Genomic characterization of the dominating Beta, V2 variant carrying vaccinated (Oxford-AstraZeneca) and nonvaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole-genome approach.
Adolescent
Adult
Aged
Bacteria
/ classification
Bacterial Infections
/ epidemiology
Bangladesh
/ epidemiology
COVID-19
/ epidemiology
ChAdOx1 nCoV-19
/ administration & dosage
Coinfection
/ epidemiology
Drug Resistance, Bacterial
/ genetics
Female
Genome, Bacterial
/ genetics
Genome, Viral
/ genetics
Humans
Male
Metagenomics
Microbiota
/ genetics
Middle Aged
Mutation
Phylogeny
SARS-CoV-2
/ classification
Selection, Genetic
Vaccination
Viral Proteins
/ genetics
Young Adult
SARS-CoV-2
antimicrobial resistance gene (AMR)
coinfection
metatranscriptomics (mRNA)
variants
Journal
Journal of medical virology
ISSN: 1096-9071
Titre abrégé: J Med Virol
Pays: United States
ID NLM: 7705876
Informations de publication
Date de publication:
04 2022
04 2022
Historique:
revised:
17
12
2021
received:
15
07
2021
accepted:
20
12
2021
pubmed:
24
12
2021
medline:
25
2
2022
entrez:
23
12
2021
Statut:
ppublish
Résumé
Bangladesh is experiencing a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approaches. Screening for SARS-CoV-2 by reverse transcriptase polymerase chain reaction and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated = 10, nonvaccinated = 7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the coinfected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta, V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthily, the receptor binding domain (RBD) region of S protein of all the isolates harbored similar substitutions including K417N, E484K, and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F, and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS = 0.621). Furthermore, we found different bacterial coinfections like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoniae, and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and nonvaccinated patients in Bangladesh.
Substances chimiques
Viral Proteins
0
ChAdOx1 nCoV-19
B5S3K2V0G8
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1670-1688Informations de copyright
© 2021 Wiley Periodicals LLC.
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