Genomic analysis of SARS-CoV-2 variants of concern identified from the ChAdOx1 nCoV-19 immunized patients from Southwest part of Bangladesh

Hassan M. Al-Emran; Md. Shazid Hasan; Md. Ali Ahasan Setu; M. Shaminur Rahman; ASM Rubayet Ul Alam; Shovon Lal Sarkar; Md. Tanvir Islam; Mir Raihanul Islam; Mohammad Mahfuzur Rahman; Ovinu Kibria Islam; Iqbal Kabir Jahid; M. Anwar Hossain

Journal of Infection and Public Health (Feb 2022)

Genomic analysis of SARS-CoV-2 variants of concern identified from the ChAdOx1 nCoV-19 immunized patients from Southwest part of Bangladesh

Hassan M. Al-Emran,
Md. Shazid Hasan,
Md. Ali Ahasan Setu,
M. Shaminur Rahman,
ASM Rubayet Ul Alam,
Shovon Lal Sarkar,
Md. Tanvir Islam,
Mir Raihanul Islam,
Mohammad Mahfuzur Rahman,
Ovinu Kibria Islam,
Iqbal Kabir Jahid,
M. Anwar Hossain

Affiliations

Hassan M. Al-Emran: Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh
Md. Shazid Hasan: Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
Md. Ali Ahasan Setu: Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh
M. Shaminur Rahman: Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
ASM Rubayet Ul Alam: Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
Shovon Lal Sarkar: Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
Md. Tanvir Islam: Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
Mir Raihanul Islam: Poverty, Health, and Nutrition Division, International Food Policy Research Institute, Dhaka, Bangladesh
Mohammad Mahfuzur Rahman: Department of Environmental Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
Ovinu Kibria Islam: Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
Iqbal Kabir Jahid: Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Corresponding authors at: Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh.
M. Anwar Hossain: Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh; Vice-Chancellor, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Corresponding authors at: Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh.

Journal volume & issue: Vol. 15, no. 2
pp. 156 – 163

Abstract

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Background: Bangladesh introduced ChAdOx1 nCoV-19 since February, 2021 and in six months, only a small population (12.8%) received either one or two dose of vaccination like other low-income countries. The COVID-19 infections were continued to roll all over the places although the information on genomic variations of SARS-CoV-2 between both immunized and unimmunized group was unavailable. The objective of this study was to compare the proportion of immune escaping variants between those groups. Methods: A total of 4718 nasopharygeal samples were collected from March 1 until April 15, 2021, of which, 834 (18%) were SARS-CoV-2 positive. The minimum sample size was calculated as 108 who were randomly selected for telephone interview and provided consent. The prevalence of SARS-CoV-2 variants and disease severity among both immunized and unimmunized groups was measured. A total of 63 spike protein sequences and 14 whole-genome sequences were performed from both groups and phylogenetic reconstruction and mutation analysis were compared. Results: A total of 40 respondents (37%, N = 108) received single-dose and 2 (2%) received both doses of ChAdOx1 nCoV-19 vaccine, which significantly reduce dry cough, loss of appetite and difficulties in breathing compared to none. There was no significant difference in hospitalization, duration of hospitalization or reduction of other symptoms like running nose, muscle pain, shortness of breathing or generalized weakness between immunized and unimmunized groups. Spike protein sequence assumed 21 (87.5%) B.1.351, one B.1.526 and two 20B variants in immunized group compared to 27 (69%) B.1.351, 5 (13%) B.1.1.7, 4 (10%) 20B, 2 B.1.526 and one B.1.427 variant in unimmunized group. Whole genome sequence analysis of 14 cases identified seven B.1.351 Beta V2, three B.1.1.7 Alpha V1, one B.1.526 Eta and the rest three 20B variants. Conclusion: Our study observed that ChAdOx1 could not prevent the new infection or severe COVID-19 disease outcome with single dose while the infections were mostly caused by B.1.351 variants in Bangladesh.

Published in Journal of Infection and Public Health

ISSN: 1876-0341 (Print); 1876-035X (Online)
Publisher: Elsevier
Country of publisher: United Kingdom
LCC subjects: Medicine: Internal medicine: Infectious and parasitic diseases; Medicine: Public aspects of medicine
Website: https://www.journals.elsevier.com/journal-of-infection-and-public-health

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