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Molecular Epidemiology of SARS-CoV-2, 4th Edition

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

Deadline for manuscript submissions: 31 July 2026 | Viewed by 7653

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Dr. Marta Giovanetti

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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, MG, Brazil
Interests: phylogenetic; phylodynamic; molecular evolution; genomic surveillance; WGS; emerging and re-emerging viral pathogens
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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

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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 250 words) can be sent to the Editorial Office for assessment.

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.

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Keywords

SARS-CoV-2
genomic monitoring
phylodynamic
molecular epidemiology

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Related Special Issues

Molecular Epidemiology of SARS-CoV-2 in Viruses (34 articles)
Molecular Epidemiology of SARS-CoV-2: 2nd Edition in Viruses (15 articles)
Molecular Epidemiology of SARS-CoV-2, 3rd Edition in Viruses (13 articles)

Published Papers (8 papers)

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Research

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15 pages, 9332 KB

Open AccessArticle

Genomic Characterization and Evolutionary Dynamics of SARS-CoV-2 Lineage NB.1.8.1 in Thailand, 2025

by Jiratchaya Puenpa, Preeyaporn Vichaiwattana, Ratchadawan Aeemjinda, Sumeth Korkong, Ritthideach Yorsaeng and Yong Poovorawan

Viruses 2026, 18(4), 450; https://doi.org/10.3390/v18040450 - 8 Apr 2026

Viewed by 169

Abstract

SARS-CoV-2 continues to cause recurrent waves in the post-pandemic period, yet genomic data from Southeast Asia remain limited for several emerging Omicron lineages, including NB.1.8.1. In this study, routine acute respiratory infection (ARI) surveillance performed in Bangkok, Thailand, from January to December 2025 was integrated with real-time RT-PCR testing and complete spike-gene sequencing for lineage assignment and evolutionary analysis. Among 4756 ARI specimens, 473 (9.9%) tested positive for SARS-CoV-2. Positivity increased in late April, peaked in May (epidemiological week 21; 58.4%), and declined through late June. Lineage typing was successful for 165/473 positive samples (34.9%), identifying 16 Pango lineages. Early 2025 showed heterogeneous circulation, including XEC- and XEC.8-related lineages, whereas NB.1.8.1 predominated during the main wave, accounting for 92.4% of typed cases in May and 89.8% in June. No recombination signals meeting predefined criteria were detected in the spike dataset. The mean spike substitution rate was estimated at 1.11 × 10⁻³ substitutions/site/year (95% HPD, 9.13 × 10⁻⁴–1.31 × 10⁻³), and the major Thai-containing NB.1.8.1 clade had an estimated tMRCA of 17 July 2024. These findings show that routine ARI surveillance combined with spike-based genomics can provide timely insights into SARS-CoV-2 circulation, lineage replacement, and ongoing viral evolution in Thailand. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 4th Edition)

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14 pages, 708 KB

Open AccessArticle

Disentangling SARS-CoV-2 Sustained Viremia Cases: Evolution, Persistence and Reinfection

by Brunna M. Alves, Filipe R. R. Moreira, Marianne M. Garrido, Pedro S. de Carvalho, Élida M. de Oliveira, Caroline C. de Sá, James Arthos, Claudia Cicala, João P. B. Viola, Livia R. Goes, Juliana D. Siqueira and Marcelo A. Soares

Viruses 2026, 18(3), 393; https://doi.org/10.3390/v18030393 - 21 Mar 2026

Viewed by 575

Abstract

Based on the follow-up of patients who recovered from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, several reports of people who re-tested positive have been described. This may result from viral reactivation, true reinfection, superinfection, or an initial infection by more than one virus (multiple infection). These scenarios can only be correctly distinguished through viral quasispecies analysis. Herein, 26 cancer patients under extended follow-up for SARS-CoV-2 infection were submitted to multiple longitudinal analyses through nucleic acid isolation, PCR amplification and high-throughput sequencing. SARS-CoV-2 classification and the definition of cases as persistent or repeated infections were based on phylogenetic reconstruction. Supported by their viral complete genomes and intrahost quasispecies over time, the different scenarios were identified. Nine confirmed and 12 plausible persistence cases were identified. Virus evolution dynamics in the intrahost population from patients with persistent infection was shown for the first time. Regarding reinfection, three confirmed and two plausible cases were identified, including one case of multiple infection. Altogether, this is the first study that analyzes the plethora of SARS-CoV-2 within-host minor variants and describes reinfections, multiple infections and viral evolution across time in cancer patients, contributing to the understanding of SARS-CoV-2’s within-host population dynamics in the natural history of COVID-19. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 4th Edition)

