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Microorganisms
Special Issues
Emerging Viruses: New Challenges in Detection, Prevention and Control
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Emerging Viruses: New Challenges in Detection, Prevention and Control

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Virology".

Deadline for manuscript submissions: closed (15 February 2024) | Viewed by 9606

Special Issue Editors

Dr. Sarah Temmam

E-Mail Website
Guest Editor
Pathogen Discovery Laboratory, Institut Pasteur, 75015 Paris, France
Interests: emerging viruses; zoonoses; arboviruses; one health; virus discovery
Dr. Janin Nouhin

E-Mail Website
Guest Editor
Virology Unit, Institut Pasteur du Cambodge, 120210 Phnom Penh, Cambodia
Interests: emerging viruses; zoonoses; one health; virus evolution

Special Issue Information

Dear Colleagues,

Emerging viruses are one of the main concerns for both public and animal health of the last decades. Climate changes, geographical expansion of vectors and increasing contacts with wildlife are few examples of anthropogenic factors that can lead to the emergence of novel viruses. Novel viruses are continuously crossing the species barrier between their animal reservoir and human or livestock populations, leading to difficulties in detecting and preventing such events, as illustrated with the recent emergence of SARS-CoV-2.

In this Special Issue entitled “Emerging viruses: new challenges in detection, prevention and control”, we encourage colleagues to contribute to this important topic with their recent research findings and technological developments. The goal of this Special Issue is to serve as a collection of the most recent knowledge related to the discovery, the prediction, or the prevention of the emergence of novel or unexpected emerging viruses, including zoonoses and arboviruses. We welcome original research articles and reviews on recent advances in the field of emerging viruses. Topics of interest include, but are not limited to, research on the mechanisms of spillover, tools for virus discovery, ecology and transmission of emerging viruses, or original concepts to better anticipate the emergence of viruses.

We hope that this Special Issue highlights current insights into emerging viruses and serves as a springboard of ideas for future advances in our understanding of these pathogens and how to combat their increasing risk to public health.

Dr. Sarah Temmam
Dr. Janin Nouhin
Guest Editors

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. Microorganisms 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 2700 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
  • zoonoses
  • arboviruses
  • one health
  • spillover
  • virus discovery
  • virus evolution
  • animal reservoir
  • arthropod vector
  • prediction
  • surveillance, tools

Published Papers (6 papers)

