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

Author

Kawser, Zannat, Rahman, Saikt, Westeel, Emilie, Habib, Mohammad Tanbir, Hossain, Mohabbat, Bulbul, Md. Rakibul Hassan, Mukta, Sharmin Aktar, Islam, Md. Zahirul, Hossain, Md. Zakir, Afrad, Mokibul Hassan, Khan, Manjur Hossain, Shirin, Tahmina, Ahmed, Md. Shakeel, Berland, Jean-Luc, Komurian-Pradel, Florence, and Qadri, Firdausi

Subjects
SARS-CoV-2, WHOLE genome sequencing, REVERSE transcriptase polymerase chain reaction, GENETIC mutation
Abstract

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. [ABSTRACT FROM AUTHOR]

Published
2024
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3. Coding-complete genomes of 18 SARS-CoV-2 Omicron JN.1, JN.1.4, and JN.1.11 sub-lineages in Bangladesh

Author

Tahsin, Anika, primary, Hasan, Mahin, additional, Rahman, Saikt, additional, Jubair, Mohammad, additional, Afrad, Mokibul Hassan, additional, Khan, Manjur Hossain, additional, Alam, Md Shaheen, additional, Begum, Mst Noorjahan, additional, Karim, Md Yeasir, additional, Mukta, Sharmin Aktar, additional, Habib, Mohammad Tanbir, additional, Alam, Ahmed Nawsher, additional, Chowdhury, Emran Kabir, additional, Rahman, Md Rofiqur, additional, Ryan, Edward T., additional, Shirin, Tahmina, additional, Rahman, Mustafizur, additional, and Qadri, Firdausi, additional

Published
2024
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4. Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh

Author

Cowley, Lauren A., Afrad, Mokibul Hassan, Rahman, Sadia Isfat Ara, Mamun, Md Mahfuz Al, Chin, Taylor, Mahmud, Ayesha, Rahman, Mohammed Ziaur, Billah, Mallick Masum, Khan, Manjur Hossain, Sultana, Sharmin, Khondaker, Tilovatul, Baker, Stephen, Banik, Nandita, Alam, Ahmed Nawsher, Mannoor, Kaiissar, Banu, Sayera, Chowdhury, Anir, Flora, Meerjady Sabrina, Thomson, Nicholas R., Buckee, Caroline O., Qadri, Firdausi, and Shirin, Tahmina

Published
2021
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5. Comprehensive Analysis of SARS-CoV-2 Dynamics in Bangladesh: Infection Trends and Variants (2020–2023).

Author

Begum, Mst. Noorjahan, Tony, Selim Reza, Jubair, Mohammad, Alam, Md. Shaheen, Karim, Yeasir, Patwary, Mohammad Hridoy, Rahman, Sezanur, Habib, Mohammad Tanbir, Ahmed, Anisuddin, Hossain, Mohammad Enayet, Rahman, Mohammed Ziaur, Khan, Manjur Hossain, Shirin, Tahmina, Qadri, Firdausi, and Rahman, Mustafizur

Subjects
COVID-19, SARS-CoV-2, WHOLE genome sequencing, COVID-19 pandemic, SARS-CoV-2 Omicron variant
Abstract

The first case of COVID-19 was detected in Bangladesh on 8 March 2020. Since then, the Government of Bangladesh (GoB) has implemented various measures to limit the transmission of COVID-19, including widespread testing facilities across the nation through a laboratory network for COVID-19 molecular testing. This study aimed to analyze the dynamics of SARS-CoV-2 in Bangladesh by conducting COVID-19 testing and genomic surveillance of the virus variants throughout the pandemic. Nasopharyngeal swabs were collected from authorized GoB collection centers between April 2020 and June 2023. The viral RNA was extracted and subjected to real-time PCR analysis in icddr,b's Virology laboratory. A subset of positive samples underwent whole-genome sequencing to track the evolutionary footprint of SARS-CoV-2 variants. We tested 149,270 suspected COVID-19 cases from Dhaka (n = 81,782) and other districts (n = 67,488). Of these, 63% were male. The highest positivity rate, 27%, was found in the >60 years age group, followed by 26%, 51–60 years, 25% in 41–50 years, and the lowest, 9% in under five children. Notably, the sequencing of 2742 SARS-CoV-2 genomes displayed a pattern of globally circulating variants, Alpha, Beta, Delta, and Omicron, successively replacing each other over time and causing peaks of COVID-19 infection. Regarding the risk of SARS-CoV-2 infection, it was observed that the positivity rate increased with age compared to the under-5 age group in 2020 and 2021. However, these trends did not remain consistent in 2022, where older age groups, particularly those over 60, had a lower positivity rate compared to other age groups due to vaccination. The study findings generated data on the real-time circulation of different SARS-CoV-2 variants and the upsurge of COVID-19 cases in Bangladesh, which impacted identifying hotspots and restricting the virus from further transmission. Even though there is currently a low circulation of SARS-CoV-2 in Bangladesh, similar approaches of genomic surveillance remain essential for monitoring the emergence of new SARS-CoV-2 variants or other potential pathogens that could lead to future pandemics. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Antibody responses after COVID-19 infection in patients who are mildly symptomatic or asymptomatic in Bangladesh

