European ancestry and the CCR5 ∆32 mutation frequency, underscoring its relevance in donor selection. African and American ancestry showed negative but non-significant associations with CCR5 ∆32 frequency, which may be attributed to the study's limitations. These results emphasize the potential importance of considering ancestry in donor selection strategies, reveal the scarcity of potential donors in Colombia, and underscore the need to consider donors from other populations with mainly European ancestry if the CCR5 ∆32 stem cell transplant becomes a routine treatment for HIV/AIDS in Colombia.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105680"},"PeriodicalIF":2.6,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395364","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}
Data on HIV drug resistance in Madagascar are rare and outdated. In this study, we assessed the prevalence of HIV drug resistance mutations to antiretrovirals (ARVs) and genetic diversity of circulating strains in treatment-naive people living with HIV (PLHIV) in Madagascar.
Materials and methods
We amplified the protease (PR), fragments of the Reverse Transcriptase (RT) and Integrase (IN) genes according to the French ANRS protocol. The amplicons were sequenced using next-generation sequencing technology on an Illumina platform (MiSeq). We determined HIV-1 subtypes through phylogenetic analysis using maximum likelihood in PhyML. Resistance interpretation was performed using the Stanford algorithm (version 9.5.1).
Results
We included 239 HIV-infected adults and children, sampled between January 2019 and November 2023, with a median age of 30 years and a mean plasma HIV viral load of 6.3 Log copies/mL. We sequenced at least one genomic fragment (PR or RT or IN) of the 239 samples, but 9 were excluded from analysis (mean depth < 10,000×). Phylogenetic analysis of 230 sequences revealed the presence of subtype C (33.91 %), A1 (11.30 %), B (11.30 %), CRF02_AG (9.56 %), subtype G (3.04 %), subtype D (0.43 %), CRF01_AE (0.43 %), and a significant proportion of unique recombinant forms (URFs) (30.30 %). The prevalence of transmitted drug resistance (TDR) was 4.95 % (10/202) among patients aged 15 years and older. When stratified by ARV class, this prevalence was 4.79 % for non-nucleoside reverse transcriptase inhibitors (NNRTIs), 0.59 % for Nucleoside Reverse Transcriptase inhibitors (NRTIs), and 0.50 % for integrase strand transfer inhibitors (INSTIs). Among children under 15 years old (n = 28), the prevalence of TDR was 14.28 % (4/28), with all mutations conferring resistance to NNRTIs. No mutation conferring resistance to protease inhibitors was found, neither in children nor in adults.
Conclusion
Our results show a low prevalence of ARV resistance mutations among adult treatment-naive PLHIV in Madagascar. In children under 15 years old, 92 % were infants under two years old, the high resistance rate is likely related to mother-to-child transmission. No resistance mutation to dolutegravir was detected. We also observed high frequencies of subtypes C, B, A1 and a high proportion of URFs, highlighting an ongoing dynamic epidemic.
{"title":"High HIV-1 genetic diversity and low prevalence of transmitted drug resistance among treatment-naive people living with HIV in Madagascar","authors":"Fetra Angelot Rakotomalala , Christelle Butel , Tahinamandranto Rasamoelina , Laetitia Serrano , Nicole Vidal , Santatriniaina Hajanirina Dauphin Randriarimanana , Luca Maharavo , Hajanirina Nathanaella Randriamananjara , Nicolas Fernandez-Nuñez , Felana Ranaivo Rabetokotany , Danielle Aurore Doll Rakoto , Eric Delaporte , Martine Peeters , François-Xavier Babin , Luc Hervé Samison , Eric Nerrienet , Ahidjo Ayouba","doi":"10.1016/j.meegid.2024.105679","DOIUrl":"10.1016/j.meegid.2024.105679","url":null,"abstract":"<div><h3>Background and objectives</h3><div>Data on HIV drug resistance in Madagascar are rare and outdated. In this study, we assessed the prevalence of HIV drug resistance mutations to antiretrovirals (ARVs) and genetic diversity of circulating strains in treatment-naive people living with HIV (PLHIV) in Madagascar.</div></div><div><h3>Materials and methods</h3><div>We amplified the protease (PR), fragments of the Reverse Transcriptase (RT) and Integrase (IN) genes according to the French ANRS protocol. The amplicons were sequenced using next-generation sequencing technology on an Illumina platform (MiSeq). We determined HIV-1 subtypes through phylogenetic analysis using maximum likelihood in PhyML. Resistance interpretation was performed using the Stanford algorithm (version 9.5.1).