Biology subjects

Joffrin, L.

Publications and source records attributed to Joffrin, L..

11 recordsLinked to original sources

bioRxiv2025

High genetic diversity of mpox virus (MPXV) in three different rodent species in the Democratic Republic of the Congo (DRC)

Altough zoonotic spillover events continue to drive human mpox outbreaks in the Democratic Republic of the Congo (DRC), the wildlife reservoir of mpox virus (MPXV) remains unkown. To address this gap, we screened samples from 2,701 wild mammals, mainly rodents (59.7%), bats (26.4%) and shrews (12.1%). Only six (0.2%) animals were Orthopoxvirus (OPV) PCR positive. Near full-length MPXV sequences were obtained from two squirrels (Funisciurus anerythrus and Paraxerus sp.) and one soft furred mouse (Praomys jacksoni). A novel Taterapox virus was identified in a shrew (Crocidura cf. denti). All newly identified MPXV strains belong to clade Ia, but they cluster into different groups or subgroups, despite being collected from geographically close locations, and all are closely related to human MPXV strainsfrom the same regions. Our study provides for the first time clear evidence that MPXV diversity is not restricted to a single rodent host species nor confined to a geographic area. Importantly, MPXV positive Paraxerus and Praomys specimens were sampled close to Kisangani, a city with more than one million inhabitants, highlighting that spillover events can als ooccur in or near major cities, with more favorable conditions for interhuman transmissions and potential emergence of new lineages.

microbiology↗

bioRxiv2024

A wide diversity of viruses detected in African mammals involved in the wild meat supply chain

The processes involved in acquiring, trading, preparing, and consuming wild meat pose significant risks for the emergence of zoonotic infectious diseases. Several major viral outbreaks have been directly linked to the wild meat supply chain, yet our knowledge of the virome in many mammals involved in this chain remains limited and disproportionately focused on certain mammalian taxa and pathogens. This report presents the findings of a metagenomic viral screening of 99 specimens belonging to 27 wild African mammal species and one domesticated species, all traded for their meat. The study focuses on tissue and swab samples collected from various regions in the Democratic Republic of the Congo and in Brussels, Belgium. A total of fifteen virus strains were detected, belonging to the families Arteriviridae, Retroviridae and Sedoreoviridae (primates), Picobirnaviridae (primates and rodents), Picornaviridae (rodents), Hepadnaviridae (hyrax), Orthoherpesviridae (artiodactylid and carnivore) and Spinareoviridae (carnivore). Several strains were detected in mammalian hosts for the first time, expanding their host range and genetic diversity. Of note is the presence of viruses genetically related to recognised zoonotic pathogens, i.e., human picobirnavirus (Orthopicobirnavirus hominis) (primates and rodents), simian foamy viruses (Simiispumavirus) (primates), and rotavirus A (Rotavirus alphagastroenteritidis) (primates). The presence of these viruses in primates is concerning as non-human primates are phylogenetically closely related to humans, which can facilitate interspecies viral transmission. These findings underscore the high diversity of mammalian viruses and the potential risk of human infection through cross-species transmission during the close interactions with wildlife in the wild meat supply chain.

genomics↗

bioRxiv2024

Assessing Ebola Virus Circulation in the Tshuapa Province (Democratic Republic of the Congo): A One Health Investigation of Wildlife and Human Interactions

