Biology subjects

Tarlinton, R. E.

Publications and source records attributed to Tarlinton, R. E..

9 recordsLinked to original sources

bioRxiv2026

Expression of Retroviruses in Guinea Pig Lymphomas.

Retroviruses commonly cause neoplasia in many species but have not been described in guinea pigs. While historical evidence exists for the presence of an active retrovirus in domestic guinea pigs (Cavia porcella), there has been no description of the sequence of these viruses or their role in disease in guinea pigs. This paper uses genome mining of the published domestic and wild (Cavia aperea) guinea pig genomes for retroviral sequences to identify the gamma and beta-retroviral complement of the Cavia genome, describing eight groups of viruses with evidence of recombination between virus groups. The most intact group, gamma-like retroviruses related to HERV-T (integration estimates of 855,000 to 3.8 million years ago), has five near full length loci that are likely capable of active infection. RNA-Scope In-situ Hybridisation of archived formalin-fixed, paraffin embedded (FFPE) guinea pig lymphoma sections with a probe for one of these loci demonstrated viral RNA expression in lymphoma tissue, strengthening the case for a role of these viruses in the high incidence of leukaemia and lymphoma in this species.

microbiology↗

bioRxiv2025

Cross-species Transmission and Host Adaptation of Feline Leukaemia Virus between Domestic Cats and the Wild Felid Leopardus guigna.

2.Feline leukaemia virus (FeLV) is widespread in domestic cats and frequently spills over into wild felid populations, causing severe outbreaks in non-domestic felid populations. Domestic cats carry both endogenous FeLV (enFeLV) and exogenous variants of FeLV (exFeLV), which can recombine to generate novel variants with alternate receptor usage. In contrast, most non-domestic felids, including the guigna are lack enFeLV This study applied amplification of the FeLV envelope gene combined with Illumina sequencing to characterise FeLV envelope gene diversity and transmission dynamics in guignas (Leopardus guigna), a small wild felid native to Chile and Argentina. Seven PCR amplicons from five free ranging guignas were sequenced. Illumina contigs demonstrated that infections originated from Chilean domestic cats; however, a distinct guigna-specific cluster with unique sequence variations was identified, suggesting that FeLV transmission also occurs among guignas independent of domestic cats. Phylogenetic analysis showed that all guigna sequences formed a Chile-specific FeLV clade, closely related to domestic cat viruses but clearly separated from international FeLV-A strains.

microbiology↗

bioRxiv2023

COMPARISON BETWEEN SANGER, ILLUMINA AND NANOPORE SEQUENCING EVIDENCING INTRA-HOST VARIATION OF FELINE LEUKEMIA VIRUS THAT INFECTS DOMESTIC CATS.

Knowledge of Feline Leukemia Virus (FeLV) sequence variation has mainly been developed using Sanger sequencing methods. However, advances in next generation sequencing methods and their broad use in laboratories has been changing our understanding of viral genetics. FeLV sequencing has specific complications with the presence of both exogenous (exFeLV) and endogenous (enFeLV) virus with frequent recombination between them, limiting sequencing approaches. Here we report an FeLV-A and FeLV-B amplicon-based comparison between Sanger, Illumina, and Oxford Nanopore sequencing methods in Chilean domestic cats. We analysed the hypervariable envelope gene, where a higher number of variants as well as recombination with endogenous strains occurs. We detected multiple variants and viral quasispecies infecting the cats. We compared these three methods to evaluate the advantages and disadvantages between them. Although the Sanger method is highly reliable, it showed a high fail rate (many amplicons did not produce useable sequence) and the sequences obtained showed artificial sequence clustering when compared with the NGS methods. Illumina sequencing showed a lower error rate but could not discriminate between exogenous and endogenous viruses. Finally, Oxford Nanopore (MinION) sequencing could successfully detect low-abundance sequences and discriminate between FeLV-A and FeLV-B sequences, although its higher error-rate requires caution in interpretation of the results. Our results indicate advantages and disadvantages for each method, with the purpose of sequencing needing to be considered in the choice of method. Results of large viral phylogenetic trees combing sequences derived from mixed sequencing methods, such as those combining historical and contemporary sequencing need to be considered with some caution as artificial clustering by sequencing method may occur.

microbiology↗

bioRxiv2023

Lack of detection of SARS-CoV-2 in Wildlife from Kerala, India in 2020-21

2.Spill over of SARs-CoV-2 into a variety of wild and domestic animals has been an ongoing feature of the human pandemic. The establishment of a new reservoir in white tailed deer in North America and increasing divergence of the viruses circulating in them from those circulating in the human population has highlighted the ongoing risk this poses for global health. Some parts of the world have seen more intensive monitoring of wildlife species for SARS-CoV-2 and related coronaviruses but there are still very large gaps in geographical and species-specific information. This paper reports negative results for SARS-CoV-2 PCR based testing using a pan coronavirus end point RDRP PCR and a Sarbecovirus specific E gene qPCR on lung and or gut tissue from wildlife from the Indian State of Kerala. These animals included: 121 Rhinolophus rouxii (Rufous Horsehoe Bat), 6 Rhinolophus bedommei (Lesser Woolly Horseshoe Bat), 15 Rossettus leschenaultii (Fulvous Fruit Bat), 47 Macaca radiata (Bonnet macaques), 35 Paradoxurus hermaphroditus (Common Palm Civet), 5 Viverricula indica (Small Indian Civet), 4 Herpestes edwardsii (Common Mongoose), 10 Panthera tigris (Bengal Tiger), 8 Panthera pardus fusca (Indian Leopard), 4 Prionailurus bengalensis (Leopard cats), 2 Felis chaus (Jungle cats), 2 Cuon alpinus (Wild dogs) and 1 Melursus ursinus (sloth bear).