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Research

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10 pages, 1125 KiB  
Communication
Metagenomic Analysis for Diagnosis of Hemorrhagic Fever in Minas Gerais, Brazil
by Felipe Campos de Melo Iani, Gabriel Montenegro de Campos, Talita Emile Ribeiro Adelino, Anielly Sarana da Silva, Simone Kashima, Luiz Carlos Junior Alcantara, Sandra Coccuzzo Sampaio, Marta Giovanetti, Maria Carolina Elias and Svetoslav Nanev Slavov
Microorganisms 2024, 12(4), 769; https://doi.org/10.3390/microorganisms12040769 - 11 Apr 2024
Viewed by 675
Abstract
Viral hemorrhagic fever poses a significant public health challenge due to its severe clinical presentation and high mortality rate. The diagnostic process is hindered by similarity of symptoms across different diseases and the broad spectrum of pathogens that can cause hemorrhagic fever. In [...] Read more.
Viral hemorrhagic fever poses a significant public health challenge due to its severe clinical presentation and high mortality rate. The diagnostic process is hindered by similarity of symptoms across different diseases and the broad spectrum of pathogens that can cause hemorrhagic fever. In this study, we applied viral metagenomic analysis to 43 serum samples collected by the Public Health Laboratory (Fundação Ezequiel Dias, FUNED) in Minas Gerais State, Brazil, from patients diagnosed with hemorrhagic fever who had tested negative for the standard local hemorrhagic disease testing panel. This panel includes tests for Dengue virus (DENV) IgM, Zika virus IgM, Chikungunya virus IgM, yellow fever IgM, Hantavirus IgM, Rickettsia rickettsii IgM/IgG, and Leptospira interrogans IgM, in addition to respective molecular tests for these infectious agents. The samples were grouped into 18 pools according to geographic origin and analyzed through next-generation sequencing on the NextSeq 2000 platform. Bioinformatic analysis revealed a prevalent occurrence of commensal viruses across all pools, but, notably, a significant number of reads corresponding to the DENV serotype 2 were identified in one specific pool. Further verification via real-time PCR confirmed the presence of DENV-2 RNA in an index case involving an oncology patient with hemorrhagic fever who had initially tested negative for anti-DENV IgM antibodies, thereby excluding this sample from initial molecular testing. The complete DENV-2 genome isolated from this patient was taxonomically classified within the cosmopolitan genotype that was recently introduced into Brazil. These findings highlight the critical role of considering the patient’s clinical condition when deciding upon the most appropriate testing procedures. Additionally, this study showcases the potential of viral metagenomics in pinpointing the viral agents behind hemorrhagic diseases. Future research is needed to assess the practicality of incorporating metagenomics into standard viral diagnostic protocols. Full article
(This article belongs to the Special Issue Emerging Viruses: New Challenges in Detection, Prevention and Control)
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12 pages, 3008 KiB  
Article
Investigation of Yellow Fever Virus at the Human–Animal Interface after a Zika Virus Outbreak in Midwest Brazil
by Lis Alvarez Baranowski, Helver Gonçalves Dias, Débora Familiar-Macedo, Gilberto Sabino-Santos, Heitor Miraglia Herrera, Renata Dezengrini Slhessarenko, Flávia Barreto dos Santos and Alex Pauvolid-Corrêa
Microorganisms 2024, 12(3), 594; https://doi.org/10.3390/microorganisms12030594 - 16 Mar 2024
Viewed by 696
Abstract
Following the first report of zika virus in March 2015, Brazil experienced its largest sylvatic yellow fever outbreak between 2016 and 2019. This study aimed to investigate the circulation of yellow fever virus (YFV) in non-human primates (NHPs) and mosquitoes collected in urban [...] Read more.
Following the first report of zika virus in March 2015, Brazil experienced its largest sylvatic yellow fever outbreak between 2016 and 2019. This study aimed to investigate the circulation of yellow fever virus (YFV) in non-human primates (NHPs) and mosquitoes collected in urban parks and other metropolitan areas of midwest Brazil between 2017 and 2018. Whole blood samples from 80 NHPs, including 48 black-tailed marmosets (Mico melanurus) and 2332 mosquitoes from six different genera, were collected in the states of Mato Grosso (MT) and Mato Grosso do Sul (MS) and then tested for YFV by RT-qPCR. Additionally, 23 plasma samples of NHPs were tested for neutralizing antibodies for YFV by a plaque reduction neutralization test (PRNT). No YFV RNA or neutralizing antibodies for YFV were detected in NHPs and mosquitoes from MT and MS. The continuous monitoring of YFV circulation in different species of NHPs and vectors in urban areas is instrumental to quickly assess potentially unknown maintenance cycles of yellow fever at the human–animal interface in Brazil. Full article
(This article belongs to the Special Issue Emerging Viruses: New Challenges in Detection, Prevention and Control)
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11 pages, 2694 KiB  
Article
Genetic Diversity, Regional Distribution, and Clinical Characteristics of Severe Fever with Thrombocytopenia Syndrome Virus in Gangwon Province, Korea, a Highly Prevalent Region, 2019–2021
by Mi-Young Moon, Hyeon Kyu Kim, Se-Jin Chung, Jae Hwan Byun, Ha-Na Kim, Woan Lee, Soon-Won Lee, Sezim Monoldorova, Sungkyeong Lee, Bo-Young Jeon and Eun-Joo Lim
Microorganisms 2023, 11(9), 2288; https://doi.org/10.3390/microorganisms11092288 - 11 Sep 2023
Viewed by 986
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is an arthropod-borne viral disease with a high mortality rate with high fever and thrombocytopenia. We investigated the clinical and epidemiological characteristics and viral genotypes from 2019 to 2021 in Gangwon Province, Korea. Of the 776 suspected [...] Read more.
Severe fever with thrombocytopenia syndrome (SFTS) is an arthropod-borne viral disease with a high mortality rate with high fever and thrombocytopenia. We investigated the clinical and epidemiological characteristics and viral genotypes from 2019 to 2021 in Gangwon Province, Korea. Of the 776 suspected cases, 62 were SFTS. The fatality rate was 11.5–28.6% (average rate, 19.4%), and the frequent clinical symptoms were high fever (95.2%), thrombocytopenia (95.2%), and leukopenia (90.3%). Hwacheon had the highest incidence rate per 100,000 persons at 8.03, followed by Inje and Yanggu (7.37 and 5.85, respectively). Goseong, Yangyang, and Hoengseong had rates of 2 or higher; Samcheok, Hongcheon, Jeongsen, and Yeonwol were 1.70–1.98, and Wonju, Gangneung, and Donghae were slightly lower, ranging from 0.31 to 0.74. Of the 57 cases with identified genotypes, eight genotypes (A, B1, B2, B3, C, D, E, and F) were detected, and the B2 genotype accounted for 54.4% (31 cases), followed by the A genotype at 22.8% (13 cases). The B2 and A genotypes were detected throughout Gangwon Province, and other genotypes, B1, B3, C, D, and F, were discovered in a few regions. In particular, genotype A could be further classified into subtypes. In conclusion, SFTS occurred throughout Gangwon Province, and Hwacheon had the highest incidence density. Multiple genotypes of SFTS were identified, with B2 and A being the most common. These findings provide important insights for the understanding and management of SFTS in this region. Full article
(This article belongs to the Special Issue Emerging Viruses: New Challenges in Detection, Prevention and Control)
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16 pages, 1733 KiB  
Article
E7 Oncogene HPV58 Variants Detected in Northeast Brazil: Genetic and Functional Analysis
by Bárbara Simas Chagas, Elias Tibúrcio Júnior, Ruany Cristyne de Oliveira Silva, Daffany Luana dos Santos, Marconi Rego Barros Junior, Rita de Cássia Pereira de Lima, Maria da Conceição Viana Invenção, Vanessa Emanuelle Pereira Santos, Pedro Luiz França Neto, Antônio Humberto Silva Júnior, Jacinto Costa Silva Neto, Marcus Vinícius de Aragão Batista and Antonio Carlos de Freitas
Microorganisms 2023, 11(8), 1915; https://doi.org/10.3390/microorganisms11081915 - 27 Jul 2023
Viewed by 1149
Abstract
Cervical cancer is associated with persistent infections by high-risk Human Papillomavirus (HPV) types that may have nucleotide polymorphisms and, consequently, different oncogenic potentials. Therefore, this study aimed to evaluate the genetic variability and structural effects of the E7 oncogene of HPV58 in cervical [...] Read more.
Cervical cancer is associated with persistent infections by high-risk Human Papillomavirus (HPV) types that may have nucleotide polymorphisms and, consequently, different oncogenic potentials. Therefore, this study aimed to evaluate the genetic variability and structural effects of the E7 oncogene of HPV58 in cervical scraping samples from Brazilian women. The study was developed with patients from hospitals in the metropolitan area of Recife, PE, Brazil. The most frequent HPV types were, in descending order of abundance, HPV16, 31, and 58. Phylogenetic analysis demonstrated that the isolates were classified into sublineages A2, C1, and D2. Two positively selected mutations were found in E7: 63G and 64T. The mutations G41R, G63D, and T64A in the E7 protein reduced the stability of the protein structure. Utilizing an NF-kB reporter assay, we observed a decrease in the NK-kB pathway activity with the HPV58-E7 variant 54S compared to the WT E7. The other detected E7 HPV58 variants presented similar NF-kB pathway activity compared to the WT E7. In this study, it was possible to identify mutations that may interfere with the molecular interaction between the viral oncoproteins and host proteins. Full article
(This article belongs to the Special Issue Emerging Viruses: New Challenges in Detection, Prevention and Control)
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Review

