Monitoring SARS-CoV-2 variants in wastewater of Dhaka City, Bangladesh: approach to complement public health surveillance systems.

Publication date: Jul 07, 2023

Wastewater-based epidemiological surveillance has been considered a powerful tool for early detection and monitoring of the dynamics of SARS-CoV-2 and its lineages circulating in a community. This study is aimed to investigate the complexity of SARS-CoV-2 infection dynamics in Dhaka city by examining its genetic variants in wastewater. Also, the study seeks to determine a connection between the SARS-CoV-2 variations detected in clinical testing and those found in wastewater samples. Out of 504 samples tested in RT-qPCR, 185 (36. 7%) tested positive for SARS-CoV-2 viral RNA. The median log concentration of SARS-CoV-2 N gene copies/Liter of wastewater (gc/L) was 5. 2, and the median log concentration of ORF1ab was 4. 9. To further reveal the genetic diversity of SARS-CoV-2, ten samples with ORF1ab real-time RT-PCR cycle threshold (Ct) values ranging from 28. 78 to 32. 13 were subjected to whole genome sequencing using nanopore technology. According to clade classification, sequences from wastewater samples were grouped into 4 clades: 20A, 20B, 21A, 21J, and the Pango lineage, B. 1, B. 1.1, B. 1.1. 25, and B. 1.617. 2, with coverage ranging from 94. 2 to 99. 8%. Of them, 70% belonged to clade 20B, followed by 10% to clade 20A, 21A, and 21J. Lineage B. 1.1. 25 was predominant in Bangladesh and phylogenetically related to the sequences from India, the USA, Canada, the UK, and Italy. The Delta variant (B. 1.617. 2) was first identified in clinical samples at the beginning of May 2021. In contrast, we found that it was circulating in the community and was detected in wastewater in September 2020. Environmental surveillance is useful for monitoring temporal and spatial trends of existing and emerging infectious diseases and supports evidence-based public health measures. The findings of this study supported the use of wastewater-based epidemiology and provided the baseline data for the dynamics of SARS-CoV-2 variants in the wastewater environment in Dhaka, Bangladesh.

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Concepts Keywords
Canada COVID-19
Environmental Lineages
Italy Low-middle-income countries
Pcr Sequencing
Viral Variants


Type Source Name
disease MESH SARS-CoV-2 infection
pathway REACTOME SARS-CoV-2 Infection
disease VO gene
drug DRUGBANK Pentaerythritol tetranitrate
disease VO time
disease VO USA
disease VO Canada
disease MESH emerging infectious diseases
disease MESH viral shedding
disease IDO infectivity
disease VO Glycoprotein
drug DRUGBANK Water
disease MESH infection
disease IDO site
disease IDO pathogen
disease VO viable
disease VO Viruses
drug DRUGBANK Medical air
disease VO organization
drug DRUGBANK Trestolone
drug DRUGBANK Polyethylene glycol
disease VO protocol
drug DRUGBANK Ademetionine
disease IDO quality
disease VO efficiency
disease IDO process
drug DRUGBANK Coenzyme M
drug DRUGBANK Etoperidone
drug DRUGBANK Calcium
drug DRUGBANK Microcrystalline cellulose
disease VO storage
disease VO volume
drug DRUGBANK Cefoxitin
drug DRUGBANK Creatinolfosfate
drug DRUGBANK Indoleacetic acid
drug DRUGBANK Flunarizine
disease VO report
disease IDO assay
disease VO frequency
disease IDO country
disease VO NS3
drug DRUGBANK Tropicamide
disease VO efficient
disease VO population
drug DRUGBANK Ethionamide
disease MESH asymptomatic infections
disease MESH polio
disease MESH hepatitis
disease MESH infectious diseases
drug DRUGBANK Tretamine
disease VO effectiveness
disease VO Equity
drug DRUGBANK Guanosine
drug DRUGBANK Isosorbide Mononitrate
disease VO vaccine
drug DRUGBANK Azelaic acid
drug DRUGBANK Gold
drug DRUGBANK Oxymetazoline
drug DRUGBANK Vorinostat
disease MESH genetic markers
disease VO Monkeypox virus
disease VO Optaflu
disease IDO infection prevalence

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