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Advances in Alphavirus and Flavivirus Research, 2nd Edition

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 8099

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Special Issue Editors

Dr. Young Chan Kim

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Guest Editor

1. Centre for Human Genetics, Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
2. Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK
Interests: alphaviruses; flaviviruses; bacteria; vaccines; diagnostics; immunology; immunoassays
Special Issues, Collections and Topics in MDPI journals

Dr. Arturo Reyes-Sandoval

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Guest Editor

1. The Jenner Institute, ORCRB, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
2. Instituto Politécnico Nacional, IPN. Av. Luis Enrique Erro s/n. Unidad Adolfo López Mateos, Mexico City, Mexico
Interests: plasmodium vivax; pre-erythrocytic malaria vaccines; flavivirus vaccines; alphavirus-based vaccines; zika vaccines; dengue vaccines; chikungunya vaccines; VLP; recombinant viral vectors; chimpanzee adenovirus (ChAdOx); MVA
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, Advances in Alphavirus and Flavivirus Research (https://www.mdpi.com/journal/viruses/special_issues/alphavirus_flavivirus_research).

As we have seen during the last decade and the most recent pandemics, the emergence or re-emergence of zoonotic viral diseases has become one of the most important public health concerns globally. In particular, mosquito-borne viruses such as Dengue (DENV), Zika (ZIKV), and Chikungunya (CHIKV) viruses have emerged in recent decades, affecting millions of people worldwide. These alphaviruses and flaviviruses can be classified into a broader category of arboviruses, and they cause significant disease burdens and public health concerns. This Special Issue entitled “Advances in Alphavirus and Flavivirus Research” is devoted to publishing advances made in alphavirus and flavivirus research.

We welcome the submission of all types of articles, including short reports, original research, and reviews, for this Special Issue. We look forward to receiving your contributions.

Dr. Young Chan Kim
Dr. Arturo Reyes-Sandoval
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. 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

arbovirus
alphavirus
flavivirus
Chikungunya
Mayaro
Zika
dengue
diagnostics
surveillance
vaccine
antivirals
animal models

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Published Papers (9 papers)

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Research

21 pages, 7879 KiB

Open AccessArticle

Identification of TRIM21 and TRIM14 as Antiviral Factors Against Langat and Zika Viruses

by Pham-Tue-Hung Tran, Mir Himayet Kabir, Naveed Asghar, Matthew R. Hathaway, Assim Hayderi, Roger Karlsson, Anders Karlsson, Travis Taylor, Wessam Melik and Magnus Johansson

Viruses 2025, 17(5), 644; https://doi.org/10.3390/v17050644 (registering DOI) - 29 Apr 2025

Abstract

Flaviviruses are usually transmitted to humans via mosquito or tick bites, whose infections may lead to severe diseases and fatality. During intracellular infection, they remodel the endoplasmic reticulum (ER) membrane to generate compartments scaffolding the replication complex (RC) where replication of the viral genome takes place. In this study, we purified the ER membrane fraction of virus infected cells to identify the proteins that were enriched during flavivirus infection. We found that tripartite motif-containing proteins (TRIMs) including TRIM38, TRIM21, and TRIM14 were significantly enriched during infection with mosquito-borne (West Nile virus strain Kunjin and Zika virus (ZIKV)) and tick-borne (Langat virus (LGTV)) flaviviruses. Further characterizations showed that TRIM21 and TRIM14 act as restriction factors against ZIKV and LGTV, while TRIM38 hinders ZIKV infection. These TRIMs worked as interferon-stimulated genes to mediate IFN-I response against LGTV and ZIKV infections. Restriction of ZIKV by TRIM14 and TRIM38 coincides with their colocalization with ZIKV NS3. TRIM14-mediated LGTV restriction coincides with its colocalization with LGTV NS3 and NS5 proteins. However, TRIM21 did not colocalize with ZIKV and LGTV NS3 or NS5 protein suggesting its antiviral activity is not dependent on direct targeting the viral enzyme. Finally, we demonstrated that overexpression of TRIM21 and TRIM14 restricted LGTV replication. Full article

(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 2nd Edition)

13 pages, 2757 KiB

Open AccessArticle

Retrospective Study of Arbovirus Circulation in Northeast Brazil in 2019 and 2022: Insights into the Re-Emergence of DENV-3 and the Co-Infection of DENV-1 and CHIKV

by Sêmilly Suélen da Silva Sousa, Ana Cecília Ribeiro Cruz, Carine Fortes Aragão, Glennda Juscely Galvão Pereira Cereja, Sandro Patroca da Silva, Raira Maria Morais de Sousa, Murilo Tavares Amorim, Eliana Vieira Pinto da Silva, Bruno Tardelli Diniz Nunes and Valéria Cristina Soares Pinheiro

