Viruses

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13 pages, 9232 KiB

Open AccessArticle

A Novel Nobecovirus in an Epomophorus wahlbergi Bat from Nairobi, Kenya

by Meredith C. VanAcker, Koray Ergunay, Paul W. Webala, Maureen Kamau, Janerose Mutura, Rashid Lebunge, Griphin Ochieng Ochola, Brian P. Bourke, Emily G. McDermott, Nicole L. Achee, Le Jiang, John P. Grieco, Erick Keter, Audrey Musanga, Suzan Murray, Jared A. Stabach, Meggan E. Craft, Eric M. Fèvre, Yvonne-Marie Linton and James Hassell

Viruses 2025, 17(4), 557; https://doi.org/10.3390/v17040557 - 12 Apr 2025

Viewed by 574

Abstract

Most human emerging infectious diseases are zoonotic, originating in animal hosts prior to spillover to humans. Prioritizing the surveillance of wildlife that overlaps with humans and human activities can increase the likelihood of detecting viruses with a high potential for human infection. Here, [...] Read more.

Most human emerging infectious diseases are zoonotic, originating in animal hosts prior to spillover to humans. Prioritizing the surveillance of wildlife that overlaps with humans and human activities can increase the likelihood of detecting viruses with a high potential for human infection. Here, we obtained fecal swabs from two fruit bat species—Eidolon helvum (n = 6) and Epomophorus wahlbergi (n = 43) (family Pteropodidae)—in peridomestic habitats in Nairobi, Kenya, and used metagenome sequencing to detect microorganisms. A near-complete genome of a novel virus assigned taxonomically to the Coronaviridae family Betacoronavirus genus and Nobecovirus subclade was characterized from E. wahlbergi. Phylogenetic analysis indicates this unique Nobecovirus clade shares a common ancestor with Eidolon/Rousettus Nobecovirus subclades isolated from Madagascar, Kenya, and Cameroon. Recombination was detected across open reading frames, except the spike protein, in all BOOTSCAN analyses, indicating intra-host coinfection and genetic exchange between genome regions. Although Nobecoviruses are currently bat-specific and are not known to be zoonotic, the propensity of coronaviruses to undergo frequent recombination events and the location of the virus alongside high human and livestock densities in one of East Africa’s most rapidly developing cities justifies continued surveillance of animal viruses in high-risk urban landscapes. Full article

(This article belongs to the Special Issue Bat- and Rodent-Borne Zoonotic Viruses)

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14 pages, 3792 KiB

Open AccessArticle

Detection of Bombali Virus in a Mops condylurus Bat in Kyela, Tanzania

by Ariane Düx, Sudi E. Lwitiho, Ahidjo Ayouba, Caroline Röthemeier, Kevin Merkel, Sabrina Weiss, Guillaume Thaurignac, Angelika Lander, Leonce Kouadio, Kathrin Nowak, Victor Corman, Christian Drosten, Emmanuel Couacy-Hymann, Detlev H. Krüger, Andreas Kurth, Sébastien Calvignac-Spencer, Martine Peeters, Nyanda E. Ntinginya, Fabian H. Leendertz and Chacha Mangu

Viruses 2024, 16(8), 1227; https://doi.org/10.3390/v16081227 - 31 Jul 2024

Cited by 1 | Viewed by 1786

Abstract

Bombali virus (BOMV) is a novel Orthoebolavirus that has been detected in free-tailed bats in Sierra Leone, Guinea, Kenya, and Mozambique. We screened our collection of 349 free-tailed bat lungs collected in Côte d’Ivoire and Tanzania for BOMV RNA and tested 228 bat [...] Read more.

