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

Al-Emran, H. M.; Hasan, M. S.; Setu, M. A. A.; Rahman, M. S.; Alam, A. R. U.; Sarkar, S. L.; Islam, M. T.; Islam, M. R.; Rahman, M. M.; Islam, M. A.; Jahid, I. K.; Hossain, M. A.

Introduction Bangladesh introduced ChAdOx1 nCoV-19 since February, 2021 and in six months, only a small population (3.5%) received their first dose of vaccination like other low-income countries. The remaining populations are struggling with increased rate of infection due to beta and delta variants. Although this uncontrolled COVID-19 pandemic did not leave even the immunized group because of immune escaping capacity of those new variants. Methods A total of 4718 nasopharygeal samples were collected from 1st March until 15th April, 2021, of which, 834 (18%) were SARS-CoV-2 positive. Randomly generated 135 positive cases were selected for telephone interview and 108 were available and provided consent. The prevalence of SARS-CoV-2 variants and disease severity among both immunized and unimmunized group was measured. A total of 63 spike protein sequence 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 group. 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. Those variants were further confirmed by 14 whole genome sequence analysis. Complete genome analysis included seven B.1.351 Beta V2, three B.1.1.7 Alpha V1, one B.1.526 Eta and rest three 20B variant. Conclusion Single dose of ChAdOx1 could not prevent the new infection or disease severity by the COVID-19 variants of concern, B.1.351, in Bangladesh.