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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.
J Med Virol. 2022 04; 94(4):1670-1688.JM

Abstract

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.

Authors+Show Affiliations

Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh.Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh.Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh.Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh.Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh.Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh.Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh.Department of Microbiology, University of Dhaka, Dhaka, Bangladesh. Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh.Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

34939673

Citation

Rahaman, Md Mizanur, et al. "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." Journal of Medical Virology, vol. 94, no. 4, 2022, pp. 1670-1688.
Rahaman MM, Sarkar MMH, Rahman MS, et al. 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. J Med Virol. 2022;94(4):1670-1688.
Rahaman, M. M., Sarkar, M. M. H., Rahman, M. S., Islam, M. R., Islam, I., Saha, O., Akter, S., Banu, T. A., Jahan, I., Habib, M. A., Goswami, B., Bari, L., Malek, M. A., & Khan, M. S. (2022). 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. Journal of Medical Virology, 94(4), 1670-1688. https://doi.org/10.1002/jmv.27537
Rahaman MM, et al. 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. J Med Virol. 2022;94(4):1670-1688. PubMed PMID: 34939673.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 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. AU - Rahaman,Md Mizanur, AU - Sarkar,Md Murshed Hasan, AU - Rahman,M Shaminur, AU - Islam,M Rafiul, AU - Islam,Israt, AU - Saha,Otun, AU - Akter,Shahina, AU - Banu,Tanjian Akhtar, AU - Jahan,Iffat, AU - Habib,Md Ahasan, AU - Goswami,Barna, AU - Bari,Latiful, AU - Malek,Md Abdul, AU - Khan,Md Salim, Y1 - 2022/01/07/ PY - 2021/12/17/revised PY - 2021/07/15/received PY - 2021/12/20/accepted PY - 2021/12/24/pubmed PY - 2022/2/25/medline PY - 2021/12/23/entrez KW - SARS-CoV-2 KW - antimicrobial resistance gene (AMR) KW - coinfection KW - metatranscriptomics (mRNA) KW - variants SP - 1670 EP - 1688 JF - Journal of medical virology JO - J Med Virol VL - 94 IS - 4 N2 - 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. SN - 1096-9071 UR - https://www.unboundmedicine.com/medline/citation/34939673/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_ DB - PRIME DP - Unbound Medicine ER -