SARS-CoV-2 Infection in Captive Hippos (Hippopotamus amphibius), Belgium.

Two adult female hippos in Zoo Antwerp who were naturally infected with SARS-CoV-2 showed nasal discharge for a few days. Virus was detected by immunocytochemistry and PCR in nasal swab samples and by PCR in faeces and pool water. Serology was also positive. No treatment was necessary

Bat pathogens hit the road: But which one?

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Analysis of partial sequences of the RNA-dependent RNA polymerase gene as a tool for genus and subgenus classification of coronaviruses

International audienceThe 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 standardization 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 387 nt 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 whole-genome 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 are 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

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 hippopotamuses in December 2021. A total of 1523 faecal samples from 103 mammal species were tested for SARS-CoV-2 via real-time PCR. None of the samples tested positive for SARS-CoV-2. Additional surrogate virus neutralisation tests conducted on 50 routinely collected serum samples from 26 mammal species were all negative. This study is the 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

Astrovirus in Reunion Free-Tailed Bat (Mormopterus francoismoutoui)

International audienceAstroviruses (AstVs) are RNA viruses infecting 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 21 June 2016 to 4 September 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. 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

Astroviruses in bats, Madagascar

International audienceDear Editor, Astroviruses (AstVs) (family Astroviridae) are positive-sense, single-stranded RNA viruses that infect a large diversity of mammalian and avian species. 1 In humans, eight serotypes have been described worldwide, accounting for 2%–9% of all acute non-bacterial gastro-enteritis cases in children. 2 AstVs have been detected from over 80 non-human host species, including a large diversity of bat species in Asia, Europe and Africa, 3 and recent phylogenetic analyses suggest that the long-term evolution of AstVs is determined by frequent cross-species transmission events. 4,5 During the past decade, numerous AstVs with potential zoonotic transmission have been described, highlighting the need for improved knowledge on their biology to prevent future health threats. 2 Bats are recognized as a major reservoir of infectious agents. Madagascar shelters over 46 bat species, of which nearly 80% are endemic, occupying different types of day roosts, including natural and synanthropic sites. Recent investigations have shown that the compositions of Malagasy bat species assemblages are correlated with factors associated with the diversity and transmission of infectious agents, such as paramyxoviruses and Leptospira. 6,7 The detection of new Betacoronaviruses in endemic Malagasy fruit bats also underlined the urgent need to better understand bat-associated infectious agents, and thus assess the potential for spillover to human populations in this major biodiversity hotspot.

A population in perpetual motion: Highly dynamic roosting behavior of a tropical island endemic bat

Abstract Although island endemic bats are a source of considerable conservation concerns, their biology remains poorly known. Here, we studied the phenology and roosting behavior of a tropical island endemic species: the Reunion free‐tailed bat (Mormopterus francoismoutoui). This widespread and abundant species occupies various natural and anthropogenic environments such as caves and buildings. We set up fine‐scale monitoring of 19 roosts over 27 months in Reunion Island and analyzed roost size and composition, sexual and age‐associated segregation of individuals, as well as the reproductive phenology and body condition of individuals. Based on extensive data collected from 6721 individuals, we revealed a highly dynamic roosting behavior, with marked seasonal sex‐ratio variation, linked to distinct patterns of sexual aggregation among roosts. Despite the widespread presence of pregnant females all over the island, parturition was localized in a few roosts, and flying juveniles dispersed rapidly toward all studied roosts. Our data also suggested a 7‐month delay between mating and pregnancy, highlighting a likely long interruption of the reproductive cycle in this tropical bat. Altogether, our results suggest a complex social organization in the Reunion free‐tailed bat, with important sex‐specific seasonal and spatial movements, including the possibility of altitudinal migration. Bat tracking and genetic studies would provide additional insights into the behavioral strategies that shape the biology of this enigmatic bat species. The fine‐scale spatiotemporal data revealed by our study will serve to the delineation of effective conservation plans, especially in the context of growing urbanization and agriculture expansion in Reunion Island

Bat Astrovirus in Mozambique

Abstract Astroviruses (AstVs) are responsible for infection of a large diversity of mammalian and avian species, including bats, aquatic birds, livestock and humans. We investigated AstVs circulation in bats in Mozambique and Mayotte, a small island in the Comoros Archipelago located between east Africa and Madagascar. Biological material was collected from 338 bats and tested for the presence of the AstV RNA-dependent RNA-polymerase gene with a pan-AstV semi-nested polymerase chain reaction assay. None of the 79 samples obtained from Mayotte bats (Pteropus seychellensis comorensis and Chaerephon pusillus) tested positive; however, 20.1% of bats sampled in Mozambique shed AstVs at the time of sampling and significant interspecific variation in the proportion of positive bats was detected. Many AstVs sequences obtained from a given bat species clustered in different phylogenetic lineages, while others seem to reflect some level of host-virus association, but also with AstVs previously reported from Malagasy bats. Our findings support active circulation of a large diversity of AstVs in bats in the western Indian Ocean islands, including the southeastern African coast, and highlight the need for more detailed assessment of its risk of zoonotic transmission to human populations

Bat coronavirus phylogeography in the Western Indian Ocean

International audienceBats 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 α-and β-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. 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

SARS-CoV-2 Infection in Captive Hippos (Hippopotamus amphibius), Belgium

Two adult female hippos in Zoo Antwerp who were naturally infected with SARS-CoV-2 showed nasal discharge for a few days. Virus was detected by immunocytochemistry and PCR in nasal swab samples and by PCR in faeces and pool water. Serology was also positive. No treatment was necessary