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Pathogens
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Molecular Epidemiology of Emerging Viruses
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Molecular Epidemiology of Emerging Viruses

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Emerging Pathogens".

Deadline for manuscript submissions: 15 August 2025 | Viewed by 11451

Special Issue Editor

Dr. Vagner Fonseca

E-Mail Website
Guest Editor
Department of Exact and Earth Sciences, University of the State of Bahia, Salvador 41150-000, Brazil
Interests: bioinformatics; viral evolution; molecular epidemiology; mathematical models; phylogenetic and phylodynamic trees
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the ever-evolving landscape of infectious diseases, the study of emerging viruses stands at the forefront of scientific inquiry. As the global community grapples with the challenges posed by novel viral threats, the need for a comprehensive understanding of their molecular epidemiology becomes increasingly paramount. We are pleased to announce a Special Issue of Pathogens entitled "Molecular Epidemiology of Emerging Viruses". In this Special Issue, we aim to provide new genomic and epidemiological data on viral strains circulating worldwide and offer an overview of the real-time global evolution of viruses.

This Special Issue invites contributions, welcoming original research articles, reviews, and methodological papers that span a broad spectrum of themes, including bioinformatics in viral research, viral evolution and dynamics, epidemiological investigations, mathematical models for emerging and recurrent viruses, and other topics related to the molecular epidemiology of emerging viruses.

Please feel free to submit your contributions, as we aim to create a comprehensive collection that advances our understanding of the intricate dynamics of emerging viruses. Manuscripts should adhere to the guidelines outlined by the journal and be submitted through the online platform.

Dr. Vagner Fonseca
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. Pathogens 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 2200 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

  • emerging viruses
  • molecular epidemiology
  • genomic data
  • genome evolution
  • viral evolution
  • epidemiological investigations
  • bioinformatics
  • mathematical models
  • phylogenetic and phylodynamic trees

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (5 papers)