The wildlife reservoir and spillover mechanisms of the Ebola virus remain elusive despite extensive research efforts in endemic areas. This study employed a One Health approach to examine the virus circulation in wildlife and the associated human exposure risks in the Tshuapa province of the Democratic Republic of the Congo. In 2021, we collected 1015 samples from 888 animals, predominantly small mammals, and 380 inhabitants of Inkanamongo village, the site of an Ebola virus disease outbreak in 2014. These samples were screened for evidence of current (RNA) or past (IgG antibodies) Ebola virus infections. We also conducted interviews with 167 individuals in the surrounding districts to assess their interactions with wildlife. While no Ebola virus RNA was detected in the wildlife samples, anti-orthoebolavirus IgG antibodies were found in 13 bats and 38 rodents. Among the human participants, 120 individuals had IgG antibodies against at least one orthoebolavirus antigen, with 12 showing seropositivity for two antigens of the same orthoebolavirus, despite not having a prior Ebola disease diagnosis. Furthermore, over 50% of respondents reported frequent visits to the forest to hunt a variety of wild animals, particularly ungulates and rodents, which could account for occasional viral spillovers. The absence of active Ebola virus circulation in wildlife may reflect seasonal patterns in reservoir ecology, like those observed in bats. Similarly, seasonal human activities, like hunting and foraging, may result in periodic exposure risks. These findings highlight the importance of continuous, multidisciplinary surveillance to monitor changes in seasonal spillover risks.

molecular biology↗

bioRxiv2024

Role of individual and population heterogeneity in shaping dynamics of multi-pathogen excretion in an island endemic bat

Understanding processes driving pathogen transmission in bats is critical to prevent spillovers and emergence events. Although substantial research has addressed this topic, few studies have directly examined shedding dynamics (as opposed to serological studies) and co-infection patterns using fine-scale spatio-temporal datasets. Here, based on the monitoring of 5,714 Reunion free-tailed bats (Mormopterus francoismoutoui) in 17 roosts over 24 months, we studied the co-shedding dynamics of paramyxoviruses (PMV) and Leptospira bacteria (LEPTO) in urine, and herpesviruses (HSV) in saliva. We evidenced all year long shedding with high prevalence of all three infectious agents (37% - 87%), as well as an exceptionally high level of co-shedding (59%), with both positive and negative interactions between infectious agents. Shedding patterns displayed temporal synchrony among roosts, with a peak during summer months, but were not influenced by roost size. Repeated shedding in recaptured bats supports within-host persistence, though underlying mechanisms remain to be identified. Our results also showed rapid HSV infection of juveniles (< 6 months), and suggest longer protection of juveniles by maternal antibodies for PMV and LEPTO. Reproductive individuals (both during the pregnancy and mating) were associated to increased PMV and LEPTO shedding, which can result from tradeoffs between reproduction and infection in both sexes, and/or an age-related bias with the progressive infection of older juveniles during reproductive periods. This study highlights the significance of persistent shedding of multiple pathogens, including bacteria, and their intricate interactions within bat populations. Understanding how human-driven ecological changes may disrupt within-host processes and influence pathogen shedding in bats will help assessing the risk of pathogen spillover from bats to other species, including humans. Author summaryUnderstanding risks of bat-borne pathogen spillover is challenging because of the difficulty in studying shedding dynamics in wild bat populations. Here, we used an original island-endemic bat species to build up a fine-scale spatio-temporal shedding analysis of two viruses (paramyxoviruses and herpesviruses) and a bacterium (Leptospira) at both population- (roost) and individual- (through recaptured bats) levels. Shedding patterns are driven by the age of bats and associated to the reproductive periods in both females and males. Results also suggest that persistence, as well as interactions between infectious agents, are important within-host processes that contribute to the transmission of infections in bat populations. More research is essential to understand how human activities may influence these co-shedding patterns and the risk of cross- species transmission.

evolutionary biology↗

bioRxiv2024

First report of astroviruses in Tanzanian bats

Emerging and re-emerging infectious diseases have posed significant global health threats, with many attributed to zoonotic RNA viruses. These pathogens can, under some conditions, cross species barriers, facilitating transmission from animal hosts to humans. Bats, characterised by unique physiological and ecological features, and remarkable species diversity, are recognized to host numerous viruses with cross-species transmission potential. This study aimed to investigate the presence of RNA viruses from a broad diversity of Tanzanian bats while valorising archived biological samples. RNA was extracted from 125 samples (28 faeces and 97 oral swabs) of 17 bat species, followed by PCR amplification targeting five distinct viral genera (Filovirus, Coronavirus, Hantavirus, Paramyxovirus and Astrovirus). Overall, 1.6 % (3/125) of the samples from two bat species (Scotophilus dinganii and Miniopterus fraterculus) tested positive for astrovirus, with the coinfection of one bat with two AstV strains. No samples tested positive for Filovirus, Coronavirus, Hantavirus and Paramyxovirus. Phylogenetic analysis based on RNA-dependent RNA polymerase sequences revealed these sequences are respectively clustering with astroviruses detected in other bat species from the genus Scotophilus from East Asia and with astroviruses detected in Miniopterus bats from Africa and Asia. Altogether, these results are the first report of astroviruses in Tanzanian bats.