</div></div><div><h3>Results</h3><div>We included 239 HIV-infected adults and children, sampled between January 2019 and November 2023, with a median age of 30 years and a mean plasma HIV viral load of 6.3 Log copies/mL. We sequenced at least one genomic fragment (PR or RT or IN) of the 239 samples, but 9 were excluded from analysis (mean depth < 10,000×). Phylogenetic analysis of 230 sequences revealed the presence of subtype C (33.91 %), A1 (11.30 %), B (11.30 %), CRF02_AG (9.56 %), subtype G (3.04 %), subtype D (0.43 %), CRF01_AE (0.43 %), and a significant proportion of unique recombinant forms (URFs) (30.30 %). The prevalence of transmitted drug resistance (TDR) was 4.95 % (10/202) among patients aged 15 years and older. When stratified by ARV class, this prevalence was 4.79 % for non-nucleoside reverse transcriptase inhibitors (NNRTIs), 0.59 % for Nucleoside Reverse Transcriptase inhibitors (NRTIs), and 0.50 % for integrase strand transfer inhibitors (INSTIs). Among children under 15 years old (<em>n</em> = 28), the prevalence of TDR was 14.28 % (4/28), with all mutations conferring resistance to NNRTIs. No mutation conferring resistance to protease inhibitors was found, neither in children nor in adults.</div></div><div><h3>Conclusion</h3><div>Our results show a low prevalence of ARV resistance mutations among adult treatment-naive PLHIV in Madagascar. In children under 15 years old, 92 % were infants under two years old, the high resistance rate is likely related to mother-to-child transmission. No resistance mutation to dolutegravir was detected. We also observed high frequencies of subtypes C, B, A1 and a high proportion of URFs, highlighting an ongoing dynamic epidemic.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105679"},"PeriodicalIF":2.6,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378635","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}
Pub Date : 2024-10-01DOI: 10.1016/j.meegid.2024.105677
Alexandra V. Tóth , Péter Berta , Balázs Harrach , Krisztina Ursu , Ana Paula Jejesky de Oliveira , Fernando Vicentini , João Luiz Rossi , Tibor Papp , Győző L. Kaján
Turtles are an evolutionarily unique and morphologically distinctive order of reptiles, and many species are globally endangered. Although a high diversity of adenoviruses in scaled reptiles is well-documented, turtle adenoviruses remain largely understudied. To investigate their molecular diversity, we focused on the identification and characterisation of adenoviruses in turtle-derived organ, swab and egg samples. Since reptile circoviruses have been scarcely reported and no turtle circoviruses have been documented to date, we also screened our samples for circoviruses. Host−virus coevolution is a common feature of these viral families, so we aimed to investigate possible signs of this as well. Two screening projects were conducted: one on Brazilian samples collected from animals in their natural habitat, and the other on Hungarian pet shop samples. Nested PCR systems were used for the detection of adeno- and circoviruses and purified PCR products were Sanger sequenced. Phylogenetic trees for the viruses were reconstructed based on the adenoviral DNA polymerase and hexon genes, circoviral Rep genes, and for the turtle hosts based on mitochondrial cytochrome b amino acid sequences. During the screening, testadeno-, siadeno-, and circovirus strains were detected. The circovirus strains were classified into the genus Circovirus, exhibiting significant evolutionary divergence but forming a monophyletic clade within a group of fish circoviruses. The phylogenetic tree of turtles reflected their taxonomic relationships, showing a deep bifurcation between suborders and distinct monophyletic clades corresponding to families. A similar clustering pattern was observed among the testadenovirus strains in their phylogenetic tree. As a result, this screening of turtle samples revealed at least three new testadenoviruses, including the first sea turtle adenovirus, evidence of coevolution between testadenoviruses and their hosts, and the first turtle associated circoviruses. These findings underscore the need for further research on viruses in turtles, and more broadly in reptiles, to better understand their viral diversity and the evolutionary processes shaping host–virus interactions.
