Genome Sequences of 23 SARS-CoV-2 Omicron-Lineage Strains from Bangladesh

Hossain, M. Pear; Manjur, Omar Hamza Bin; Hasda, Lincon; Habib, Mohammad Tanbir; Afrad, Mokibul Hassan; Khan, Manjur Hossain; Banik, Nandita; Afreen, Nawroz; Alam, Ahmed Nawsher; Ayub, Mustak Ibn; Rahman, Mohammed Ziaur; Rahman, Mustafizur; Khanam, Farhana; Thomson, Nicholas R.; Shirin, Tahmina; Qadri, Firdausi

doi:10.1128/mra.00950-22

Cited by 2 publications

(1 citation statement)

References 4 publications

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“…A several contagious variants of SARS-CoV-2 evolved globally over the time, and classified by Whole Genome Sequencing process (28). Even after mass vaccination program, a swift surge of the delta variant, later replaced by the omicron variant of SARS-CoV-2 caused a fatal increase in hospitalization (29). Furthermore, different types sub-variant of the omicron (Eris, Pirola) are identified in symptomatic subjects (30, 31).…”

Section: Introductionmentioning

confidence: 99%

Unveiling the occurrence of COVID-19 in a diverse Bangladeshi population during the pandemic

Hossain,

Mannan,

Islam

et al. 2024

Front. Public Health

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IntroductionCOVID-19 pandemic hit Bangladesh with relatively low intensity, unlike its neighbors India and European countries and USA.MethodsThe present report included data of 8,480 individuals tested for COVID-19 RT-PCR of the workers and officials from readymade garments (RMG) industry in Chandra area in Gazipur. The present data looked into the clinic-demographic factors associated with the susceptibility of the condition.ResultThe data elucidated the susceptibility of the individuals to SARS-CoV-2 based on age, gender, pre-existing health conditions, and the presence of symptoms. It was observed that individuals aged over 60 had the highest rate of COVID-19 positivity, and men exhibited a higher infection rate compared to women. Regardless of age, fever and cough were the most frequently reported symptoms. Two-thirds of the individuals included in this report appeared to be asymptomatic carriers. The prevalence of comorbidities among individuals who tested positive for COVID-19 was notably higher, and this exhibited a gender-specific pattern.DiscussionAlthough our study provides important epidemiological insights into the initial year of the pandemic among Bangladeshi populations, it can also add value for future drug and vaccine development. However, it is essential to acknowledge the limitations like - restriction of public movement, unavailability of vehicle yielding a selection bias, due to the lockdown conditions imposed owing to the pandemic and the diverse characteristics of the participants. The report emphasizes the significance of figuring out how age, gender, and underlying health conditions impact susceptibility to and transmission of COVID-19, thereby providing valuable insights for public health strategies and future research initiatives.

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Section: Introductionmentioning

confidence: 99%

Unveiling the occurrence of COVID-19 in a diverse Bangladeshi population during the pandemic

Hossain,

Mannan,

Islam

et al. 2024

Front. Public Health

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SARS-CoV-2 variant survey: Comparison of RT-PCR screening with TGS and variant distribution across two divisions of Bangladesh

Kawser,

Rahman,

Westeel

et al. 2024

PLoS ONE

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Background The widespread increase in multiple variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) since 2020 is causing significant health concerns worldwide. While whole-genome sequencing (WGS) has played a leading role in surveillance programs, many local laboratories lack the expertise and resources. Thus, we aimed to investigate the circulating SARS-CoV-2 variants and evaluate the performance of multiplexed real-time reverse transcription-PCR (RT-PCR) for screening and monitoring the emergence of new SARS-CoV-2 variants in Bangladesh. Methods A total of 600 confirmed SARS-CoV-2-positive cases were enrolled either prospectively or retrospectively from two divisions of Bangladesh. The samples were screened by variant RT-PCR targeting five mutations of the spike gene (N501Y, P681R, L452R, E484K, E484Q). A subsample of the study population was also selected for third-generation sequencing (TGS) and the results were compared to the variant RT-PCR screening. An in-depth comparison was made between the two methods in terms of congruence and cost-benefit. Result Seven variants were detected among samples, with similar distributions of the variants across both divisions. Variant RT-PCR for the targeted mutations lead to a 98.5% call rate; only nine samples failed to be determined. No association was found regarding the demographic features, clinical criteria, or routine RT-PCR Ct values across the variants. The clade diversity of the sequenced subpopulation (n = 99) exhibited similar distributions across the two study sites and other epidemiologic variables. Variant RT-PCR successfully distinguished variants of concern (VOCs) and variants of interest (VOIs); however, 8% discrepancy was observed for the closest lineages. Moreover, the variant RT-PCR represented an ideal balance of cost, time, and accuracy that outweigh their limitations. Conclusion Based on the strong agreement of variant RT-PCR with TGS, such rapid, easily accessible approaches of rapid strain typing are essential in the context of pandemic responses to guide both treatment decisions and public health measures.

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Genome Sequences of 23 SARS-CoV-2 Omicron-Lineage Strains from Bangladesh

Cited by 2 publications

References 4 publications

Unveiling the occurrence of COVID-19 in a diverse Bangladeshi population during the pandemic

Unveiling the occurrence of COVID-19 in a diverse Bangladeshi population during the pandemic

SARS-CoV-2 variant survey: Comparison of RT-PCR screening with TGS and variant distribution across two divisions of Bangladesh

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