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Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh.
Islam, Ariful; Sayeed, Md Abu; Rahman, Md Kaisar; Zamil, Shafayat; Abedin, Josefina; Saha, Otun; Hassan, Mohammad Mahmudul.
  • Islam A; EcoHealth Alliance, New York, NY 10018, USA; Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Geelong Campus, VIC 3216, Australia. Electronic address: arif@ecohealthalliance.org.
  • Sayeed MA; EcoHealth Alliance, New York, NY 10018, USA; Department of Medicine, Jhenaidah Government Veterinary College, Jhenaidah 7300, Bangladesh; Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka 1212, Bangladesh.
  • Rahman MK; EcoHealth Alliance, New York, NY 10018, USA; Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka 1212, Bangladesh.
  • Zamil S; Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Zakir Hossain Road, Khulshi, Chattogram 4225, Bangladesh.
  • Abedin J; EcoHealth Alliance, New York, NY 10018, USA; Institute of Epidemiology, Disease Control and Research (IEDCR), Mohakhali, Dhaka 1212, Bangladesh.
  • Saha O; Department of Microbiology, University of Dhaka, Dhaka 1207, Bangladesh.
  • Hassan MM; Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Zakir Hossain Road, Khulshi, Chattogram 4225, Bangladesh.
Infect Genet Evol ; 92: 104884, 2021 08.
Article in English | MEDLINE | ID: covidwho-1208478
ABSTRACT
Epidemiological and molecular characterization of SARS-CoV-2 is essential for identifying the source of the virus and for effective control of the spread of local strains. We estimated case fatality rate, cumulative recovery number, basic reproduction number (R0) and future incidence of COVID-19 in Bangladesh. We illustrated the spatial distribution of cases throughout the country. We performed phylogenetic and mutation analysis of SARS-CoV-2 sequences from Bangladesh. As of July 31, 2020, Bangladesh had a case fatality rate of 1.32%. The cases were initially clustered in Dhaka and its surrounding districts in March but spreads throughout the country over time. The R0 calculated as 1.173 in Exponential Growth method. For the projection, a 20% change in R0 with subsequent infection trend has been calculated. The genomic analysis of 292 Bangladeshi SARS-CoV-2 strains suggests diverse genomic clades L, O, S, G, GH, where predominant circulating clade was GR (83.9%; 245/292). The GR clades' phylogenetic analysis revealed distinct clusters (I to XIII) with intra-clade variations. The mutation analysis revealed 1634 mutations where 94.6% and 5.4% were non-synonymous and unique mutation, respectively. The Spike, Nucleocapsid, NSP2, and RdRP showed substantially high mutation but no mutation was recorded in NSP9 and NSP11 protein. In spike (S) protein, 355 predominant mutations were recorded, highest in D614G. Alternatively, I120F in NSP2 protein, R203K and G204R in nucleocapsid protein, and P323L in RdRp were more recurrent. The Bangladeshi genomes belonged to phylogenetic lineages A, B, B.1, B.1.1, B.1.1.23, B.1.1.25, B.1.113, and B.1.36, among which 50.0% sequences owned by the pangolin lineage B.1.1.25. The study illustrates the spatial distribution of SARS-CoV-2, and molecular epidemiology of Bangladeshi isolates. We recommend continuous monitoring of R0 and genomic surveillance to understand the transmission dynamics and detect new variants of SARS-CoV-2 for proper control of the current pandemic and evaluate the effectiveness of vaccination globally.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Genetic Variation / SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Adolescent / Adult / Child / Child, preschool / Female / Humans / Infant / Male / Middle aged / Young adult Country/Region as subject: Asia Language: English Journal: Infect Genet Evol Journal subject: Biology / Communicable Diseases / Genetics Year: 2021 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Genetic Variation / SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Adolescent / Adult / Child / Child, preschool / Female / Humans / Infant / Male / Middle aged / Young adult Country/Region as subject: Asia Language: English Journal: Infect Genet Evol Journal subject: Biology / Communicable Diseases / Genetics Year: 2021 Document Type: Article