Bombali virus (BOMV) is a novel Orthoebolavirus that has been detected in free-tailed bats in Sierra Leone, Guinea, Kenya, and Mozambique. We screened our collection of 349 free-tailed bat lungs collected in Côte d’Ivoire and Tanzania for BOMV RNA and tested 228 bat blood samples for BOMV antibodies. We did not detect BOMV-specific antibodies but found BOMV RNA in a Mops condylurus bat from Tanzania, marking the first detection of an ebolavirus in this country. Our findings further expand the geographic range of BOMV and support M. condylurus’ role as a natural BOMV host. Full article

(This article belongs to the Special Issue Bat- and Rodent-Borne Zoonotic Viruses)

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16 pages, 4678 KiB

Open AccessArticle

Hantavirus Expansion Trends in Natural Host Populations in Brazil

by José Henrique Fortes Mello, Renata L. Muylaert and Carlos Eduardo Viveiros Grelle

Viruses 2024, 16(7), 1154; https://doi.org/10.3390/v16071154 - 17 Jul 2024

Viewed by 1472

Abstract

Hantaviruses are zoonotic agents responsible for causing Hantavirus Cardiopulmonary Syndrome (HCPS) in the Americas, with Brazil ranking first in number of confirmed HCPS cases in South America. In this study, we simulate the monthly spread of highly lethal hantavirus in natural hosts by [...] Read more.

Hantaviruses are zoonotic agents responsible for causing Hantavirus Cardiopulmonary Syndrome (HCPS) in the Americas, with Brazil ranking first in number of confirmed HCPS cases in South America. In this study, we simulate the monthly spread of highly lethal hantavirus in natural hosts by conjugating a Kermack–McCormick SIR model with a cellular automata model (CA), therefore simultaneously evaluating both in-cell and between-cell infection dynamics in host populations, using recently compiled data on main host species abundances and confirmed deaths by hantavirus infection. For both host species, our models predict an increase in the area of infection, with 22 municipalities where no cases have been confirmed to date expected to have at least one case in the next decade, and a reduction in infection in 11 municipalities. Our findings support existing research and reveal new areas where hantavirus is likely to spread within recognized epicenters. Highlighting spatial-temporal trends and potential expansion, we emphasize the increased risk due to pervasive habitat fragmentation and agricultural expansion. Consistent prevention efforts and One Health actions are crucial, especially in newly identified high-risk municipalities. Full article

(This article belongs to the Special Issue Bat- and Rodent-Borne Zoonotic Viruses)

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22 pages, 1312 KiB

Open AccessArticle

Host–Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts

by Wanlin Li and Nadia Tahiri

Viruses 2024, 16(7), 1133; https://doi.org/10.3390/v16071133 - 15 Jul 2024

Cited by 2 | Viewed by 1340

Abstract

Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provides vital insights into transmission dynamics and host adaptation. Prior research has yielded valuable [...] Read more.

Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provides vital insights into transmission dynamics and host adaptation. Prior research has yielded valuable insights into phenomena such as host switching, cospeciation, and other dynamics concerning the interaction between CoVs and bats. Nonetheless, a distinct gap exists in the current literature concerning a comparative cophylogenetic analysis focused on elucidating the contributions of sequence fragments to the co-evolution between hosts and viruses. In this study, we analyzed the cophylogenetic patterns of 69 host–virus connections. Among the 69 host–virus links examined, 47 showed significant cophylogeny based on ParaFit and PACo analyses, affirming strong associations. Focusing on two proteins, ORF1ab and spike, we conducted a comparative analysis of host and CoV phylogenies. For ORF1ab, the specific window ranged in multiple sequence alignment (positions 520–680, 770–870, 2930–3070, and 4910–5080) exhibited the lowest Robinson–Foulds (RF) distance (i.e., 84.62%), emphasizing its higher contribution in the cophylogenetic association. Similarly, within the spike region, distinct window ranges (positions 0–140, 60–180, 100–410, 360–550, and 630–730) displayed the lowest RF distance at 88.46%. Our analysis identified six recombination regions within ORF1ab (positions 360–1390, 550–1610, 680–1680, 700–1710, 2060–3090, and 2130–3250), and four within the spike protein (positions 10–510, 50–560, 170–710, and 230–730). The convergence of minimal RF distance regions with combination regions robustly affirms the pivotal role of recombination in viral adaptation to host selection pressures. Furthermore, horizontal gene transfer reveals prominent instances of partial gene transfer events, occurring not only among variants within the same host species but also crossing host species boundaries. This suggests a more intricate pattern of genetic exchange. By employing a multifaceted approach, our comprehensive strategy offers a nuanced understanding of the intricate interactions that govern the co-evolutionary dynamics between bat hosts and CoVs. This deeper insight enhances our comprehension of viral evolution and adaptation mechanisms, shedding light on the broader dynamics that propel viral diversity. Full article