Viruses 2025, 17(4), 475; https://doi.org/10.3390/v17040475 - 26 Mar 2025

Viewed by 274

Abstract

Arboviruses transmitted by Aedes aegypti cause high number of cases and deaths annually. The aim was to investigate the presence of the presence of Dengue (DENV), Zika (ZIKV) and Chikungunya (CHIKV) viruses in endemic areas of Maranhão, northeastern Brazil. The study was carried out in Caxias, Codó, Peritoró, and São Mateus do Maranhão in 2019 (Caxias) and 2022. The blood samples were subjected to RNA extraction and then tested by RT-qPCR. Cell culture was used to attempt viral isolation and subsequent sequencing. In total, 171 samples were analyzed (32 from 2019, 18.7%) and 72 (42.1%) were found to have arboviruses: 68 (39.7%) from Caxias; 2 (1.1%) from Codó; 1 (0.6%) from Peritoró; and 1 (0.6%) from São Mateus. Overall, 85.3% (n = 58) of the positive samples were infected with DENV-1, 4 (four) (5.9%) with DENV-2 (Caxias), 1 (one) (1.5%) with DENV-3 (Caxias), and in 6 (six) (7.3%) samples CHIKV was detected, with one co-infection of DENV-1 and CHIKV (Caxias). The DENV-1 genotype V and the ECSA genotype of CHIKV were characterized in samples from Caxias. The detection of DENV-1, DENV-2, DENV-3, and more CHIKV in the interior of Maranhão alerts to the importance of virological studies in these areas. Full article

(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 2nd Edition)

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16 pages, 13674 KiB

Open AccessArticle

In Vitro System for Studying Ilhéus Virus, a Neglected Arbovirus: Ultrastructural Characterization of Cytopathology, Morphology, and Morphogenesis

by Maycon Douglas do Nascimento Garcia, Igor Pinto Silva Da Costa, Marcos Alexandre Nunes da Silva, Vivian Neuza dos Santos Ferreira, Ana Luisa Teixeira de Almeida, Gabriela Cardoso Caldas, Andressa Santos de Almeida, Ana Maria Bispo de Filippis, Natalia Fintelman-Rodrigues, Aline de Paula Dias da Silva, Marcelo Alves Ferreira, Thiago Moreno L. Souza, Alex Pauvolid-Corrêa and Debora Ferreira Barreto-Vieira

Viruses 2025, 17(3), 320; https://doi.org/10.3390/v17030320 - 26 Feb 2025

Viewed by 396

Abstract

Ilhéus Virus (ILHV) was first detected in 1944 in Ilhéus, state of Bahia, northeast Brazil. During cellular infection, orthoflaviviruses induce cellular changes related both to the replication process, the formation of replication complexes, and to structures resulting from cellular damage. Although more detailed data are available in the literature for other orthoflaviviruses, the relationship between ILHV, the formation of these structures, its replication cycle, and cellular changes remains unknown. One of the main objectives of this study is to characterize the primary ultrastructural changes in green monkey kidney epithelial cell lineage (Vero cell) infected with ILHV, as well as to map its replication cycle, virion structure, and genome. To achieve these objectives, Vero cell monolayers were infected with an MOI of 0.01 and collected at different times post-infection. Cell monolayers were evaluated under bright-field microscopy and transmission electron microscopy. Ultrastructural analyses confirmed that ILHV can induce the formation of double-membrane vesicles, convoluted membranes, and vesicular packets. These structures, like those observed in zika (ZIKV) and dengue (DENV) viruses, form replication complexes that aid ILHV’s replication process in cells. Our preliminary results reveal that ILHV infection induces cytopathogenesis like that observed in vitro studies for other arboviruses. Full article

(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 2nd Edition)

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16 pages, 3530 KiB

Open AccessArticle

Attenuation of Chikungunya Virus by a Single Amino Acid Substitution in the nsP1 Component of a Non-Structural Polyprotein

by John Chamberlain, Stuart D. Dowall, Jack Smith, Geoff Pearson, Victoria Graham, John Raynes and Roger Hewson