molecular biology↗

bioRxiv2023

Stuck on a small tropical island: wide in-situ diversification of an urban-dwelling bat

Bats are often the only mammals naturally colonizing isolated islands and are thus an excellent model to study evolutionary processes of insular ecosystems. Here, we studied the Reunion free-tailed bat (Mormopterus francoismoutoui), an endemic species to Reunion Island that has adapted to urban settings. At regional scale, we investigated the evolutionary history of Mormopterus species, as well as on Reunion Island sex-specific and seasonal patterns of genetic structure. We used an extensive spatio-temporal sampling including 1,136 individuals from 18 roosts and three biological seasons (non-reproductive/winter, pregnancy/summer, and mating), with additional samples from Mormopterus species from neighbouring islands (M. jugularis of Madagascar and M. acetabulosus of Mauritius). Complementary information gathered from both microsatellite and mitochondrial markers revealed a high genetic diversity but no signal of spatial genetic structure and weak evidence of female philopatry. Regional analysis suggests a single colonization event for M. francoismoutoui, dated around 175,000 years ago, and followed by in-situ diversification and the evolution of divergent ancestral lineages, which today form a large metapopulation. Population expansion was relatively ancient (55,000 years ago) and thus not linked to human colonization of the island and the availability of new anthropic day-roost sites. Discordant structure between mitochondrial and microsatellite markers suggests the presence of yet-unknown mating sites, or the recent evolution of putative ecological adaptations. Our study illustrates how understanding mechanisms involved in speciation can be challenging and the importance of both mitochondrial and nuclear DNA in resolving the wide in-situ diversification of an urban-dwelling bat, endemic to a small island.

genetics↗

bioRxiv2023

SARS-CoV-2 surveillance between 2020 and 2021 of all mammalian species in two Flemish zoos (Antwerp Zoo and Planckendael Zoo)

The COVID-19 pandemic has led to millions of human infections and deaths worldwide. Several other mammal species are also susceptible to SARS-CoV-2, and multiple instances of transmission from humans to pets, farmed mink, wildlife and zoo animals have been recorded. We conducted a systematic surveillance of SARS-CoV-2 in all mammal species in two zoos in Belgium between September and December 2020 and July 2021 in four sessions, and a targeted surveillance of selected mammal enclosures following SARS-CoV-2 infection in hippos in December 2021. A total of 1523 faecal samples were tested for SARS-CoV-2 via real-time PCR. None of the samples tested positive for SARS-CoV-2. Additional surrogate virus neutralization tests conducted on 50 routinely collected serum samples during the same period were all negative. This study is a first to our knowledge to conduct active SARS-CoV-2 surveillance for several months in all mammal species of a zoo. We conclude that at the time of our investigation, none of the screened animals were excreting SARS-CoV-2.

