ideSHi’s SARS-CoV-2 Genomic Surveillance Report

The COVID-19 pandemic in Bangladesh is part of the global coronavirus disease pandemic which is caused by SARS-CoV-2. The virus was first identified in Bangladesh on March 8, 2020. Since then, it has spread over the whole country, with the number of infections rising steadily. As the most impacted country in South Asia after India, Bangladesh has been hit by four waves of COVID-19 thus far, with the omicron epidemic being the most recent.

Pattern of COVID-19 Variants at ideSHi

ideSHi is part of a nationwide genomic surveillance project of SARS-CoV-2 variants in collaboration with IEDCR and icddr,b. We use Oxford Nanopore Technology-based MinION sequencing facilities to track down the trend of variant circulation. The graph illustrates the sequencing summary from April 2021 to February 2022. In April 2021, the beta variant (B.1.351) was found all around Bangladesh. However, from May 2021 to December 2021, several sub-lineages of the delta variant (B.1.617.2) were predominant. Finally, omicron arrived in Dhaka in 6 December, 2021 and has become the most common variant within a short period of time.

ideSHi was the first to detect the omicron variant in Bangladesh. The initial omicron cases were carried by two passengers returning from Zimbabwe. Omicron's BA.2 sub-lineage is currently circulating across the country.

Our latest findings are published in reputed journals like Nature, American Society of Microbiology (ASM) etc. Selected publications are listed:

  1. Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh. Lauren A Cowley, Mokibul Hassan Afrad, Sadia Isfat Ara Rahman, Md Mahfuz Al Mamun, Taylor Chin, Ayesha Mahmud, Mohammed Ziaur Rahman, Mallick Masum Billah, Manjur Hossain Khan, Sharmin Sultana, Tilovatul Khondaker, Stephen Baker, Nandita Banik, Ahmed Nawsher Alam, Kaiissar Mannoor, Sayera Banu, Anir Chowdhury, Meerjady Sabrina Flora, Nicholas R Thomson, Caroline O Buckee, Firdausi Qadri, Tahmina Shirin Nature microbiology.
  2. Genome sequences of 15 SARS-CoV-2 sublineage B. 1.617. 2 strains in Bangladesh Mokibul Hassan Afrad, Manjur Hossain Khan, Sadia Isfat Ara Rahman, Omar Hamza Bin Manjur, Mohabbat Hossain, Ahmed Nawsher Alam, Farzana Islam Khan, Nawroz Afreen, Farsim Tarannum Haque, Nicholas R Thomson, Tahmina Shirin, Firdausi Qadri Microbiology Resource Announcements.
  1. Genome Sequences of 25 SARS-CoV-2 Sublineage B.1.1.529 Omicron Strains in Bangladesh. Omar Hamza Bin Manjur, Mokibul Hassan Afrad, Manjur Hossain Khan, Mohabbat Hossain, Zannat Kawser, Ahmed Nawsher Alam, Nandita Banik, Saruar Alam, Mallick Masum Billah, Nawroz Afreen, Farhana Khanam, Taufiqur Rahman Bhuiyan, Mohammed Ziaur Rahman, Emilie Westeel, Jean-Luc Berland, Florence Pradel, Sayera Banu, Mustafizur Rahman, Nicholas R. Thompson, Firdausi Qadri, Tahmina Shirin Microbiology Resource Announcements.