Author

Shirin, Tahmina, Bhuiyan, Taufiqur Rahman, Charles, Richelle C., Amin, Shaheena, Bhuiyan, Imran, Kawser, Zannat, Rahat, Asifuzaman, Alam, Ahmed Nawsher, Sultana, Sharmin, Aleem, Md Abdul, Khan, Manjur Hossain, Khan, Samsad Rabbani, LaRocque, Regina C., Calderwood, Stephen B., Ryan, Edward T., Slater, Damien M., Banu, Sayera, Clemens, John, Harris, Jason B., Flora, Meerjady Sabrina, and Qadri, Firdausi

Published
2020
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7. Coding-complete genomes of XBB.1.16, XBB.2.3, FL.4 (alias of XBB.1.9.1.4), and XBB.3 of SARS-CoV-2 Omicron isolated from Bangladesh

Author

Rahman, Saikt, primary, Habib, Mohammad Tanbir, additional, Afrad, Mokibul Hassan, additional, Hasan, Mahin, additional, Tahsin, Anika, additional, Jubair, Mohammad, additional, Khan, Manjur Hossain, additional, Alam, Ahmed Nawsher, additional, Chowdhury, Emran Kabir, additional, Rahman, Mustafizur, additional, Ryan, Edward Thomas, additional, Shirin, Tahmina, additional, and Qadri, Firdausi, additional

Published
2023
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8. Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh

Author

Habib, Mohammad Tanbir, primary, Rahman, Saikt, additional, Afrad, Mokibul Hassan, additional, Howlader, Arif Mahmud, additional, Khan, Manjur Hossain, additional, Khanam, Farhana, additional, Alam, Ahmed Nawsher, additional, Chowdhury, Emran Kabir, additional, Rahman, Ziaur, additional, Rahman, Mustafizur, additional, Shirin, Tahmina, additional, and Qadri, Firdausi, additional

Published
2023
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9. Oral cholera vaccine coverage evaluation survey: Forcibly Displaced Myanmar Nationals and host community in Cox's Bazar, Bangladesh

Author

Qayum, Md. Omar, primary, Billah, Mallick Masum, additional, Sarker, Mohammad Ferdous Rahman, additional, Alamgir, A. S. M., additional, Nurunnahar, Mehejabin, additional, Khan, Manjur Hossain, additional, Salim Uzzaman, M., additional, Henderson, Alden, additional, Shirin, Tahmina, additional, and Flora, Meerjady Sabrina, additional

Published
2023
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12. Genome Sequences of 23 SARS-CoV-2 Omicron-Lineage Strains from Bangladesh

Author

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

Published
2023
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13. Seroprevalence of SARS-CoV-2 antibodies among Forcibly Displaced Myanmar Nationals in Cox’s Bazar, Bangladesh 2020: a population-based cross-sectional study

Author

Rahman, Mahbubur, primary, Khan, Samsad Rabbani, additional, Alamgir, A S M, additional, Kennedy, David S, additional, Hakim, Ferdous, additional, Evers, Egmond Samir, additional, Afreen, Nawroz, additional, Alam, Ahmed Nawsher, additional, Islam, Md Sahidul, additional, Paul, Debashish, additional, Bhuiyan, Rijwan, additional, Islam, Raisul, additional, Moureen, Adneen, additional, Salimuzzaman, M, additional, Billah, Mallick Masum, additional, Sharif, Ahmed Raihan, additional, Akter, Mst Khaleda, additional, Sultana, Sharmin, additional, Khan, Manjur Hossain, additional, von Harbou, Kai, additional, Zaman, Mohammad Mostafa, additional, Shirin, Tahmina, additional, and Flora, Meerjady Sabrina, additional

Published
2022
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15. The 2022 dengue outbreak in Bangladesh: hypotheses for the late resurgence of cases and fatalities

Author

Haider, Najmul, Hasan, Mohammad Nayeem, Khalil, Ibrahim, Tonge, Daniel, Hegde, Shivanand, Chowdhury, Muhammad Abdul Baker, Rahman, Mahbubur, Khan, Manjur Hossain, Ansumana, Rashid, Zumla, Alimuddin, and Uddin, Md Jamal

