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Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh.
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; Shirin, Tahmina.
  • Cowley LA; Department of Biology and Biochemistry, University of Bath, Bath, UK.
  • Afrad MH; Infectious Diseases Division, International Centre for Diarrheal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh.
  • Rahman SIA; Infectious Diseases Division, International Centre for Diarrheal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh.
  • Mamun MMA; Institute for Developing Science and Health Initiatives, Dhaka, Bangladesh.
  • Chin T; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
  • Mahmud A; Department of Demography, University of California, Berkeley, CA, USA.
  • Rahman MZ; Infectious Diseases Division, International Centre for Diarrheal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh.
  • Billah MM; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh.
  • Khan MH; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh.
  • Sultana S; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh.
  • Khondaker T; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh.
  • Baker S; Department of Medicine, University of Cambridge, Cambridge, UK.
  • Banik N; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh.
  • Alam AN; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh.
  • Mannoor K; Institute for Developing Science and Health Initiatives, Dhaka, Bangladesh.
  • Banu S; Infectious Diseases Division, International Centre for Diarrheal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh.
  • Chowdhury A; Aspire to Innovate (a2i) Program, ICT Division/Cabinet Division, Government of Bangladesh/UNDP, Dhaka, Bangladesh.
  • Flora MS; Directorate General of Health Services, Mohakhali, Dhaka, Bangladesh.
  • Thomson NR; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
  • Buckee CO; London School of Hygiene and Tropical Medicine, London, UK.
  • Qadri F; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
  • Shirin T; Infectious Diseases Division, International Centre for Diarrheal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh. fqadri@icddrb.org.
Nat Microbiol ; 6(10): 1271-1278, 2021 10.
Article in English | MEDLINE | ID: covidwho-1402078
ABSTRACT
Genomics, combined with population mobility data, used to map importation and spatial spread of SARS-CoV-2 in high-income countries has enabled the implementation of local control measures. Here, to track the spread of SARS-CoV-2 lineages in Bangladesh at the national level, we analysed outbreak trajectory and variant emergence using genomics, Facebook 'Data for Good' and data from three mobile phone operators. We sequenced the complete genomes of 67 SARS-CoV-2 samples (collected by the IEDCR in Bangladesh between March and July 2020) and combined these data with 324 publicly available Global Initiative on Sharing All Influenza Data (GISAID) SARS-CoV-2 genomes from Bangladesh at that time. We found that most (85%) of the sequenced isolates were Pango lineage B.1.1.25 (58%), B.1.1 (19%) or B.1.36 (8%) in early-mid 2020. Bayesian time-scaled phylogenetic analysis predicted that SARS-CoV-2 first emerged during mid-February in Bangladesh, from abroad, with the first case of coronavirus disease 2019 (COVID-19) reported on 8 March 2020. At the end of March 2020, three discrete lineages expanded and spread clonally across Bangladesh. The shifting pattern of viral diversity in Bangladesh, combined with the mobility data, revealed that the mass migration of people from cities to rural areas at the end of March, followed by frequent travel between Dhaka (the capital of Bangladesh) and the rest of the country, disseminated three dominant viral lineages. Further analysis of an additional 85 genomes (November 2020 to April 2021) found that importation of variant of concern Beta (B.1.351) had occurred and that Beta had become dominant in Dhaka. Our interpretation that population mobility out of Dhaka, and travel from urban hotspots to rural areas, disseminated lineages in Bangladesh in the first wave continues to inform government policies to control national case numbers by limiting within-country travel.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / Cell Phone / Social Media / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: Asia Language: English Journal: Nat Microbiol Year: 2021 Document Type: Article Affiliation country: S41564-021-00955-3

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / Cell Phone / Social Media / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: Asia Language: English Journal: Nat Microbiol Year: 2021 Document Type: Article Affiliation country: S41564-021-00955-3