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17 pages, 793 KiB  
Review
Emerging Infectious Diseases Are Virulent Viruses—Are We Prepared? An Overview
by Jasmine J. Han, Hannah A. Song, Sarah L. Pierson, Jane Shen-Gunther and Qingqing Xia
Microorganisms 2023, 11(11), 2618; https://doi.org/10.3390/microorganisms11112618 - 24 Oct 2023
Cited by 3 | Viewed by 3542
Abstract
The recent pandemic caused by SARS-CoV-2 affected the global population, resulting in a significant loss of lives and global economic deterioration. COVID-19 highlighted the importance of public awareness and science-based decision making, and exposed global vulnerabilities in preparedness and response systems. Emerging and [...] Read more.
The recent pandemic caused by SARS-CoV-2 affected the global population, resulting in a significant loss of lives and global economic deterioration. COVID-19 highlighted the importance of public awareness and science-based decision making, and exposed global vulnerabilities in preparedness and response systems. Emerging and re-emerging viral outbreaks are becoming more frequent due to increased international travel and global warming. These viral outbreaks impose serious public health threats and have transformed national strategies for pandemic preparedness with global economic consequences. At the molecular level, viral mutations and variations are constantly thwarting vaccine efficacy, as well as diagnostic, therapeutic, and prevention strategies. Here, we discuss viral infectious diseases that were epidemic and pandemic, currently available treatments, and surveillance measures, along with their limitations. Full article
(This article belongs to the Special Issue Emerging Viruses: New Challenges in Detection, Prevention and Control)
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Other