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Research

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8 pages, 3015 KiB  
Communication
First Detection of a Novel Posavirus 2 Strain Identified from Pigs in China
by Li Chen, Haohao Lu, Xue Gao, Han Zhou, Jinghao Wang, Zhidong Zhang, Bin Chen, Chun Li, Luqi Liang, Long Zhou and Yi Zhang
Pathogens 2024, 13(12), 1036; https://doi.org/10.3390/pathogens13121036 - 24 Nov 2024
Viewed by 949
Abstract
Porcine stool-associated RNA virus (Posavirus) is an unclassified virus with sequence similarity to viruses in the order of Picornaviridae. In China, lineage 1 Posavirus (Posavirus 1) has been circulating in the field since its initial emergence in 2014 however no other lineages have [...] Read more.
Porcine stool-associated RNA virus (Posavirus) is an unclassified virus with sequence similarity to viruses in the order of Picornaviridae. In China, lineage 1 Posavirus (Posavirus 1) has been circulating in the field since its initial emergence in 2014 however no other lineages have been reported. To investigate the genetic diversity of Posavirus in China, 1200 diarrheic samples were collected from pigs in China. Following high-throughput and Sanger sequencing, one complete genome sequence of a Posavirus (designated SC01) strain was obtained. The genome of SC01 strain was 10217 nucleotides in length and encoded a polyprotein of 3346 amino acids. Genome comparative analysis revealed that SC01 shared 85.6% nucleotide similarity to Posavirus 2 strains, but only 35.2–58.0% sequence identity with Posavirus 1 and 3–12 strains. Phylogenetic analysis showed that the SC01 was classified in Posavirus 2 and clustered into a separate branch with the American Posavirus 2 isolates, indicating that the SC01 is a Posavirus 2 strain. Notably, a novel 1-amino acid deletion was observed in polyprotein at amino acid position 147. This is the first report of the presence of Posavirus 2 in China, and the genomic data of SC01 provides insights into the genetic diversity and evolution of Posavirus in the region. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Emerging Viruses)
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10 pages, 794 KiB  
Communication
Detection of Multiple Human Viruses, including Mpox, Using a Wastewater Surveillance Approach in Brazil
by Juliana Calabria de Araujo, Ana Paula Assad Carvalho, Cintia D. Leal, Manuelle Natividade, Marcus Borin, Augusto Guerra, Natália Carobin, Adriano Sabino, Mariana Almada, Maria Cristina M. Costa, Flavia Saia, Livia V. Frutuoso, Felipe C. M. Iani, Talita Adelino, Vagner Fonseca, Marta Giovanetti and Luiz Carlos Junior Alcantara
Pathogens 2024, 13(7), 589; https://doi.org/10.3390/pathogens13070589 - 16 Jul 2024
Cited by 4 | Viewed by 2209
Abstract
Sewage surveillance can be used as an effective complementary tool for detecting pathogens in local communities, providing insights into emerging threats and aiding in the monitoring of outbreaks. In this study using qPCR and whole genomic sewage surveillance, we detected the Mpox virus [...] Read more.
Sewage surveillance can be used as an effective complementary tool for detecting pathogens in local communities, providing insights into emerging threats and aiding in the monitoring of outbreaks. In this study using qPCR and whole genomic sewage surveillance, we detected the Mpox virus along with other viruses, in municipal and hospital wastewaters in Belo Horizonte, Brazil over a 9-month period (from July 2022 until March 2023). MPXV DNA detection rates varied in our study, with 19.6% (11 out of 56 samples) detected through the hybrid capture method of whole-genome sequencing and 20% (12 out of 60 samples) through qPCR. In hospital wastewaters, the detection rate was higher, at 40% (12 out of 30 samples) compared to 13.3% (4 out of 30 samples) in municipal wastewaters. This variation could be attributed to the relatively low number of MPXV cases reported in the city, which ranged from 106 to 341 cases during the study period, and the dilution effects, given that each of the two wastewater treatment plants (WWTP) investigated serves approximately 1.1 million inhabitants. Additionally, nine other virus families were identified in both hospitals and municipal wastewaters, including Adenoviridade, Astroviridae, Caliciviridae, Picornaviridade, Polyomaviridae, Coronaviridae (which includes SARS-CoV-2), Herspesviridae, Papillomaviridae and Flaviviridae (notably including Dengue). These findings underscore the potential of genomic sewage surveillance as a robust public health tool for monitoring a wide range of viruses circulating in both community and hospitals environments, including MPXV. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Emerging Viruses)
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13 pages, 2079 KiB  
Article
High Frequencies of kdr Mutation and Chikungunya Infection in Aedes aegypti Population from Minas Gerais, Brazil
by Pedro Augusto Almeida-Souza, Cirilo Henrique de Oliveira, Luiz Paulo Brito, Thaynara de Jesus Teixeira, Iago Alves Celestino, Gabriele Barbosa Penha, Ronaldo Medeiros dos Santos, Wexley Miranda Mendes, Bergmann Morais Ribeiro, Fabrício Souza Campos, Paulo Michel Roehe, Natalia Rocha Guimarães, Felipe C. M. Iani, Ademir Jesus Martins and Filipe Vieira Santos de Abreu
Pathogens 2024, 13(6), 457; https://doi.org/10.3390/pathogens13060457 - 28 May 2024
Cited by 2 | Viewed by 2873
Abstract
The Chikungunya virus (CHIKV) presents global health challenges, with Brazil experiencing outbreaks since its introduction in 2014. In 2023, following a CHIKV outbreak in Minas Gerais (MG), social media was used to optimize an entomological survey aimed at identifying vectors and viral lineages [...] Read more.
The Chikungunya virus (CHIKV) presents global health challenges, with Brazil experiencing outbreaks since its introduction in 2014. In 2023, following a CHIKV outbreak in Minas Gerais (MG), social media was used to optimize an entomological survey aimed at identifying vectors and viral lineages and assessing insecticide resistance. Following Instagram posts, residents with suspected CHIKV infection were able to schedule mosquito aspirations. In total, 421 mosquitoes (165 Aedes aegypti and 256 Culex quinquefasciatus) were captured from 40 households in Salinas city (MG) and tested for the Dengue, Zika, and Chikungunya viruses through RT-qPCR. Twelve of 57 pools (10 Ae. aegypti and two Cx. quinquefasciatus) tested positive for CHIKV RNA. Viral RNA was also detected in the heads of nine Ae. aegypti, indicating viral dissemination but not in Cx. quinquefasciatus. Genome sequencing yielded the first near-complete genome from the 2023 outbreak, unveiling that the CHIKV strain belonged to the East/Central/South African (ECSA) genotype. Additionally, genetic analyses revealed high frequencies of kdr alleles, including in CHIKV-infected mosquitoes, suggesting resistance to pyrethroid insecticides in this Ae. aegypti population. Social media was important for guiding mosquito-capture efforts in CHIKV transmission hotspots, thus optimizing the opportunity for viral detection. These findings emphasize the urgent need for innovative vector studies and control strategies, as well as interdisciplinary approaches in public health interventions. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Emerging Viruses)
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Review

