Whole genome sequencing and phylogenetic classification of Tunisian SARS-CoV-2 strains from patients of the Military Hospital in Tunis.
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ABSTRACT:
SUBMITTER: Handrick S
PROVIDER: S-EPMC7545018 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background & objectivesSeveral phylogenetic classification systems have been devised to trace the viral lineages of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, inconsistency in the nomenclature limits uniformity in its epidemiological understanding. This study provides an integration of existing classifications and describes evolutionary trends of the SARS-CoV-2 strains circulating in India.MethodsThe whole genomes of 330 SARS-CoV-2 samples were sequenced using next-generation sequencing (NGS). Phylogenetic and sequence analysis of a total of 3014 Indian SARS-CoV-2 sequences from 20 different States/Union Territories (January to September 2020) from the Global Initiative on Sharing All Influenza Data (GISAID) database was performed to observe the clustering of Nextstrain and Phylogenetic Assignment of Named Global Outbreak LINeages (Pangolin) lineages with the GISAID clades. The identification of mutational sites under selection pressure was performed using Mixed Effects Model of Evolution and Single-Likelihood Ancestor Counting methods available in the Datamonkey server.ResultsTemporal data of the Indian SARS-CoV-2 genomes revealed that except for Uttarakhand, West Bengal and Haryana that showed the circulation of GISAID clade O even after July 2020, the rest of the States showed a complete switch to GR/GH clades. Pangolin lineages B.1.1.8 and B.1.113 identified within GR and GH clades, respectively, were noted to be indigenous evolutions. Sites identified to be under positive selection pressure within these clades were found to occur majorly in the non-structural proteins coded by ORF1a and ORF1b.Interpretation & conclusionsThis study interpreted the geographical and temporal dominance of SARS-CoV-2 strains in India over a period of nine months based on the GISAID classification. An integration of the GISAID, Nextstrain and Pangolin classifications is also provided. The emergence of new lineages B.1.1.8 and B.1.113 was indicative of host-specific evolution of the SARS-CoV-2 strains in India. The hotspot mutations such as those driven by positive selection need to be further characterized.
| S-EPMC8184080 | biostudies-literature
Project description:The present study describes the strains of hepatitis C virus (HCV) isolated from Tunisian hemodialysis patients. Thirty-three HCV strains isolated from different dialysis centers in Tunis City were amplified by RT-PCR in a region of the NS5b gene, genotyped by sequencing, and compared to international sequences by phylogenetic analysis. The phylogenetic tree showed that 16 HCV isolates have been identified as subtype 4k (48.5%), 7 as unspecified HCV-4 subtype (21.2%), 5 as subtype 4a et 1b (each 15.2%). The analysis of this tree revealed that the HCV-1b strains were closely related to Anglo-Saxon and European isolates, while the HCV-4 isolates are genetically similar to Egyptian and African strains. Phylogenic analysis of 33 Tunisian isolates with international HCV strains on a region of the NS5b gene demonstrated that the subtype 4k submerged the Tunis city and a new subtype of HCV4 seems to be suspect in this area.
| S-EPMC3578366 | biostudies-literature
Project description:Rotaviruses (RVs) are a major etiological agent of acute viral gastroenteritis in humans and young animals, with rotavirus B (RVB) often detected in suckling and weaned pigs. Group A rotavirus classification is currently based on the two outer capsid proteins, VP7 and VP4, and the middle layer protein, VP6. Using RVB strains generated in this study and reference sequences from GenBank, pairwise identity frequency graphs and phylogenetic trees were constructed for the eleven gene segments of RVB to estimate the nucleotide identity cutoff values for different genotypes and determine the genotype diversity per gene segment. Phylogenetic analysis of VP7, VP4, VP6, VP1–VP3, and NSP1–NSP5 identified 26G, 5P, 13I, 5R, 5C, 5M, 8A, 10N, 6T, 4E, and 7H genotypes, respectively. The analysis supports the previously proposed cutoff values for the VP7, VP6, NSP1, and NSP3 gene segments (80%, 81%, 76% and 78%, respectively) and suggests new cutoff values for the VP4, VP1, VP2, VP3, NSP2, NSP4, and NSP5 (80%, 78%, 79%, 77% 83%, 76%, and 79%, respectively). Reassortment events were detected between the porcine RVB strains from our study. This research describes the genome constellations for the complete genome of Group B rotaviruses in different host species.