(This article belongs to the Special Issue Bat- and Rodent-Borne Zoonotic Viruses)

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14 pages, 873 KiB

Open AccessArticle

Sosuga Virus Detected in Egyptian Rousette Bats (Rousettus aegyptiacus) in Sierra Leone

by Brian R. Amman, Alusine H. Koroma, Amy J. Schuh, Immah Conteh, Tara K. Sealy, Ibrahim Foday, Jonathan Johnny, Ibrahim A. Bakarr, Shannon L. M. Whitmer, Emily A. Wright, Aiah A. Gbakima, James Graziano, Camilla Bangura, Emmanuel Kamanda, Augustus Osborne, Emmanuel Saidu, Jonathan A. Musa, Doris F. Bangura, Sammuel M. T. Williams, George M. Fefegula, Christian Sumaila, Juliet Jabaty, Fatmata H. James, Amara Jambai, Kate Garnett, Thomas F. Kamara, Jonathan S. Towner and Aiah Lebbie Show full author list Hide full author list

Viruses 2024, 16(4), 648; https://doi.org/10.3390/v16040648 - 22 Apr 2024

Cited by 5 | Viewed by 2150

Abstract

Sosuga virus (SOSV), a rare human pathogenic paramyxovirus, was first discovered in 2012 when a person became ill after working in South Sudan and Uganda. During an ecological investigation, several species of bats were sampled and tested for SOSV RNA and only one [...] Read more.

Sosuga virus (SOSV), a rare human pathogenic paramyxovirus, was first discovered in 2012 when a person became ill after working in South Sudan and Uganda. During an ecological investigation, several species of bats were sampled and tested for SOSV RNA and only one species, the Egyptian rousette bat (ERBs; Rousettus aegyptiacus), tested positive. Since that time, multiple other species have been sampled and ERBs in Uganda have continued to be the only species of bat positive for SOSV infection. Subsequent studies of ERBs with SOSV demonstrated that ERBs are a competent host for SOSV and shed this infectious virus while exhibiting only minor infection-associated pathology. Following the 2014 Ebola outbreak in West Africa, surveillance efforts focused on discovering reservoirs for zoonotic pathogens resulted in the capture and testing of many bat species. Here, SOSV RNA was detected by qRT-PCR only in ERBs captured in the Moyamba District of Sierra Leone in the central region of the country. These findings represent a substantial range extension from East Africa to West Africa for SOSV, suggesting that this paramyxovirus may occur in ERB populations throughout its sub-Saharan African range. Full article

(This article belongs to the Special Issue Bat- and Rodent-Borne Zoonotic Viruses)

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12 pages, 690 KiB

Open AccessArticle

Presence of Alphacoronavirus in Tree- and Crevice-Dwelling Bats from Portugal

by Mahima Hemnani, Priscilla Gomes da Silva, Gertrude Thompson, Patrícia Poeta, Hugo Rebelo and João R. Mesquita

Viruses 2024, 16(3), 434; https://doi.org/10.3390/v16030434 - 12 Mar 2024

Cited by 2 | Viewed by 1873

Abstract

Coronaviruses (CoVs) are RNA viruses capable of infecting a wide range of hosts, including mammals and birds, and have caused significant epidemics such as the ongoing COVID-19 pandemic. Bats, the second most diverse mammalian order, are hosts for various CoVs due to their [...] Read more.

Coronaviruses (CoVs) are RNA viruses capable of infecting a wide range of hosts, including mammals and birds, and have caused significant epidemics such as the ongoing COVID-19 pandemic. Bats, the second most diverse mammalian order, are hosts for various CoVs due to their unique immune responses and ecological traits. This study investigates CoV prevalence in crevice- and tree-dwelling bats in Portugal, a country with limited prior research on bat CoVs. Using nested RT-PCR and sequencing, we screened 87 stool samples from bats, identifying one sample (1.15%) that was positive for Alphacoronavirus, belonging to Pipistrellus pipistrellus. Phylogenetic analysis revealed close genetic relationships with Alphacoronavirus strains from the same bat species in Europe. The low prevalence suggests habitat-specific differences in viral transmission, with cave-dwelling bats exhibiting higher CoV prevalence due to population density and behaviour. These findings underscore the necessity for sustained surveillance efforts aimed at comprehending CoV dynamics within bat populations, especially concerning the risk of spillover events and viral evolution. Vital to this understanding is the monitoring of bat migration patterns, which serves as a crucial tool for elucidating CoV ecology and epidemiology. Such efforts are essential for ongoing research endeavours aimed at mitigating the potential for future zoonotic disease outbreaks. Full article