Viruses 2025, 17(2), 281; https://doi.org/10.3390/v17020281 - 18 Feb 2025

Viewed by 464

Abstract

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that, since its re-emergence in 2004, has become recognised as a major public health concern throughout many tropical and sub-tropical regions of the world. Amongst the insights gained from studies on other alphaviruses, several key determinants of virulence have been identified, including one present at the P3 position in the nsP1/nsP2 cleavage domain of the S.A.AR86 Sindbis (SINV) strain. This strain is associated with neurovirulence in adult mice; however, when a threonine-to-isoleucine substitution is engineered at this P3 position, an attenuated phenotype results. A reverse genetics system was developed to evaluate the phenotype that resulted from the substitution of alanine, present at the P3 position in the wild-type CHIKV clone, with valine. The A533V-mutant CHIKV induced milder disease symptoms in the C57BL/6 mouse model than the wild-type virus, in terms of severity of inflammation, length of viraemic period, and histological changes. Furthermore, the induction of type I IFN occurred more rapidly in both CHIKV-infected cell cultures and the mouse model with the mutant CHIKV. Full article

(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 2nd Edition)

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14 pages, 1054 KiB

Open AccessArticle

Elevated Plasma Angiopoietin-like 4 Protein Levels in Adult Patients with Dengue

by Win Khaing, Suk Hiang Lau, Tun-Linn Thein, Nguan Soon Tan, Sylvie Alonso, Shawn Vasoo, Po Ying Chia, David Chien Boon Lye, Yee Sin Leo and Vincent T. K. Chow

Viruses 2025, 17(2), 226; https://doi.org/10.3390/v17020226 - 6 Feb 2025

Viewed by 798

Abstract

Dengue virus infection can cause severe complications due to vascular leakage. Angiopoietin-like protein 4 (ANGPTL4) regulates vascular permeability, but its role in dengue pathogenesis is unclear. This study investigated the association between plasma ANGPTL4 levels and dengue severity in Singapore adults. Plasma samples from 48 dengue patients (24 severe and 24 non-severe) during acute and convalescent phases were selected from the prospective COhort study on progression of DENgue severity in Singapore adults (CODEN) cohort. The CODEN was conducted at the National Centre for Infectious Diseases, Tan Tock Seng Hospital, from June 2016 to January 2020. ANGPTL4 levels were measured and compared to 152 healthy controls. Logistic regression assessed the relationship between plasma ANGPTL4 concentrations and disease severity. There were no statistically significant differences in ANGPTL4 levels between severe and non-severe dengue patients during acute (677.4 vs. 909.1 pg/mL, p = 0.4) or convalescent phases (793.7 vs. 565.6 pg/mL, p = 0.96). Plasma ANGPTL4 levels were significantly elevated during acute dengue (4634.3 pg/mL) versus healthy controls (907.4 pg/mL), declining during convalescence. Compared to the lowest tertile, the adjusted odds ratios for severe dengue were 0.36 (95%CI: 0.08–1.65, p = 0.190) for medium tertile and 0.57 (95%CI: 0.13–2.49, p = 0.456) for high tertile. Among patients with high ANGPTL4 levels (>5000 pg/mL), 36.4% developed severe complications, including significant plasma leakage. Plasma ANGPTL4 levels were significantly higher in dengue patients than controls, suggesting its potential as a biomarker, which warrants future detailed investigations. Larger prospective studies with serial sampling, including pediatric populations, may clarify the role of ANGPTL4 in severe dengue. Full article

(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 2nd Edition)

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12 pages, 1349 KiB

Open AccessArticle

Establishment of a New Real-Time Molecular Assay for the Detection of Babanki Virus in Africa

by Martin Faye, Mathilde Ban, Fatou Kiné Top, El Hadji Ndiaye, Fatou Diène Thiaw, Gamou Fall, Moussa Moise Diagne, Amadou Alpha Sall, Mawlouth Diallo, Valérie Choumet and Ousmane Faye

Viruses 2024, 16(12), 1841; https://doi.org/10.3390/v16121841 - 27 Nov 2024

Viewed by 830

Abstract

Babanki virus is a subtype of the Sindbis virus, a widespread arthropod-borne alphavirus circulating in Eurasia, Africa, and Oceania. Characterized by rashes and arthritis, clinical infections due to Sindbis were mainly reported in Africa, Australia, Asia, and Europe. However, its sub-type, Babanki virus, was reported in Northern Europe and Africa, where its epidemiology potential remains poorly understood. The diagnosis of alphaviruses is mainly based on serological testing and conventional PCR methods, which have considerable limits. In this study, we developed a real-time qRT-PCR assay for the detection of Babanki virus. The analytical sensitivity and specificity of the newly established assay were evaluated using in vitro standard RNA and related viruses relevant to the African context, respectively. In addition, its diagnostic sensitivity was assessed using a subset of Babanki virus-positive and -negative mosquito pools collected from the field. The new real-time qRT-PCR assay exhibited a 100% specificity, a 95% detection limit of 1 RNA molecule/reaction, and a diagnostic sensitivity of up to 120 pfu/reaction. This newly established assay could be useful not only for the detection of Babanki virus during epidemics but also in future experimental and surveillance studies focusing on their epidemiology and pathogenicity. Full article