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20 pages, 7004 KB

Open AccessArticle

Genetic Diversity of SARS-CoV-2 in Kazakhstan from 2020 to 2022

by Altynay Gabiden, Andrey Komissarov, Aknur Mutaliyeva, Aidar Usserbayev, Kobey Karamendin, Alexander Perederiy, Artem Fadeev, Ainagul Kuatbaeva, Dariya Jussupova, Askar Abdaliyev, Manar Smagul, Yelizaveta Khan, Marat Kumar, Temirlan Sabyrzhan, Aigerim Abdimadiyeva and Aidyn Kydyrmanov

Viruses 2026, 18(1), 138; https://doi.org/10.3390/v18010138 - 21 Jan 2026

Viewed by 757

Abstract

Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had major social and economic consequences worldwide. Whole genome sequencing (WGS) is essential for genomic monitoring, enabling tracking of viral evolution, detection of emerging variants, and identification of introductions and transmission chains to inform timely public health responses. Here, we compile and harmonize SARS-CoV-2 genomic data generated by multiple laboratories across Kazakhstan together with publicly available sequences to provide a national overview of genomic dynamics across successive epidemic waves from 2020 to 2022. We analyzed 4462 genomes deposited in GISAID (including 340 generated in this study), of which 3299 passed Nextclade quality filters, and summarized lineage turnover across major phases (pre-VOC, Alpha, Delta, Omicron BA.1/BA.2, Omicron BA.4/BA.5, and a later recombinant-dominant period). Sequencing intensity varied markedly over time (0.60‰ of confirmed cases during Delta vs. 11.57‰ during the Omicron BA.5 wave), suggesting that lineage diversity and persistence may be underestimated. Pre-VOC circulation included ≥12 Pango lineages with evidence of multiple introductions and sustained local transmission, including a Kazakhstan-restricted B.4.1 lineage that emerged in Nur-Sultan/Astana and disappeared after April 2020. The Tengizchevroil oilfield outbreak comprised B.1.1 viruses with phylogenetic support for ≥three independent introductions. Alpha and Omicron waves were characterized by repeated introductions and heterogeneous origins, whereas Delta was dominated by AY.122 with an additional distinct AY.122 cluster; a notable BF.7 local transmission event was observed during BA.5. We also highlight locally enriched non-lineage-defining mutations. Overall, recurrent importations and variable local amplification shaped SARS-CoV-2 dynamics in Kazakhstan, while interpretation is constrained by strongly time-skewed sequencing. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 4th Edition)

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11 pages, 495 KB

Open AccessArticle

Sociodemographic Associations and COVID-19 Symptoms Following One Year of Molecular Screening for SARS-CoV-2 Among Healthcare Workers

by Viviane Campos Barbosa de Sena, Michelle Oliveira, Rejane Alencar Saldanha, Larissa Vicenza, Tais Hanae Kasai Brunswick, Bernardo Tura, Helena Cramer Veiga Rey, Adriana Bastos Carvalho, Antônio Carlos Campos de Carvalho, Djane Braz Duarte, Dayde Lane Mendonça da Silva and Daniel Arthur Barata Kasal

Viruses 2025, 17(12), 1622; https://doi.org/10.3390/v17121622 - 16 Dec 2025

Viewed by 482

Abstract

Background: During the COVID-19 pandemic, high rates of infection with SARS-CoV-2 were reported in healthcare workers (HCWs), among whom asymptomatic individuals had high potential to spread the virus while assisting high-risk patients. This study conducted routine SARS-CoV-2 screening among the staff of a specialized cardiology hospital in Brazil during 2022 and 2023, while also evaluating variables associated with infection and the occurrence of symptoms. Methods: A prospective cohort study of 94 HCWs with biweekly RT-PCR screening was performed, employing RT-PCR from nasal swabs. Results: Participants aged 50.9 ± 10.2 years and were predominantly female (85.1%) and non-white (56.4%). The follow-up period was 576.4 ± 185.9 days, and most participants worked in the intensive care unit/emergency department (34%). Although the HCWs with the highest COVID-19 rates before inclusion were technicians/graduates (67.3%) and non-white individuals (57.7%), these groups presented lower infection rates at follow-up (p < 0.001, CI 95% 2.924–27.93; and p = 0.02, CI 95% 0.129–0.859, respectively). The number of asymptomatic cases increased during the study (p = 0.001), and simultaneous infection upsurges occurred in different hospital departments. Interpretation: These data highlight the association between educational level and the risk of SARS-CoV-2 infection in HCWs. The synchronicity of cases in different hospital departments offers insights about the nosocomial spread of SARS-CoV-2. The increase in the number of asymptomatic infections with repeated infections suggests that regular molecular screening may contribute to increasing the safety of both patients and HCWs in a pandemic context. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 4th Edition)