乌龟是爬行动物中进化独特、形态各异的一种，许多物种在全球濒临灭绝。虽然鳞甲爬行动物中腺病毒的多样性已得到充分证实，但龟类腺病毒在很大程度上仍未得到充分研究。为了研究其分子多样性，我们重点对龟类器官、拭子和蛋样本中的腺病毒进行了鉴定和表征。由于爬行动物圆环病毒的报道很少，而迄今为止还没有乌龟圆环病毒的记录，因此我们也对样本进行了圆环病毒筛查。宿主-病毒共同进化是这些病毒家族的共同特征，因此我们也旨在调查这方面的可能迹象。我们开展了两个筛查项目：一个是在巴西的自然栖息地采集动物样本，另一个是在匈牙利的宠物店采集样本。使用巢式 PCR 系统检测腺病毒和圆环病毒，并对纯化的 PCR 产物进行桑格测序。根据腺病毒 DNA 聚合酶和 hexon 基因、环状病毒 Rep 基因以及龟类宿主的线粒体细胞色素 b 氨基酸序列，重建了病毒的系统发生树。在筛选过程中，检测到了试腺病毒株、双腺病毒株和圆环病毒株。这些圆环病毒毒株被归入圆环病毒属，在进化过程中出现了显著的分化，但在鱼类圆环病毒群中形成了一个单系支系。龟类的系统发生树反映了它们的分类关系，显示出亚目和与科相对应的独特单系支系之间的深刻分叉。在其系统发育树中，也观察到了类似的睾丸腺病毒毒株聚类模式。因此，这次对海龟样本的筛选发现了至少三种新的试变种病毒，包括第一种海龟腺病毒、试变种病毒与其宿主共同进化的证据以及第一种与海龟相关的循环病毒。这些发现强调了进一步研究海龟病毒以及更广泛的爬行动物病毒的必要性，以便更好地了解它们的病毒多样性以及形成宿主-病毒相互作用的进化过程。
{"title":"Discovery of the first sea turtle adenovirus and turtle associated circoviruses","authors":"Alexandra V. Tóth , Péter Berta , Balázs Harrach , Krisztina Ursu , Ana Paula Jejesky de Oliveira , Fernando Vicentini , João Luiz Rossi , Tibor Papp , Győző L. Kaján","doi":"10.1016/j.meegid.2024.105677","DOIUrl":"10.1016/j.meegid.2024.105677","url":null,"abstract":"<div><div>Turtles are an evolutionarily unique and morphologically distinctive order of reptiles, and many species are globally endangered. Although a high diversity of adenoviruses in scaled reptiles is well-documented, turtle adenoviruses remain largely understudied. To investigate their molecular diversity, we focused on the identification and characterisation of adenoviruses in turtle-derived organ, swab and egg samples. Since reptile circoviruses have been scarcely reported and no turtle circoviruses have been documented to date, we also screened our samples for circoviruses. Host−virus coevolution is a common feature of these viral families, so we aimed to investigate possible signs of this as well. Two screening projects were conducted: one on Brazilian samples collected from animals in their natural habitat, and the other on Hungarian pet shop samples. Nested PCR systems were used for the detection of adeno- and circoviruses and purified PCR products were Sanger sequenced. Phylogenetic trees for the viruses were reconstructed based on the adenoviral DNA polymerase and hexon genes, circoviral Rep genes, and for the turtle hosts based on mitochondrial cytochrome <em>b</em> amino acid sequences. During the screening, testadeno-, siadeno-, and circovirus strains were detected. The circovirus strains were classified into the genus <em>Circovirus</em>, exhibiting significant evolutionary divergence but forming a monophyletic clade within a group of fish circoviruses. The phylogenetic tree of turtles reflected their taxonomic relationships, showing a deep bifurcation between suborders and distinct monophyletic clades corresponding to families. A similar clustering pattern was observed among the testadenovirus strains in their phylogenetic tree. As a result, this screening of turtle samples revealed at least three new testadenoviruses, including the first sea turtle adenovirus, evidence of coevolution between testadenoviruses and their hosts, and the first turtle associated circoviruses. These findings underscore the need for further research on viruses in turtles, and more broadly in reptiles, to better understand their viral diversity and the evolutionary processes shaping host–virus interactions.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105677"},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373606","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}
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