(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 2nd Edition)

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18 pages, 2219 KiB

Open AccessArticle

The Low-Density Lipoprotein Receptor-Related Protein-1 Is Essential for Dengue Virus Infection

by Vivian Huerta, Alejandro M. Martin, Mónica Sarría, Osmany Guirola, Alexis Yero, Yassel Ramos, Dianne Pupo, Dayron Martin, Tea Carletti, Luis G. González-Lodeiro, Alessandro Marcello and Glay Chinea

Viruses 2024, 16(11), 1692; https://doi.org/10.3390/v16111692 - 30 Oct 2024

Cited by 1 | Viewed by 1506

Abstract

Dengue virus (DENV) causes the most prevalent and rapidly spreading arboviral disease of humans. It enters human cells by receptor-mediated endocytosis. Numerous cell-surface proteins were proposed as DENV entry factors. Among these, the phosphatidylserine receptor TIM-1 is the only one known to mediate virus internalization. However, several cellular models lacking TIM-1 are permissive to DENV infection, suggesting that other receptors exist. Here, we show that the low-density lipoprotein receptor-related protein-1 (LRP1) binds DENV virions by interacting with the DIII of the viral envelope glycoprotein. DENV infection is effectively inhibited by the purified receptor at 5 × 10⁻⁸ mol/L, and the interaction of the envelope protein with LRP1 is also blocked by a natural ligand of LRP1. The depletion of LRP1 causes 100-fold lower production of infectious virus than controls. Our results indicate that LRP1 is another DENV receptor, thus becoming an attractive target to evaluate for the development of effective antiviral drugs against DENV. Full article

(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 2nd Edition)

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16 pages, 4189 KiB

Open AccessArticle

Membrane Retention of West Nile Virus NS5 Depends on NS1 or NS3 for Enzymatic Activity

by Alanna C. Tseng, Vivek R. Nerurkar, Kabi R. Neupane, Helmut Kae and Pakieli H. Kaufusi

Viruses 2024, 16(8), 1303; https://doi.org/10.3390/v16081303 - 16 Aug 2024

Viewed by 1129

Abstract

West Nile virus (WNV) nonstructural protein 5 (NS5) possesses multiple enzymatic domains essential for viral RNA replication. During infection, NS5 predominantly localizes to unique replication organelles (ROs) at the rough endoplasmic reticulum (RER), known as vesicle packets (VPs) and convoluted membranes (CMs), with a portion of NS5 accumulating in the nucleus. NS5 is a soluble protein that must be in the VP, where its enzymatic activities are required for viral RNA synthesis. However, the mechanistic processes behind the recruitment of NS5 from the cytoplasm to the RER membrane remain unclear. Here, we utilize high-resolution confocal microscopy and sucrose density gradient ultracentrifugation to investigate whether the association of NS5 with other NS proteins contributes to its membrane recruitment and retention. We demonstrate that NS1 or NS3 partially influences the NS5 association with the membrane. We further demonstrate that processed NS5 is predominantly in the cytoplasm and nucleus, indicating that the processing of NS5 from the viral polyprotein does not contribute to its membrane localization. These observations suggest that other host or viral factors, such as the enwrapment of NS5 by the RO, may also be necessary for the complete membrane retention of NS5. Therefore, studies on the inhibitors that disrupt the membrane localization of WNV NS5 are warranted for antiviral drug development. Full article

(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 2nd Edition)

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16 pages, 2174 KiB

Open AccessArticle

Elucidation of the Epitranscriptomic RNA Modification Landscape of Chikungunya Virus

by Belinda Baquero-Pérez, Enrico Bortoletto, Umberto Rosani, Anna Delgado-Tejedor, Rebeca Medina, Eva Maria Novoa, Paola Venier and Juana Díez

Viruses 2024, 16(6), 945; https://doi.org/10.3390/v16060945 - 12 Jun 2024

Cited by 2 | Viewed by 1973

Abstract

The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. Among the 32 distinct RNA modifications analysed by mass spectrometry, inosine was found enriched in the genomic CHIKV RNA. However, orthogonal validation by Illumina RNA-seq analyses did not identify any inosine modification along the CHIKV RNA genome. Moreover, CHIKV infection did not alter the expression of ADAR1 isoforms, the enzymes that catalyse the adenosine to inosine conversion. Together, this study highlights the importance of a multidisciplinary approach to assess the presence of RNA modifications in viral RNA genomes. Full article

(This article belongs to the Special Issue Advances in Alphavirus and Flavivirus Research, 2nd Edition)

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