| S-EPMC6027208 | biostudies-literature
Project description:BackgroundIn Tunisia a first SARS-CoV-2 confirmed case was reported in March 03, 2020. Since then, an increase of cases number was observed from either imported or local cases. The aim of this preliminary study was to better understand the molecular epidemiology and genetic variability of SARS-CoV-2 viruses circulating in Tunisia and worldwide.MethodsWhole genome sequencing was performed using NGS approach on six SARS. CoV-2 highly positive samples detected during the early phase of the outbreak.ResultsFull genomes sequences of six Tunisian SARS-CoV-2 strains were obtained from imported and locally transmission cases during the COVID-19 outbreak. Reported sequences were non-identical with 0.1% nucleotide divergence rate and clustered into 6 different clades with worldwide sequences. SNPs results favor the distribution of the reported Tunisian sequences into 3 major genotypes. These SNP mutations are critical for diagnosis and vaccine development.ConclusionsThese results indicate multiple introductions of the virus in Tunisia and add new genomic data on SARS-CoV-2 at the international level.
| S-EPMC8278182 | biostudies-literature
Project description:BackgroundStaphylococcus aureus is an opportunistic pathogen and a leading cause of nosocomial infections. It can acquire resistance to all the antibiotics that entered the clinics to date, and the World Health Organization defined it as a high-priority pathogen for research and development of new antibiotics. A deeper understanding of the genetic variability of S. aureus in clinical settings would lead to a better comprehension of its pathogenic potential and improved strategies to contrast its virulence and resistance. However, the number of comprehensive studies addressing clinical cohorts of S. aureus infections by simultaneously looking at the epidemiology, phylogenetic reconstruction, genomic characterisation, and transmission pathways of infective clones is currently low, thus limiting global surveillance and epidemiological monitoring.MethodsWe applied whole-genome shotgun sequencing (WGS) to 184 S. aureus isolates from 135 patients treated in different operative units of an Italian paediatric hospital over a timespan of 3 years, including both methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) from different infection types. We typed known and unknown clones from their genomes by multilocus sequence typing (MLST), Staphylococcal Cassette Chromosome mec (SCCmec), Staphylococcal protein A gene (spa), and Panton-Valentine Leukocidin (PVL), and we inferred their whole-genome phylogeny. We explored the prevalence of virulence and antibiotic resistance genes in our cohort, and the conservation of genes encoding vaccine candidates. We also performed a timed phylogenetic investigation for a potential outbreak of a newly emerging nosocomial clone.ResultsThe phylogeny of the 135 single-patient S. aureus isolates showed a high level of diversity, including 80 different lineages, and co-presence of local, global, livestock-associated, and hypervirulent clones. Five of these clones do not have representative genomes in public databases. Variability in the epidemiology is mirrored by variability in the SCCmec cassettes, with some novel variants of the type IV cassette carrying extra antibiotic resistances. Virulence and resistance genes were unevenly distributed across different clones and infection types, with highly resistant and lowly virulent clones showing strong association with chronic diseases, and highly virulent strains only reported in acute infections. Antigens included in vaccine formulations undergoing clinical trials were conserved at different levels in our cohort, with only a few highly prevalent genes fully conserved, potentially explaining the difficulty of developing a vaccine against S. aureus. We also found a recently diverged ST1-SCCmecIV-t127 PVL- clone suspected to be hospital-specific, but time-resolved integrative phylogenetic analysis refuted this hypothesis and suggested that this quickly emerging lineage was acquired independently by patients.ConclusionsWhole genome sequencing allowed us to study the epidemiology and genomic repertoire of S. aureus in a clinical setting and provided evidence of its often underestimated complexity. Some virulence factors and clones are specific of disease types, but the variability and dispensability of many antigens considered for vaccine development together with the quickly changing epidemiology of S. aureus makes it very challenging to develop full-coverage therapies and vaccines. Expanding WGS-based surveillance of S. aureus to many more hospitals would allow the identification of specific strains representing the main burden of infection and therefore reassessing the efforts for the discovery of new treatments and clinical practices.
