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Emerging Microbes, Infections and Spillovers

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

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 24900

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Dr. Laura Kakkola

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Guest Editor

Research Center for Cancer, Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
Interests: virus–cell interactions; innate and adaptive immunity to viral infections; molecular mechanisms of cytokine gene expression; emerging viruses; viral innate and adaptive immunity antagonists
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Dr. Tarja Sironen

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Guest Editor

Department of Virology, University of Helsinki, Helsinki, Finland
Interests: One Health; microbiology and microbial evolution; zoonoses; emerging infectious diseases
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Dr. Ravi Kant

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Guest Editor

Associate Professor (Docent) of Medical Microbiology, University of Helsinki, Helsinki, Finland
Interests: genomics; metagenomics; microbiology; bioinformatics; viromics
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Dr. Maciej Grzybek

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Guest Editor

Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Powstania Styczniowego 9B, 81-519 Gdynia, Poland
Interests: parasites; helminths; molecular biology; parasite ecology; rodents; next-generation sequencing; PCR bioinformatics; ecology; animal ecology; data analysis; DNA extraction; ecology and evolution; genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Emerging pathogens are a constant threat to mankind, as shown by the Ebola and Zika virus outbreaks and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. These viruses are zoonotic (i.e. they cross-species barriers), alike the majority of emerging pathogens. Internationalization and industrialization have dramatically changed the vulnerability of human and animal populations to emerging and re-emerging infectious diseases, changing both the scale and pace of disease outbreaks. New infectious diseases are expected as a major threat to global public health in coming years. Most of these are caused by microbes specially viruses that are able to cross the host species barriers as zoonoses or further establish human-to-human transmission. In order to detect these pathogens and develop control measures, studies on the reservoirs and vectors, molecular biology, and diagnostics of these pathogens are needed. This Special Issue seeks all types of manuscripts (e.g., reviews, research articles, and short communications) related to emerging pathogens and viral zoonoses. The topics may include (but are not restricted to) virus discovery, virus-host interaction, pathogenesis, cross-species transmission, virus evolution, reservoirs, cross-species transmission and zoonotic aspects are considered.

Dr. Laura Kakkola
Dr. Tarja Sironen
Dr. Ravi Kant
Dr. Maciej Grzybek
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

emerging infections
virus spillovers
microbes
cross-species transmission
virus evolution
viral disease
virus reservoirs
virus-host interaction
pathogenesis

Published Papers (10 papers)

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Editorial

Jump to: Research, Other

4 pages, 194 KiB

Open AccessEditorial

Emerging Microbes, Infections, and Spillovers: Charting a Path Forward

by Maciej Grzybek, Laura Kakkola, Tarja Sironen and Ravi Kant

Viruses 2023, 15(12), 2392; https://doi.org/10.3390/v15122392 - 08 Dec 2023

Viewed by 857

Abstract

In an age defined by rapid globalization and unprecedented technological advancements, the field of infectious diseases stands at the intersection of complex challenges and promising opportunities [...] Full article

(This article belongs to the Special Issue Emerging Microbes, Infections and Spillovers)

Research

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15 pages, 2432 KiB

Open AccessArticle

Genetic Diversity of Type A Influenza Viruses Found in Swine Herds in Northwestern Poland from 2017 to 2019: The One Health Perspective

by Lukasz Rabalski, Maciej Kosinski, Piotr Cybulski, Tomasz Stadejek and Krzysztof Lepek

Viruses 2023, 15(9), 1893; https://doi.org/10.3390/v15091893 - 07 Sep 2023

Viewed by 1091

Abstract

Influenza A viruses (IAV) are still a cause of concern for public health and veterinary services worldwide. With (−) RNA-segmented genome architecture, influenza viruses are prone to reassortment and can generate a great variety of strains, some capable of crossing interspecies barriers. Seasonal IAV strains continuously spread from humans to pigs, leading to multiple reassortation events with strains endemic to swine. Due to its high adaptability to humans, a reassortant strain based on “human-like” genes could potentially be a carrier of avian origin segments responsible for high virulence, and hence become the next pandemic strain with unseen pathogenicity. The rapid evolution of sequencing methods has provided a fast and cost-efficient way to assess the genetic diversity of IAV. In this study, we investigated the genetic diversity of swine influenza viruses (swIAVs) collected from Polish farms. A total of 376 samples were collected from 11 farms. The infection was confirmed in 112 cases. The isolates were subjected to next-generation sequencing (NGS), resulting in 93 full genome sequences. Phylogenetic analysis classified 59 isolates as genotype T (H1avN2g) and 34 isolates as genotype P (H1pdmN1pdm), all of which had an internal gene cassette (IGC) derived from the H1N1pdm09-like strain. These data are consistent with evolutionary trends in European swIAVs. The applied methodology proved to be useful in monitoring the genetic diversity of IAV at the human–animal interface. Full article

