Openly accessible

Molecular epidemiology of sars-cov-2 in diverse environmental samples globally

Islam, Ariful, Sayeed, MA, Kalam, MA, Ferdous, J, Rahman, MK, Abedin, J, Islam, S, Shano, S, Saha, O, Shirin, T and Hassan, MM 2021, Molecular epidemiology of sars-cov-2 in diverse environmental samples globally, Microorganisms, vol. 9, no. 8, pp. 1-15, doi: 10.3390/microorganisms9081696.

Attached Files
Name Description MIMEType Size Downloads

Title Molecular epidemiology of sars-cov-2 in diverse environmental samples globally
Author(s) Islam, ArifulORCID iD for Islam, Ariful orcid.org/0000-0002-9210-3351
Sayeed, MA
Kalam, MA
Ferdous, J
Rahman, MK
Abedin, J
Islam, S
Shano, S
Saha, O
Shirin, T
Hassan, MM
Journal name Microorganisms
Volume number 9
Issue number 8
Article ID 1696
Start page 1
End page 15
Total pages 15
Publisher MDPI AG
Place of publication Basel, Switzerland
Publication date 2021
ISSN 2076-2607
2076-2607
Keyword(s) alpha variant
COVID-19
mutation
phylogenetic analysis
sewage
Summary 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.
Language eng
DOI 10.3390/microorganisms9081696
HERDC Research category C1 Refereed article in a scholarly journal
Free to Read? Yes
Persistent URL http://hdl.handle.net/10536/DRO/DU:30154637

Connect to link resolver
 
Unless expressly stated otherwise, the copyright for items in DRO is owned by the author, with all rights reserved.

Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.

Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 0 times in TR Web of Science
Scopus Citation Count Cited 0 times in Scopus
Google Scholar Search Google Scholar
Access Statistics: 2 Abstract Views, 1 File Downloads  -  Detailed Statistics
Created: Thu, 26 Aug 2021, 16:22:16 EST

Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.