| S-EPMC6234625 | biostudies-literature
Project description: Not available
| EMPIAR-10493 | biostudies-other
Project description:We performed targeted genome sequencing of 11 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples collected from asymptomatic individuals. These nasopharyngeal and oropharyngeal samples were collected during the first wave of coronavirus disease 2019 (COVID-19) in Karnataka, India. Nine strains were found to be Nextstrain clade 20B (PANGO lineage B.1.1.519, GISAID clade GR), and two were identified as clade 20A (PANGO lineage B.1.619, GISAID clade G). The spike protein mutation D614G was observed across all the sequenced strains.
| S-EPMC8793731 | biostudies-literature
Project description:BackgroundDuring the SARS-CoV-2 pandemic, healthcare workers (HCWs) are exposed to infection both at work and in their communities. Determining where HCWs might have been infected is challenging based on epidemiological data alone. At Akershus University Hospital, Norway, several clusters of possible intra-hospital SARS-CoV-2 transmission were identified based on routine contact tracing. To investigate these clusters further, we added whole genome sequencing (WGS) of SARS-CoV-2 virus to routine contact tracing among HCWs and between HCWs and patients. This study illustrates both the potential power and challenges with high-resolution genotyping in outbreak settings.AimThe aim was to determine whether clusters of suspected intra-hospital SARS-CoV-2 transmission could be resolved by combining WGS of SARS-CoV-2 with contact tracing data.MethodsEpidemiological data were collected during routine contact tracing of PCR-confirmed SARS-CoV-2 positive HCWs. Possible outbreaks were identified as wards with two or more infected HCWs defined as close contacts who tested positive for SARS-CoV-2 less than three weeks apart. Viral RNA from naso-/oropharyngeal samples underwent nanopore sequencing according to the manufacturer's instructions (Oxford Nanopore Technologies) in direct compliance to the Artic Network protocol (https://artic.network/ncov-2019).ResultsFive outbreaks were suspected from contact tracing. Viral consensus sequences from 24 HCWs, two patients and seven anonymous samples were analysed. Two outbreaks were confirmed, one refuted, two remained undetermined. One new potential outbreak was discovered.ConclusionCombined with epidemiological data, nanopore WGS was a useful tool for investigating intra-hospital SARS-CoV-2 transmission. WGS helped resolve questions about possible outbreaks and guide local infection prevention and control measures.
| S-EPMC7908852 | biostudies-literature
Project description:Aim: Whole genome and peptide mutation analysis can specify effective vaccine and therapeutics against severe acute respiratory coronavirus-2 (SARS-CoV-2). Materials & methods: Whole genome similarity for Bangladeshi SARS-CoV-2 was determined using ClustalW and BLASTn. Phylogenetic analysis was conducted using neighbor-joining method. Results: 100% of isolates in Bangladesh were in the G clade. We found 99.98–100% sequence similarity among Bangladeshi isolates and isolates of England, Greece, USA, Saudi Arabia and India. Deletion of bases at 5? untranslated region and 3? untranslated region was detected. Substitution 261 (E?D) at NSP13 and 1109 (F?L) at spike (S) protein were detected. Substitution 377 (D?G) at nucleocapsid with common substitution 614 (D?G) at S were also detected. Conclusion: This study will provide baseline data for development of an effective vaccine or therapeutics against SARS-CoV-2. Graphical abstract
| S-EPMC7692877 | biostudies-literature
Project description: Not available
| S-BSST379 | biostudies-other