(This article belongs to the Special Issue Bat- and Rodent-Borne Zoonotic Viruses)

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9 pages, 1464 KiB

Open AccessArticle

Detection of Filoviruses in Bats in Vietnam

by Marat T. Makenov, Lan Anh T. Le, Olga A. Stukolova, Ekaterina V. Radyuk, Evgeny S. Morozkin, Nga T. T. Bui, Olga B. Zhurenkova, Manh N. Dao, Chau V. Nguyen, Mo T. Luong, Dung T. Nguyen, Marina V. Fedorova, Anna V. Valdokhina, Victoria P. Bulanenko, Vasiliy G. Akimkin and Lyudmila S. Karan

Viruses 2023, 15(9), 1785; https://doi.org/10.3390/v15091785 - 23 Aug 2023

Cited by 5 | Viewed by 2442

Abstract

A new filovirus named Měnglà virus was found in bats in southern China in 2015. This species has been assigned to the new genus Dianlovirus and has only been detected in China. In this article, we report the detection of filoviruses in bats [...] Read more.

A new filovirus named Měnglà virus was found in bats in southern China in 2015. This species has been assigned to the new genus Dianlovirus and has only been detected in China. In this article, we report the detection of filoviruses in bats captured in Vietnam. We studied 248 bats of 15 species caught in the provinces of Lai Chau and Son La in northern Vietnam and in the province of Dong Thap in the southern part of the country. Filovirus RNA was found in four Rousettus leschenaultii and one Rousettus amplexicaudatus from Lai Chau Province. Phylogenetic analysis of the polymerase gene fragment showed that three positive samples belong to Dianlovirus, and two samples form a separate clade closer to Orthomarburgvirus. An enzyme-linked immunosorbent assay showed that 9% of Rousettus, 13% of Eonycteris, and 10% of Cynopterus bats had antibodies to the glycoprotein of marburgviruses. Full article

(This article belongs to the Special Issue Bat- and Rodent-Borne Zoonotic Viruses)

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12 pages, 1309 KiB

Open AccessArticle

First Report of Alphacoronavirus Circulating in Cavernicolous Bats from Portugal

by Mahima Hemnani, Priscilla Gomes da Silva, Gertrude Thompson, Patricia Poeta, Hugo Rebelo and João R. Mesquita

Viruses 2023, 15(7), 1521; https://doi.org/10.3390/v15071521 - 8 Jul 2023

Cited by 4 | Viewed by 1585

Abstract

The emergence of novel coronaviruses (CoVs) has emphasized the need to understand their diversity and distribution in animal populations. Bats have been identified as crucial reservoirs for CoVs, and they are found in various bat species worldwide. In this study, we investigated the [...] Read more.

The emergence of novel coronaviruses (CoVs) has emphasized the need to understand their diversity and distribution in animal populations. Bats have been identified as crucial reservoirs for CoVs, and they are found in various bat species worldwide. In this study, we investigated the presence of CoVs of four cavernicolous bats in six locations in the centre and south of Portugal. We collected faeces, anal, and buccal swab samples, as well as air samples from the locations using a Coriolis air sampler. Our results indicate that CoVs were more readily detected in faecal samples compared to anal and buccal swab samples. No CoVs were detected in the air samples. Phylogenetic analysis showed that the detected viruses belong to the Alphacoronavirus genus. This study represents the first report of Alphacoronaviruses circulating in bats in Portugal and highlights the importance of continuous surveillance for novel CoVs in bat populations globally. Ongoing surveillance for CoVs in bat populations is essential as they are a vital source of these viruses. It is crucial to understand the ecological relationships between animals, humans, and the environment to prevent and control the emergence and transmission of infectious diseases. Further ecological studies are needed to investigate the factors contributing to the emergence and transmission of zoonotic viruses. Full article

(This article belongs to the Special Issue Bat- and Rodent-Borne Zoonotic Viruses)

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