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18 pages, 1303 KB

Open AccessArticle

Comparative Assessment of Viral Load Retention in Surgical and Fabric Masks Worn by COVID-19 Patients

by Cristiane Monteiro Eller, Milena De Paula Rebello, Andreza Sálvio, Emanuelle S. R. F. Silva, Vinícius Silva Belo, Elba Regina E. Lemos, Marta Giovanetti, José Júnior França De Barros and Marco Aurélio Horta

Viruses 2025, 17(12), 1552; https://doi.org/10.3390/v17121552 - 27 Nov 2025

Viewed by 859

Abstract

Face masks are widely recognized as a key intervention to limit SARS-CoV-2 transmission, yet the distribution and persistence of viral RNA across different mask regions and layers remain poorly understood. To address this, we analyzed 185 masks collected from 60 SARS-CoV-2-positive individuals in Rio de Janeiro between December 2020 and September 2022. Masks were sectioned into anatomical regions (nose, mouth, sides) and structural layers (inner, middle, outer), and viral RNA was quantified using RT-qPCR. Samples with the highest viral loads were selected for partial sequencing of the spike gene, and paired analyses with swab samples were performed. Statistical comparisons included non-parametric tests and a linear mixed-effects model. Our results showed that the inner layer and nose region consistently harbored the highest viral RNA levels, with no significant differences between surgical and fabric masks. Viral load decreased by an estimated 39% per day, consistent with exponential decay. Sequencing confirmed identical viral genomes in masks and swabs and allowed identification of circulating variants, including Gamma and Omicron. These findings indicate that masks serve not only as effective physical barriers but also as non-invasive sources for genomic surveillance, providing insights into viral shedding patterns and informing strategies for monitoring and controlling SARS-CoV-2 transmission. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 4th Edition)

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17 pages, 4115 KB

Open AccessArticle

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

Viewed by 1696

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 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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Review

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31 pages, 1947 KB

Open AccessReview

Integrative Insights into the Immunopathogenesis and Organ-Specific Immunological Mechanisms of Long COVID: A Narrative Review

by Supriya Mahajan, Saurabh Mahajan and Nidhi Kaushik

Viruses 2026, 18(4), 458; https://doi.org/10.3390/v18040458 - 10 Apr 2026

Viewed by 120

Abstract

Long COVID (LC), also referred to as post-acute sequelae of SARS-CoV-2 infection, is characterized by persistent symptoms originating 3 months following acute COVID-19, lasting for at least two months and frequently affecting individuals who initially experienced mild to moderate disease. The clinical spectrum is heterogeneous, involving respiratory, cardiovascular, neurological, renal, gastrointestinal, and endocrine systems, thereby posing substantial diagnostic and therapeutic challenges. Despite extensive investigation, the precise immunopathogenic mechanisms underlying LC remain incompletely defined. Accumulating evidence suggests that LC is driven by a multifactorial interplay of persistent viral antigen reservoirs, chronic immune activation, dysregulated innate and adaptive immune responses, autoimmunity, endothelial dysfunction, microvascular injury, and aberrant tissue repair. These systemic immune perturbations manifest variably across different organs, contributing to the diverse clinical phenotypes observed. However, mechanistic clarity is hindered by heterogeneity in study designs, limited longitudinal data, and the absence of standardized immunological profiling. This narrative review provides integrative insights into the immunopathogenesis of LC, synthesizing current evidence on systemic immune dysregulation and organ-specific immunological mechanisms. A conceptual framework is proposed to facilitate a structured understanding of this complex syndrome and to guide future research toward targeted immunomodulatory strategies. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 4th Edition)

18 pages, 1648 KB

Open AccessReview

Global Surveillance and Biological Characterization of the SARS-CoV-2 NB.1.8.1 Variant: An Emerging VUM Lineage Under Scrutiny

by Gaojie Cao, Chenhui Xu, Linxi Wang, Keikei Chai and Beibei Wu

Viruses 2025, 17(11), 1457; https://doi.org/10.3390/v17111457 - 31 Oct 2025

Viewed by 2159

Abstract

The continuous evolution of SARS-CoV-2 and its variants poses persistent challenges to global public health. As a sublineage of the XDV.1 variant, NB.1.8.1 has rapidly emerged as a dominant strain worldwide, triggering a new wave of infections. Representing a product of viral adaptation, this variant has acquired several critical amino acid mutations—including A435S and T478I—which enhance its transmissibility and immune evasion capabilities compared to the ancestral XDV.1 lineage. This review systematically summarizes the genomic characteristics, epidemiological features, and immune escape potential of NB.1.8.1. It emphasizes that sustained genomic surveillance and serological assessments are crucial for informing public health response strategies, guiding vaccine development, and optimizing containment measures. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 4th Edition)

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