(This article belongs to the Special Issue Emerging Microbes, Infections and Spillovers)

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18 pages, 2734 KiB

Open AccessArticle

A Novel Simian Adenovirus Associating with Human Adenovirus Species G Isolated from Long-Tailed Macaque Feces

by Nathamon Kosoltanapiwat, Lia van der Hoek, Cormac M. Kinsella, Jarinee Tongshoob, Luxsana Prasittichai, Michelle Klein, Maarten F. Jebbink, Martin Deijs, Onrapak Reamtong, Kobporn Boonnak, Wathusiri Khongsiri, Juthamas Phadungsombat, Daraka Tongthainan, Phitsanu Tulayakul and Marnoch Yindee

Viruses 2023, 15(6), 1371; https://doi.org/10.3390/v15061371 - 14 Jun 2023

Cited by 1 | Viewed by 1472 | Correction

Abstract

Metagenomics has demonstrated its capability in outbreak investigations and pathogen surveillance and discovery. With high-throughput and effective bioinformatics, many disease-causing agents, as well as novel viruses of humans and animals, have been identified using metagenomic analysis. In this study, a VIDISCA metagenomics workflow was used to identify potential unknown viruses in 33 fecal samples from asymptomatic long-tailed macaques (Macaca fascicularis) in Ratchaburi Province, Thailand. Putatively novel astroviruses, enteroviruses, and adenoviruses were detected and confirmed by PCR analysis of long-tailed macaque fecal samples collected from areas in four provinces, Ratchaburi, Kanchanaburi, Lopburi, and Prachuap Khiri Khan, where humans and monkeys live in proximity (total n = 187). Astroviruses, enteroviruses, and adenoviruses were present in 3.2%, 7.5%, and 4.8% of macaque fecal samples, respectively. One adenovirus, named AdV-RBR-6-3, was successfully isolated in human cell culture. Whole-genome analysis suggested that it is a new member of the species Human adenovirus G, closely related to Rhesus adenovirus 53, with evidence of genetic recombination and variation in the hexon, fiber, and CR1 genes. Sero-surveillance showed neutralizing antibodies against AdV-RBR-6-3 in 2.9% and 11.2% of monkeys and humans, respectively, suggesting cross-species infection of monkeys and humans. Overall, we reported the use of metagenomics to screen for possible new viruses, as well as the isolation and molecular and serological characterization of the new adenovirus with cross-species transmission potential. The findings emphasize that zoonotic surveillance is important and should be continued, especially in areas where humans and animals interact, to predict and prevent the threat of emerging zoonotic pathogens. Full article

(This article belongs to the Special Issue Emerging Microbes, Infections and Spillovers)

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16 pages, 4254 KiB

Open AccessArticle

Clinical Epidemiology, Pathology, and Molecular Investigation of Lumpy Skin Disease Outbreaks in Bangladesh during 2020–2021 Indicate the Re-Emergence of an Old African Strain

by Rokshana Parvin, Emdadul Haque Chowdhury, Md Taohidul Islam, Jahan Ara Begum, Mohammed Nooruzzaman, Anja Globig, Klaas Dietze, Bernd Hoffmann and Eeva Tuppurainen

Viruses 2022, 14(11), 2529; https://doi.org/10.3390/v14112529 - 15 Nov 2022

Cited by 10 | Viewed by 5003

Abstract

Lumpy skin disease (LSD) emerged in Bangladesh in mid-2019, leading to great economic losses for cattle farmers. This study describes the recent occurrence of the LSDV in Bangladesh and examines the clinical manifestation of the disease in local cattle breeds, characteristic epidemiological features, and pathological findings in affected animals. In addition, a full-genome sequencing of two local LSDV isolates was carried out. A total of 565 animals from 88 households were investigated, and 165 samples (skin lesions, saliva, nasal discharge, feces, and milk) were collected for virus detection. Pathology and immunohistochemistry were performed on nodule biopsies. Fever, nodular skin lesions, and swelling of the joints were the most common clinical manifestations. Skin lesions had a higher concentration of viral DNA compared to other sample types and were therefore selected for virus isolation and characterization. Pathology of the LSD skin nodules comprised a granulomatous reaction in the dermis and hypodermis that extended to the surrounding tissues. Development of the skin lesions started with swelling of keratinocytes with cytoplasmic vacuolation, vasculitis, panniculitis, thrombosis, and infarction. Altogether, the LSDV produced transmural, hemorrhagic, necrotizing, proliferative and ulcerative dermatitis. The LSD viral antigen was detected occasionally in the macrophages, epithelial cells, and vascular smooth muscle cells. The complete genome sequence analysis revealed that the two Bangladeshi field strains (BD-V392.1 and BD-V395.1) were distinct from the contemporary field strains and were closely related to the ancestral African Neethling strain. The findings of this study will improve the diagnosis, monitoring, and control of LSD in Bangladesh. Full article