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23 pages, 2519 KiB  
Review
Comprehensive Insights into Monkeypox (mpox): Recent Advances in Epidemiology, Diagnostic Approaches and Therapeutic Strategies
by Suresh Kumar, Dhanyashri Guruparan, Kalimuthu Karuppanan and K. J. Senthil Kumar
Pathogens 2025, 14(1), 1; https://doi.org/10.3390/pathogens14010001 - 26 Dec 2024
Cited by 4 | Viewed by 1906
Abstract
Monkeypox (mpox) is a viral infection closely related to smallpox, manifesting as a milder febrile rash in affected individuals. Over the past two decades, the incidence of mpox has surged, possibly linked to a declining immunity against the smallpox vaccine worldwide. Recent outbreaks [...] Read more.
Monkeypox (mpox) is a viral infection closely related to smallpox, manifesting as a milder febrile rash in affected individuals. Over the past two decades, the incidence of mpox has surged, possibly linked to a declining immunity against the smallpox vaccine worldwide. Recent outbreaks of mpox in multiple countries have sparked concerns regarding altered transmission patterns and the potential for a global menace. In this article, we present a multidimensional review encompassing the latest scientific discoveries, illuminating the intricate structure of the human mpox virus. Key findings include advancements in understanding the virus’s molecular mechanisms, which highlight its genetic adaptability and potential for zoonotic spillover. Diagnostic innovations, such as improved molecular assays, have enhanced detection accuracy, while novel therapeutic strategies, including antiviral drugs and vaccines, show promise in mitigating outbreaks. Our conclusions emphasize the importance of robust surveillance systems, vaccination programs, and rapid response strategies to curb mpox’s spread. Future recommendations include strengthening global collaboration for zoonotic disease surveillance, advancing the research on host–pathogen interactions, and developing next-generation therapeutics to address this emerging public health threat effectively. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Emerging Viruses)
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18 pages, 2582 KiB  
Review
Understanding the Transmission Dynamics of the Chikungunya Virus in Africa
by Yajna Ramphal, Houriiyah Tegally, James Emmanuel San, Martina Larissa Reichmuth, Marije Hofstra, Eduan Wilkinson, Cheryl Baxter, CLIMADE Consortium, Tulio de Oliveira and Monika Moir
Pathogens 2024, 13(7), 605; https://doi.org/10.3390/pathogens13070605 - 22 Jul 2024
Viewed by 2880
Abstract
The Chikungunya virus (CHIKV) poses a significant global public health concern, especially in Africa. Since its first isolation in Tanzania in 1953, CHIKV has caused recurrent outbreaks, challenging healthcare systems in low-resource settings. Recent outbreaks in Africa highlight the dynamic nature of CHIKV [...] Read more.
The Chikungunya virus (CHIKV) poses a significant global public health concern, especially in Africa. Since its first isolation in Tanzania in 1953, CHIKV has caused recurrent outbreaks, challenging healthcare systems in low-resource settings. Recent outbreaks in Africa highlight the dynamic nature of CHIKV transmission and the challenges of underreporting and underdiagnosis. Here, we review the literature and analyse publicly available cases, outbreaks, and genomic data, providing insights into the epidemiology, genetic diversity, and transmission dynamics of CHIKV in Africa. Our analyses reveal the circulation of geographically distinct CHIKV genotypes, with certain regions experiencing a disproportionate burden of disease. Phylogenetic analysis of sporadic outbreaks in West Africa suggests repeated emergence of the virus through enzootic spillover, which is markedly different from inferred transmission dynamics in East Africa, where the virus is often introduced from Asian outbreaks, including the recent reintroduction of the Indian Ocean lineage from the Indian subcontinent to East Africa. Furthermore, there is limited evidence of viral movement between these two regions. Understanding the history and transmission dynamics of outbreaks is crucial for effective public health planning. Despite advances in surveillance and research, diagnostic and surveillance challenges persist. This review and secondary analysis highlight the importance of ongoing surveillance, research, and collaboration to mitigate the burden of CHIKV in Africa and improve public health outcomes. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Emerging Viruses)
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