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Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally.
Islam, Ariful; Sayeed, Md Abu; Kalam, Md Abul; Ferdous, Jinnat; Rahman, Md Kaisar; Abedin, Josefina; Islam, Shariful; Shano, Shahanaj; Saha, Otun; Shirin, Tahmina; Hassan, Mohammad Mahmudul.
  • Islam A; EcoHealth Alliance, New York, NY 10001-2320, USA.
  • Sayeed MA; Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, VIC 3216, Australia.
  • Kalam MA; EcoHealth Alliance, New York, NY 10001-2320, USA.
  • Ferdous J; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh.
  • Rahman MK; Helen Keller International, Dhaka 1212, Bangladesh.
  • Abedin J; EcoHealth Alliance, New York, NY 10001-2320, USA.
  • Islam S; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh.
  • Shano S; EcoHealth Alliance, New York, NY 10001-2320, USA.
  • Saha O; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh.
  • Shirin T; EcoHealth Alliance, New York, NY 10001-2320, USA.
  • Hassan MM; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh.
Microorganisms ; 9(8)2021 Aug 10.
Article in English | MEDLINE | ID: covidwho-1348673
ABSTRACT
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swamped the global environment greatly in the current pandemic. Wastewater-based epidemiology (WBE) effectively forecasts the surge of COVID-19 cases in humans in a particular region. To understand the genomic characteristics/footprints and diversity of SARS-CoV-2 in the environment, we analyzed 807 SARS-CoV-2 sequences from 20 countries deposited in GISAID till 22 May 2021. The highest number of sequences (n = 638) were reported in Austria, followed by the Netherlands, China, and Bangladesh. Wastewater samples were highest (40.0%) to successfully yield the virus genome followed by a 24 h composite wastewater sample (32.6%) and sewage (18.5%). Phylogenetic analysis revealed that SARS-CoV-2 environmental strains are a close congener with the strains mostly circulating in the human population from the same region. Clade GRY (32.7%), G (29.2%), GR (25.3%), O (7.2%), GH (3.4%), GV (1.4%), S (0.5%), and L (0.4%) were found in environmental samples. Various lineages were identified in environmental samples; nevertheless, the highest percentages (49.4%) of the alpha variant (B.1.1.7) were detected in Austria, Liechtenstein, Slovenia, Czech Republic, Switzerland, Germany, and Italy. Other prevalent lineages were B.1 (18.2%), B.1.1 (9.2%), and B.1.160 (3.9%). Furthermore, a significant number of amino acid substitutions were found in environmental strains where the D614G was found in 83.8% of the sequences. However, the key mutations-N501Y (44.6%), S982A (44.4%), A570D (43.3%), T716I (40.4%), and P681H (40.1%) were also recorded in spike protein. The identification of the environmental belvedere of SARS-CoV-2 and its genetic signature is crucial to detect outbreaks, forecast pandemic harshness, and prepare with the appropriate tools to control any impending pandemic. We recommend genomic environmental surveillance to trace the emerging variants and diversity of SARS-CoV-2 viruses circulating in the community. Additionally, proper disposal and treatment of wastewater, sewage, and medical wastes are important to prevent environmental contamination.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Observational study Topics: Variants Language: English Year: 2021 Document Type: Article Affiliation country: Microorganisms9081696

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Observational study Topics: Variants Language: English Year: 2021 Document Type: Article Affiliation country: Microorganisms9081696