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Viruses
Special Issues
Molecular Epidemiology of SARS-CoV-2, 4th Edition
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Molecular Epidemiology of SARS-CoV-2, 4th Edition

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Coronaviruses".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 213

Special Issue Editor

Dr. Marta Giovanetti

E-Mail Website
Guest Editor
1. Department of Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, Rome, Italy
2. Instituto Rene Rachou Fundação Oswaldo Cruz, Belo Horizonte 30.190-009, Brazil
Interests: phylogenetic; phylodynamic; molecular evolution; genomic surveillance; WGS; emerging and re-emerging viral pathogens
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the course of the SARS-CoV-2 pandemic, extensive and sustained global transmission allowed for the evolution of the virus, leading to the emergence of the so-called ‘variants of concern’ (VOCs). These VOCs are characterized by several lineage-specific mutations that, it has been suggested, impact viral transmissibility, resistance to neutralizing antibodies, and virulence. The identification of such variants has recently challenged public health authorities, specifically in terms of tracking transmission and mitigating the impact of the ongoing pandemic. This Special Issue will provide new genomic data on the SARS-CoV-2 strains circulating worldwide and present an overview of the real-time global evolution of SARS-CoV-2.

Dr. Marta Giovanetti
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • SARS-CoV-2
  • genomic monitoring
  • phylodynamic
  • molecular epidemiology

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Published Papers (1 paper)

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Research

17 pages, 4115 KiB  
Article
Uncovering SARS-CoV-2 Molecular Epidemiology Across the Pandemic Transition: Insights into Transmission in Clinical and Environmental Samples
by Vrushali D. Patil, Rashmi Chowdhary, Anvita Gupta Malhotra, Jitendra Singh, Debasis Biswas, Rajnish Joshi and Jagat Rakesh Kanwar
Viruses 2025, 17(5), 726; https://doi.org/10.3390/v17050726 - 19 May 2025
Abstract
Background: Respiratory droplets are the main way in which the COVID-19 pandemic’s causal agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), spreads. Angiotensin-converting enzyme 2 (ACE2) receptors, especially in lung cells, allow the virus to enter host cells. However, ACE2 expression in intestinal cells [...] Read more.
Background: Respiratory droplets are the main way in which the COVID-19 pandemic’s causal agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), spreads. Angiotensin-converting enzyme 2 (ACE2) receptors, especially in lung cells, allow the virus to enter host cells. However, ACE2 expression in intestinal cells has sparked worries about possible fecal transfer, particularly in poor-sanitation areas like India. Methods: Between July 2021 and July 2024, clinical (nasopharyngeal, saliva, and stool samples) and sewage samples were collected from outpatient departments and sewage treatment plants (STPs), respectively, from the high-population-density area under study in order to investigate SARS-CoV-2 transmission. Results: This proof-of-concept study analyzed clinical samples from n = 60 COVID-19-positive patients at a central Indian tertiary care hospital and n = 156 samples from hospital STPs. Variants of SARS-CoV-2 were found using qRT-PCR and Next-Generation Sequencing (NGS). Of the n = 37 qRT-PCR-positive patients who gave their assent, 30% had stool samples that tested positive for viral RNA. In 70% of positive NP and 65% of positive saliva samples, along with two stool samples from immunocompromised patients, the live virus was identified using Vero E6 cell lines. Although 18% of the tests reported qRT-PCR-positive results, no live virus was detected in sewage samples despite NGS validation. The detection of SARS-CoV-2 in the absence of confirmed clinical cases may indicate the silent circulation of the virus within the community, suggesting that sewage surveillance can serve as an early warning system before an outbreak occurs. Conclusions: These findings provide critical insights into the importance of continuous environmental surveillance, silent virus circulation, changes in viral epidemiology throughout the years, and strategies to mitigate coronavirus outbreaks. Full article
(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 4th Edition)
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