molecular biology↗

bioRxiv2022

Synchronicity of viral shedding in molossid bat maternity colonies

Infection dynamics in vertebrates are driven by biological and ecological processes. For bats, population structure and reproductive cycles have major effects on RNA virus transmission. On Reunion Island, previous studies have shown that parturition of pregnant females and aggregation of juvenile Reunion free-tailed bats (Mormopterus francoismoutoui) are associated to major increase in the prevalence of bats shedding viruses. The synchronicity of such shedding pulses, however, is yet to be assessed, between viruses but also maternity colonies. Based on 3422 fresh faeces collected every two to five weeks during four consecutive birthing seasons, we report the prevalence of bats shedding astroviruses (AstVs), coronaviruses (CoVs), and paramyxoviruses (PMVs) in two maternity colonies on Reunion Island. We found that the proportion of bats shedding viruses is highly influenced by sampling collection dates, and therefore by the seasonality of parturition. We highlight that virus shedding patterns are reproducible among years and colonies for CoVs and at a lesser extent for PMVs, but not for AstVs. We also report 1% of bats harbouring double infections, mostly CoVs and PMVs, but none shedding simultaneously AstVs, CoVs and PMVs.

ecology↗

bioRxiv2020

Partial RdRp sequences offer a robust method for Coronavirus subgenus classification

The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, subfamily Orthocoronavirinae) represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardisation for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a partial region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with genome-scale analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses is sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, "MyCoV", which provides a method for attributing subgenus and assessing the reliability of the attribution. Importance StatementThe analysis of polymerase chain reaction amplicons derived from biological samples is the most common modern method for detection and classification of infecting viral agents, such as Coronaviruses. Recent updates to the official standard for taxonomic classification of Coronaviruses, however, may leave researchers unsure as to whether the viral sequences they obtain by these methods can be classified into specific viral taxa due to variations in the sequences when compared to type strains. Here, we present a plausible method for defining genetic dissimilarity cut-offs that will allow researchers to state which taxon their virus belongs to and with what level of certainty. To assist in this, we also provide the R package MyCoV which classifies user generated sequences.

evolutionary biology↗

bioRxiv2019

Astrovirus in Reunion Free-tailed Bat (Mormopterus francoismoutoui)

Astroviruses (AstVs) are RNA viruses infecting of a large diversity of avian and mammalian species, including bats, livestock, and humans. We investigated AstV infection in a free-tailed bat species, Mormopterus francoismoutoui, endemic to Reunion Island. A total of 380 guano samples were collected in a maternity colony during 38 different sampling sessions, from June 21st 2016 to September 4th 2018. Each sample was tested for the presence of the AstV RNA-dependent RNA-polymerase (RdRp) gene using a pan-AstV semi-nested polymerase chain reaction assay. In total, 27 guano samples (7.1%) tested positive, with high genetic diversity of the partial RdRp gene sequences among positive samples. A phylogenetic analysis further revealed that the detected viruses were genetically related to AstVs reported in rats, reptiles, dogs, and pigs, but did not cluster with AstVs commonly found in bats. Although more investigations need to be conducted to assess the prevalence of infected bats in the studied population, our findings show that Reunion free-tailed bats are exposed to AstVs, and suggest that cross-species transmission may occur with other hosts sharing the same habitat.

ecology↗

bioRxiv2019

Bat coronavirus phylogeography in the western Indian Ocean

Bats provide key ecosystem services such as crop pest regulation, pollination, seed dispersal, and soil fertilization. Bats are also major hosts for biological agents responsible for zoonoses, such as coronaviruses (CoVs). The islands of the Western Indian Ocean are identified as a major biodiversity hotspot, with more than 50 bat species. In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5% {+/-} 4.9%) as compared to those sampled on islands (4.5% {+/-} 1.5%). Phylogenetic analyses revealed a large diversity of - and {beta}-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites. ImportanceThis is the first study to report the presence of coronaviruses (CoVs) in bats in Mayotte, Mozambique and Reunion Island, and in insectivorous bats in Madagascar. Eight percent of the tested bats were positive for CoVs, with higher prevalence in continental Africa than on islands. A high genetic diversity of - and {beta}-CoVs was found, with strong association between bat host and virus phylogenies, supporting a long history of co-evolution between bats and their associated CoVs in the Western Indian Ocean. These results highlight that strong variation between islands does exist and is associated with the composition of the bat species community on each island. Future studies should investigate whether CoVs detected in these bats have a potential for spillover in other hosts.

evolutionary biology↗