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7 pages, 441 KiB  
Brief Report
Detection of Anti-Rift Valley Fever Virus Antibodies in Serum Samples of Patients with Suspected Arbovirus Infection
by Daniele Lapa, Eliana Specchiarello, Massimo Francalancia, Enrico Girardi, Fabrizio Maggi and Anna Rosa Garbuglia
Microorganisms 2023, 11(8), 2081; https://doi.org/10.3390/microorganisms11082081 - 14 Aug 2023
Cited by 2 | Viewed by 1137
Abstract
The definitive diagnosis of the Rift Valley fever virus (RVFV) requires a form of testing that is available only in reference laboratories. It includes indirect immunofluorescence assay (IFA), the serum neutralization assay (NA), and real-time PCR. Therefore, often, no attempts are made to [...] Read more.
The definitive diagnosis of the Rift Valley fever virus (RVFV) requires a form of testing that is available only in reference laboratories. It includes indirect immunofluorescence assay (IFA), the serum neutralization assay (NA), and real-time PCR. Therefore, often, no attempts are made to detect it, even among travelers from endemic areas. In this study, the presence of anti-RVFV IgG and IgM was retrospectively screened in stored serum samples from people who were admitted with arbovirus symptoms at the National Institute for Infectious Diseases (INMI) L. Spallanzani, Rome, Italy. Overall, 80 residual serum samples were anonymized, and sub-aliquots were prepared and tested for anti-RVFV IgG and IgM. A serum neutralization assay was used as a confirmatory test. There was a positive result in eight out of 80 samples (10%) for anti-RVFV IgG, with titers ranging from 1:40 up to 1:1280. Three of eight (2.6%) samples were confirmed as seropositive through an in-house serum neutralization assay, with antibody titers ranging from 1:10 to 1:160. All samples resulted negative for anti-RVFV IgM and RVFV RNA when tested by IFA and real-time RT-PCR, respectively. Our data highlight that several RVFV infections can possibly escape routine virological diagnosis, which suggests RVFV testing should be set up in order to monitor virus prevalence. Full article
(This article belongs to the Special Issue Emerging Viruses: New Challenges in Detection, Prevention and Control)
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