Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally.

Ariful Islam,Otun Saha,Shahanaj Shano,Md Abul Kalam,Josefina Abedin,Md Abu Sayeed,Mohammad Mahmudul Hassan,Md Kaisar Rahman,Tahmina Shirin,Shariful Islam,Jinnat Ferdous

doi:10.3390/microorganisms9081696

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.

Highlights

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)put human civilization at risk for its devastating spread
We found that 20 countries reported 807 SARS-CoV-2 sequences from different environmental samples across the globe
The SARS-CoV-2 RNA has been detected in diverse samples, namely, air, currency, environmental swab, surface swab, wastewater, sewage, and the outer packaging of cold chain products

Summary

Introduction

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)put human civilization at risk for its devastating spread. Microorganisms 2021, 9, 1696 embargoes, and many other factors, but the threat might be aggravated if there is a chance of environmental contamination by the virus [1,2]. SARS-CoV-2 is mainly a respiratory virus, but it may persist and replicate in the gastrointestinal tract and shed through feces during and after the active infectious stage in humans [3,4,5,6]. The World Health Organization (WHO) reported an occurrence of 342 cases with 42 deaths in Hong Kong due to SARS where the virus was transmitted through a water plumbing system. The SARS-CoV-2 droplet might be released through the wastewater sanitation arrangement of the building’s different floors which might cause cross-contamination [11]

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