Genomic Surveillance of SARS-CoV-2 Viruses Collected during the Ending Phase of the First Wave of the COVID-19 Pandemic in Bangladesh

Jahan, Munira; Bhattacharjee, Arittra; Rahmat, Raad; Islam, Samprity; Akhter, Tahmina; Ahammad, Ishtiaque; Hossain, Mohammad Uzzal; Munshi, Saif Ullah; Salimullah, Md.

doi:10.1128/mra.00496-21

Cited by 2 publications

(3 citation statements)

References 13 publications

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“…Our finding is supported by reports of high anti-S protein IgG on the day of positive swab among unvaccinated COVID-19 patients in the United Kingdom having confirmed SARS-CoV-2 re-infection [39]. On this basis, we conclude that the patients with the delta variant likely have pre-existing antibodies from either the first Bangladesh pandemic wave in April to June 2020 [29][30][31][32] or the second Bangladesh pandemic wave in March 2021, which were predominantly of the SARS CoV-2 alpha or beta variants [25][26][27][28]40].…”

Section: Discussionsupporting

confidence: 88%

“…The extensive genomic surveillance of SARS CoV-2 viral isolates in Bangladesh throughout the pandemic is motivated by the urgency to identify the next strains of SARS CoV-2 carrying S-protein mutations or other genetic changes [25][26][27][28][29][30][31][32][33][34]. In the first and second pandemic waves in Bangladesh, the alpha and beta variants of the B.1.1.7 and B.1.351 lineages were associated with an Ro of approximately 1.2 [27].…”

Section: Discussionmentioning

confidence: 99%

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Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021

Ghosh

Kaiser

Molla

et al. 2021

Viruses

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Novel SARS-CoV-2 variants are emerging at an alarming rate. The delta variant and other variants of concern (VoC) carry spike (S)-protein mutations, which have the potential to evade protective immunity, to trigger break-through infections after COVID-19 vaccination, and to propagate future waves of COVID-19 pandemic. To identify SARS CoV-2 variants in Bangladesh, patients who are RT-PCR-positive for COVID-19 infections in Dhaka were screened by a RT-PCR melting curve analysis for spike protein mutations. To assess the anti-SARS CoV-2 antibody responses, the levels of the anti-S -proteins IgA and IgG and the anti-N-protein IgG were measured by ELISA. Of a total of 36 RT-PCR positive samples (75%), 27 were identified as delta variants, with one carrying an additional Q677H mutation and two with single nucleotide substitutions at position 23029 (compared to Wuhan-Hu-1 reference NC 045512) in the genome sequence. Three (8.3%) were identified as beta variants, two (5.5%) were identified as alpha variants, three (8.3%) were identified as having a B.1.1.318 lineage, and one sample was identified as an eta variant (B.1.525) carrying an additional V687L mutation. The trend of higher viral load (lower Cp values) among delta variants than in the alpha and beta variants was of borderline statistical significance (p = 0.045). Prospective studies with larger Bangladeshi cohorts are warranted to confirm the emergence of S-protein mutations and their association with antibody response in natural infection and potential breakthrough in vaccinated subjects.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021

Ghosh

Kaiser

Molla

et al. 2021

Viruses

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“…In case of first wave, several SARS-CoV-2 variants tried to increase their transmissibility through certain spike protein mutations. For example, mutations such as S:P681R/H were associated with enhanced transmission [ 79 ]. It has been reported that variants with S:D614G and S:Q675H mutations are relatively less infectious [ 80 ].…”

Section: Discussionmentioning

confidence: 99%

Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh

et al. 2021

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As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of Mid-June 2021, over 1500 SARS-CoV-2 genomesequences have been deposited in the GISAID database from Bangladesh which were extracted and categorized into two waves. By analyzing these genome sequences, it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%). Wave-2 samples also had a higher frequency of deletion, and transversion events. During the first wave, the GR clade was the most predominant but it was replaced by the GH clade in the latter wave. The B.1.1.25 variant showed the highest frequency in wave-1 while in case of wave-2, the B.1.351.3 variant, was the most common one. A notable presence of the delta variant, which is currently at the center of concern, was also observed. Comparison of the Spike protein found in the reference and the 3 most common lineages found in Bangladesh namely, B.1.1.7, B.1.351, B.1.617 in terms of their ability to form stable complexes with ACE2 receptor revealed that B.1.617 had the potential to be more transmissible than others. Importantly, no indigenous variants have been detected so far which implies that the successful prevention of import of foreign variants can diminish the outbreak in the country.

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Genomic Surveillance of SARS-CoV-2 Viruses Collected during the Ending Phase of the First Wave of the COVID-19 Pandemic in Bangladesh

Cited by 2 publications

References 13 publications

Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021

Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021

Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh

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