(This article belongs to the Special Issue Emerging Microbes, Infections and Spillovers)

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10 pages, 1605 KiB

Open AccessArticle

Kiwira Virus, a Newfound Hantavirus Discovered in Free-tailed Bats (Molossidae) in East and Central Africa

by Sabrina Weiss, Lwitiho E. Sudi, Ariane Düx, Chacha D. Mangu, Nyanda Elias Ntinginya, Gabriel M. Shirima, Sophie Köndgen, Grit Schubert, Peter T. Witkowski, Jean-Jacques Muyembe, Steve Ahuka, Boris Klempa, Fabian H. Leendertz and Detlev H. Krüger

Viruses 2022, 14(11), 2368; https://doi.org/10.3390/v14112368 - 27 Oct 2022

Cited by 4 | Viewed by 3467

Abstract

A novel hantavirus, named Kiwira virus, was molecularly detected in six Angolan free-tailed bats (Mops condylurus, family Molossidae) captured in Tanzania and in one free-tailed bat in the Democratic Republic of Congo. Hantavirus RNA was found in different organs, with the highest loads in the spleen. Nucleotide sequences of large parts of the genomic S and L segments were determined by in-solution hybridisation capture and high throughput sequencing. Phylogenetic analyses placed Kiwira virus into the genus Mobatvirus of the family Hantaviridae, with the bat-infecting Quezon virus and Robina virus as closest relatives. The detection of several infected individuals in two African countries, including animals with systemic hantavirus infection, provides evidence of active replication and a stable circulation of Kiwira virus in M. condylurus bats and points to this species as a natural host. Since the M. condylurus home range covers large regions of Sub-Saharan Africa and the species is known to roost inside and around human dwellings, a potential spillover of the Kiwira virus to humans must be considered. Full article

(This article belongs to the Special Issue Emerging Microbes, Infections and Spillovers)

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7 pages, 839 KiB

Open AccessCommunication

Wild Red Deer (Cervus elaphus) Do Not Play a Role as Vectors or Reservoirs of SARS-CoV-2 in North-Eastern Poland

by Martyna Krupińska, Jakub Borkowski, Aleksander Goll, Joanna Nowicka, Karolina Baranowicz, Vincent Bourret, Tomas Strandin, Sanna Mäki, Ravi Kant, Tarja Sironen and Maciej Grzybek

Viruses 2022, 14(10), 2290; https://doi.org/10.3390/v14102290 - 18 Oct 2022

Cited by 3 | Viewed by 2897

Abstract

Several studies reported a high prevalence of SARS-CoV-2 among white-tailed deer in North America. Monitoring cervids in all regions to better understand SARS-CoV-2 infection and circulation in other deer populations has been urged. To evaluate deer exposure and/or infection to/by SARS-CoV-2 in Poland, we sampled 90 red deer shot by hunters in five hunting districts in north-eastern Poland. Serum and nasopharyngeal swabs were collected, and then an immunofluorescent assay (IFA) to detect anti-SARS-CoV-2 antibodies was performed as well as real-time PCR with reverse transcription for direct virus detection. No positive samples were detected. There is no evidence of spillover of SARS-CoV-2 from the human to deer population in Poland. Full article

(This article belongs to the Special Issue Emerging Microbes, Infections and Spillovers)

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18 pages, 2080 KiB

Open AccessArticle

I226R Protein of African Swine Fever Virus Is a Suppressor of Innate Antiviral Responses

by Jinxuan Hong, Xiaojuan Chi, Xu Yuan, Faxin Wen, Kul Raj Rai, Lei Wu, Zhongbao Song, Song Wang, Guijie Guo and Ji-Long Chen

Viruses 2022, 14(3), 575; https://doi.org/10.3390/v14030575 - 11 Mar 2022

Cited by 16 | Viewed by 3448

Abstract

African swine fever is one of the most devastating swine diseases caused by African swine fever virus (ASFV). Although ASFV encodes more than 160 viral proteins, the implication of a majority of ASFV proteins in regulating host immunity is yet to be explored, and the mechanisms of immune evasion by ASFV proteins are largely unknown. Here, we report that the I226R protein of ASFV significantly suppressed innate immune responses. The ectopic expression of ASFV I226R in 293T cells significantly inhibited the activation of interferon-stimulated response element promoters triggered by Sendai virus (SeV), poly(I:C), or cyclic GMP-AMP synthase (cGAS)/STING. The I226R protein caused a significant decrease in the expression of interferons and interferon-stimulating genes in cells infected with SeV. Similar results were obtained from experiments using I226R-overexpressed PK15 and 3D4/21 cells stimulated with vesicular stomatitis virus. We observed that I226R inhibited the activation of both nuclear factor-kappa B (NF-κB) and interferon regulatory factor 3 (IRF3). Furthermore, it was shown that overexpression of I226R suppressed IRF3 activation and caused the degradation of NF-κB essential modulator (NEMO) protein. The I226R-induced NEMO degradation could be prevented by treatment with MG132, a proteasome inhibitor. Together, these results reveal that the ASFV I226R protein impairs antiviral responses, likely through multiple mechanisms including the suppression of NF-κB and IRF3 activation, to counteract innate immune responses during the viral infection. Full article

