Seasonal dynamics of the wild rodent faecal virome

Raghwani, Jayna; Faust, Christina L.; François, Sarah; Nguyen, Dung; Raulo, Aura; Hill, Sarah C.; Parag, Kris V; Simmonds, Peter; Knowles, Sarah C. L.; Pybus, Oliver G.

doi:10.1101/2022.02.09.479684

Cited by 6 publications

(2 citation statements)

References 64 publications

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“…Other molecular surveys of viruses in rodents ( Apodemus spp. and Myodes glareolus ) has found that much of the faecal virome is seasonally transient, emphasising the need for longitudinal studies (Raghwani et al ., 2022). However, overall together these studies show that wild rodents commonly have a rich and diverse virome.…”

Section: Discussionmentioning

confidence: 99%

The Ecology of Viruses in Urban Rodents with a Focus on SARS-CoV-2

Fisher

Airey

Liu

et al. 2023

Preprint

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Wild animals are naturally infected with a range of viruses, some of which may be zoonotic for humans. During the human COIVD pandemic there was also the possibility of rodents acquiring SARS-CoV-2 from people, so-called reverse zoonoses. To investigate this we have sampled rats (Rattus norvegicus) and mice (Apodemus sylvaticus) from urban environments in 2020 during the human COVID-19 pandemic. We metagenomically sequenced lung and gut tissue and faeces for viruses, PCR screened for SARS-CoV-2, and serologically surveyed for anti-SARS-CoV-2 Spike antibodies. We describe the range of viruses that we found in these two rodent species. We found no molecular evidence of SARS-CoV-2 infection, though in rats we found lung antibody responses and evidence of neutralisation ability, that are consistent with rats being exposed to SARS-CoV-2 and / or exposed to other viruses that result in cross-reactive antibodies.

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Section: Discussionmentioning

confidence: 99%

The Ecology of Viruses in Urban Rodents with a Focus on SARS-CoV-2

Fisher

Airey

Liu

et al. 2023

Preprint

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“…This feature could make metagenomic sequencing a suitable tool to screen for zoonotic pathogens in wildlife, and it could facilitate the detection of unexpected or emerging pathogens. Although numerous microbiome‐profiling studies have been performed on humans, such studies performed on wildlife are limited (Egan et al., 2021 ; Firth et al., 2014 ; Ge et al., 2018 ; Raghwani et al., 2022 ; Razzauti et al., 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Screen the unforeseen: Microbiome‐profiling for detection of zoonotic pathogens in wild rats

Cock

Fonville

Vries

et al. 2022

Transbounding Emerging Dis

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Wild rats can host various zoonotic pathogens. Detection of these pathogens is commonly performed using molecular techniques targeting one or a few specific pathogens. However, this specific way of surveillance could lead to (emerging) zoonotic pathogens staying unnoticed. This problem may be overcome by using broader microbiome-profiling techniques, which enable broad screening of a sample's bacterial or viral composition. In this study, we investigated if 16S rRNA gene amplicon sequencing would be a suitable tool for the detection of zoonotic bacteria in wild rats. Moreover, we used virome-enriched (VirCapSeq) sequencing to detect zoonotic viruses. DNA from kidney samples of 147 wild brown rats (Rattus norvegicus) and 42 black rats (Rattus rattus) was used for 16S rRNA gene amplicon sequencing of the V3-V4 hypervariable region. Blocking primers were developed to reduce the amplification of rat host DNA. The kidney bacterial composition was studied using alphaand beta-diversity metrics and statistically assessed using PERMANOVA and SIM-PER analyses. From the sequencing data, 14 potentially zoonotic bacterial genera were identified from which the presence of zoonotic Leptospira spp. and Bartonella tribocorum was confirmed by (q)PCR or Sanger sequencing. In addition, more than 65% of all samples were dominated (>50% reads) by one of three bacterial taxa:Streptococcus (n = 59), Mycoplasma (n = 39) and Leptospira (n = 25). These taxa also showed the highest contribution to the observed differences in beta diversity. Vir-CapSeq sequencing in rat liver samples detected the potentially zoonotic rat hepatitis E virus in three rats. Although 16S rRNA gene amplicon sequencing was limited in its capacity for species level identifications and can be more difficult to interpret due to the influence of contaminating sequences in these low microbial biomass samples, we believe it has potential to be a suitable pre-screening method in the This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

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Community structure of heritable viruses in aDrosophila-parasitoids complex

Varaldi,

Lepetit,

Burlet

et al. 2023

Preprint

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The diversity and phenotypic impacts related to the presence of heritable bacteria in insects have been extensively studied in the last decades. On the contrary, heritable viruses have been overlooked for several reasons, including technical ones. This is regrettable because of the size of this gap knowledge and because case study indicate that viruses may have profound impact on the functionning of individuals and communities. Additionally, the factors that may shape viral communities are poorly known, except in some very specific viral-insect systems. Here we analyze the community structure of heritable viruses in a multi-hosts-multi-parasitoids community. Drosophilidae and their larval and pupal parasitoids were sampled in two locations, two years and two seasons. After two lab generations, putative DNA and RNA viruses were purified and sequenced. Our analysis revealed the presence of 53 viruses (including 40 previously unkown viruses), the great majority of which were RNA viruses. The "species" factor was by far the most significant one, explaining more than 50\% of the variance in viral structure. Additionally, parasitoids had a higher number of heritable viruses compared to their hosts, suggesting that this lifestyle favours the association with viruses. Finally, our community-level survey challenged previous interpretation concerning the host range of some previously described viruses.

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Seasonal dynamics of the wild rodent faecal virome

Cited by 6 publications

References 64 publications

The Ecology of Viruses in Urban Rodents with a Focus on SARS-CoV-2

The Ecology of Viruses in Urban Rodents with a Focus on SARS-CoV-2

Screen the unforeseen: Microbiome‐profiling for detection of zoonotic pathogens in wild rats

Community structure of heritable viruses in aDrosophila-parasitoids complex

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