Abstract

Bangladesh reported the highest number of annual deaths (n= 281) related to dengue virus infection in 2022 since the virus reappeared in the country in 2000. Earlier studies showed that >92% of the annual cases occurred between the months of August and September. The 2022 outbreak is characterized by late onset of dengue cases with unusually higher deaths in colder months, that is, October–December. Here we present possible hypotheses and explanations for this late resurgence of dengue cases. First, in 2022, the rainfall started late in the season. Compared to the monthly average rainfall for September and October between 2003 and 2021, there was 137 mm of additional monthly rainfall recorded in September and October 2022. Furthermore, the year 2022 was relatively warmer with a 0.71°C increased temperature than the mean annual temperature of the past 20 yr. Second, a new dengue virus serotype, DENV-4, had recently reintroduced/reappeared in 2022 and become the dominant serotype in the country for a large naïve population. Third, the post-pandemic return of normalcy after 2 yr of nonpharmaceutical social measures facilitates extra mosquito breeding habitats, especially in construction sites. Community engagement and regular monitoring and destruction of Aedes mosquitoes’ habitats should be prioritized to control dengue virus outbreaks in Bangladesh.

Published
2023
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16. Genome Sequences of 25 SARS-CoV-2 Sublineage B.1.1.529 Omicron Strains in Bangladesh

Author

Bin Manjur, Omar Hamza, primary, Afrad, Mokibul Hassan, additional, Khan, Manjur Hossain, additional, Hossain, Mohabbat, additional, Kawser, Zannat, additional, Alam, Ahmed Nawsher, additional, Banik, Nandita, additional, Alam, Saruar, additional, Billah, Mallick Masum, additional, Afreen, Nawroz, additional, Khanam, Farhana, additional, Bhuiyan, Taufiqur Rahman, additional, Rahman, Mohammed Ziaur, additional, Westeel, Emilie, additional, Berland, Jean-Luc, additional, Komurian-Pradel, Florence, additional, Banu, Sayera, additional, Rahman, Mustafizur, additional, Thompson, Nicholas R., additional, Qadri, Firdausi, additional, and Shirin, Tahmina, additional

Published
2022
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17. Genome Sequences of 15 SARS-CoV-2 Sublineage B.1.617.2 Strains in Bangladesh

Author

Afrad, Mokibul Hassan, primary, Khan, Manjur Hossain, additional, Rahman, Sadia Isfat Ara, additional, Bin Manjur, Omar Hamza, additional, Hossain, Mohabbat, additional, Alam, Ahmed Nawsher, additional, Khan, Farzana Islam, additional, Afreen, Nawroz, additional, Haque, Farsim Tarannum, additional, Thomson, Nicholas R., additional, Shirin, Tahmina, additional, and Qadri, Firdausi, additional

Published
2021
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19. Genomic and mobility data reveal mass population movement as a driver of SARS-CoV-2 dissemination and diversity in Bangladesh

Author

Cowley, Lauren A., primary, Afrad, Mokibul Hassan, additional, Rahman, Sadia Isfat Ara, additional, Mahfuz-Al-Mamun, Md., additional, Chin, Taylor, additional, Mahmud, Ayesha, additional, Rahman, Mohammed Ziaur, additional, Billah, Mallick Masum, additional, Khan, Manjur Hossain, additional, Sultana, Sharmin, additional, Khondaker, Tilovatul, additional, Baker, Stephen, additional, Banik, Nandita, additional, Alam, Ahmed Nawsher, additional, Mannor, Kaiissar, additional, Banu, Sayera, additional, Chowdhury, Anir, additional, Flora, Meerjady Sabrina, additional, Thomson, Nicholas R., additional, Buckee, Caroline O., additional, Qadri, Firdausi, additional, and Shirin, Tahmina, additional

Published
2021
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20. Antibody Responses after COVID-19 Infection in Patients Who Are Mildly Symptomatic or Asymptomatic in Bangladesh

Author

Shirin, Tahmina, primary, Bhuiyan, Taufiqur R., additional, Charles, Richelle C., additional, Amin, Shaheena, additional, Bhuiyan, Imran, additional, Kawser, Zannat, additional, Rahat, Asifuzaman, additional, Alam, Ahmed Nawsher, additional, Sultana, Sharmin, additional, Aleem, Md Abdul, additional, Khan, Manjur Hossain, additional, Khan, Samsad Rabbani, additional, LaRocque, Regina C., additional, Calderwood, Stephen B., additional, Ryan, Edward T., additional, Slater, Damien M., additional, Banu, Sayera, additional, Clemens, John D., additional, Harris, Jason B., additional, Flora, Meerjady Sabrina, additional, and Qadri, Firdausi, additional

Published
2020
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