(This article belongs to the Special Issue Emerging Microbes, Infections and Spillovers)

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11 pages, 2767 KiB

Open AccessArticle

Common Laboratory Mice Are Susceptible to Infection with the SARS-CoV-2 Beta Variant

by Ravi Kant, Lauri Kareinen, Teemu Smura, Tobias L. Freitag, Sawan Kumar Jha, Kari Alitalo, Seppo Meri, Tarja Sironen, Kalle Saksela, Tomas Strandin, Anja Kipar and Olli Vapalahti

Viruses 2021, 13(11), 2263; https://doi.org/10.3390/v13112263 - 11 Nov 2021

Cited by 21 | Viewed by 2919

Abstract

Small animal models are of crucial importance for assessing COVID-19 countermeasures. Common laboratory mice would be well-suited for this purpose but are not susceptible to infection with wild-type SARS-CoV-2. However, the development of mouse-adapted virus strains has revealed key mutations in the SARS-CoV-2 spike protein that increase infectivity, and interestingly, many of these mutations are also present in naturally occurring SARS-CoV-2 variants of concern. This suggests that these variants might have the ability to infect common laboratory mice. Herein we show that the SARS-CoV-2 beta variant attains infectibility to BALB/c mice and causes pulmonary changes within 2–3 days post infection, consistent with results seen in other murine models of COVID-19, at a reasonable virus dose (2 × 10⁵ PFU). The findings suggest that common laboratory mice can serve as the animal model of choice for testing the effectiveness of antiviral drugs and vaccines against SARS-CoV-2. Full article

(This article belongs to the Special Issue Emerging Microbes, Infections and Spillovers)

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Other

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5 pages, 732 KiB

Open AccessCorrection

Correction: Kosoltanapiwat et al. A Novel Simian Adenovirus Associating with Human Adenovirus Species G Isolated from Long-Tailed Macaque Feces. Viruses 2023, 15, 1371

Viruses 2023, 15(9), 1871; https://doi.org/10.3390/v15091871 - 04 Sep 2023

Viewed by 547

Abstract

After publication of the article, the authors received comments from a member of the Viruses editorial board who is an expert in the field of adenovirus concerning figures and references that should be included in the paper [...] Full article

(This article belongs to the Special Issue Emerging Microbes, Infections and Spillovers)

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7 pages, 835 KiB

Open AccessBrief Report

Prolonged Viability of Senecavirus A in Exposed House Flies (Musca domestica)

by Justin Heath Turner, Willian Pinto Paim, Mayara Fernanda Maggioli, Cristina Mendes Peter, Robert Miknis, Justin Talley and Fernando Vicosa Bauermann

Viruses 2022, 14(1), 127; https://doi.org/10.3390/v14010127 - 11 Jan 2022

Cited by 3 | Viewed by 1509

Abstract

House flies (Musca domestica) are often present in swine farms worldwide. These flies utilize animal secretions and waste as a food source. House flies may harbor and transport microbes and pathogens acting as mechanical vectors for diseases. Senecavirus A (SVA) infection in pigs occurs via oronasal route, and animals shed high virus titers to the environment. Additionally, SVA possesses increased environmental resistance. Due to these reasons, we investigated the tenacity of SVA in house flies. Five groups of flies, each composed of ten females and ten males, were exposed to SVA, titer of 10^9.3 tissue culture infectious dose (TCID₅₀/mL). Groups of male and female flies were collected at 0, 6, 12, 24, and 48 h post-exposure. For comparison purposes, groups of flies were exposed to Swinepox virus (SwPV). Infectious SVA was identified in all tested groups. Successful isolation of SVA demonstrated the titers varied between 10^6.8 and 10^2.8 TCID₅₀/mL in female groups and varied from 10^5.85 to 10^3.8 TCID₅₀/mL in male groups. In contrast, infectious SwPV was only detected in the female group at 6 h. The significant SVA infectious titer for prolonged periods of time, up to 48 h, indicates a potential role of flies in SVA transmission. Full article

(This article belongs to the Special Issue Emerging Microbes, Infections and Spillovers)

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