microbiology↗

bioRxiv2023

Lack of detection of SARS-CoV-2 in British wildlife 2020-21 and first description of a stoat (Mustela erminea) Minacovirus

2.Repeat spillover of SARS-CoV-2 into new hosts has highlighted the critical role of cross species transmission of coronaviruses and establishment of new reservoirs of virus in pandemic and epizootic spread of coronaviruses. Species particularly susceptible to SARS-CoV-2 spill-over include Mustelidae (mink, ferrets and related animals), cricetid rodents (hamsters and related animals), felids domestic cats and related animals) and white tailed deer. These predispositions led us to screen British wildlife with sarbecovirus specific qPCR and pan coronavirus PCR assays for SARS-CoV-2 using samples collected during the human pandemic to establish if widespread spill-over was occurring. Fourteen wildlife species (n=402) were tested, including : 2 Red Foxes (Vulpes vulpes), 101 Badgers (Meles meles), 2 wild American Mink (Neogale vison), 41 Pine Marten (Martes martes), 2 Weasels (Mustela nivalis), 7 Stoats (Mustela erminea), 108 Water Voles (Arvicola amphibius), 39 Bank voles (Myodes glareolous), 10 Field Voles (Microtus agrestis), 15 Wood Mice (Apodemus sylvaticus), 1 Common Shrew (Sorex aranaeus), 2 Pygmy Shrews (Sorex minutus), 2 Hedgehogs (Erinaceus europaeus) and 75 Eurasian Otters (Lutra lutra). No cases of SARS-CoV-2 were detected in any animals, however a novel minacovirus related to mink and ferret alphacoronaviruses was detected in stoats recently introduced to the Orkney Islands. This group of viruses is of interest due to pathogenicity in ferrets. The impact of this virus on the health of stoat populations remains to be established.

microbiology↗

bioRxiv2023

Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology

Horseshoe bats are the natural hosts of the Sarbecovirus subgenus that includes SARS-CoV-1 and 2. Despite the devastating impacts of the COVID-19 pandemic, there is still little known about the underlying epidemiology and virology of sarbecoviruses in their natural hosts, leaving large gaps in our pandemic preparedness. Here we describe the results of PCR testing for sarbecoviruses in the two horseshoe bat species (Rhinolophus hipposideros and R. ferrumequinum) present in Great Britain, collected in 2021-22 during the peak of COVID-19 pandemic. One hundred and ninety seven R. hipposideros samples from 33 roost sites and 277 R. ferremequinum samples from 20 roost sites were tested. No coronaviruses were detected in any samples from R. ferrumequinum whereas 44% and 56% of individual and pooled (respectively) faecal samples from R. hipposideros across multiple roost sites tested positive in a sarbecovirus-specific qPCR. Full genome sequences were generated from three of the positive samples (and partial genomes from two more) using Illumina RNAseq on unenriched samples. Phylogenetic analyses showed that the obtained sequences belong to the same monophyletic clade, with >95% similarity, as previously reported European isolates from R. hipposideros. The sequences differed in the presence or absence of accessory genes ORF 7b, 9b and 10. All lacked the furin cleavage site of SARS-CoV-2 spike gene and are therefore unlikely to be infective for humans. These results demonstrate a lack, or at least low incidence, of SARS-CoV-2 spill over from humans to susceptible GB bats, and confirm that sarbecovirus infection is widespread in R. hipposideros. Despite frequently sharing roost sites with R. ferrumequinum, no evidence of cross-species transmission was found.

microbiology↗

bioRxiv2023

Surveillance of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We recovered nine (two novel) complete genomes across six bat species: four alphacoronaviruses, a MERS-related betacoronavirus, and four closely related sarbecoviruses. We demonstrate that at least one of these sarbecoviruses can bind and use the human ACE2 receptor for infecting human cells, albeit suboptimally. Additionally, the spike proteins of these sarbecoviruses possess an R-A-K-Q motif, which lies only one nucleotide mutation away from a furin cleavage site (FCS) that enhances infectivity in other coronaviruses, including SARS-CoV-2. However, mutating this motif to an FCS does not enable spike cleavage. Overall, while UK sarbecoviruses would require further molecular adaptations to infect humans, their zoonotic risk is unknown and warrants closer surveillance.

genomics↗

bioRxiv2019

Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports its Classification as a Novel Species

Hantaviruses are a diverse group of single-stranded, negative-sensed RNA viruses, known to cause sporadic outbreaks of potentially fatal human disease. To date, only two Orthohantavirus species have been detected in the UK - Seoul virus and Tatenale. Whilst Seoul is known to be pathogenic in humans, only partial fragments of Tatenale have been recovered, precluding any accurate analysis of its phylogeny or potential pathogenicity. To overcome this shortfall we used a degenerate primer PCR method to identify Tatenale-infection in rodents living in two separate locations in the UK. PCR positive samples were then subjected to either unbiased high-throughput sequencing or overlapping PCR product sequencing to recover the complete coding sequence of the Tatenale virus. This analysis provided in-depth insight into the evolutionary origins of this recently identified UK Orthohantavirus and unequivocally showed that Tatenale virus meets the established criteria for classification as a novel species. Crucially, our data will facilitate in vitro investigation into the zoonotic potential of Tatenale virus.

microbiology↗

bioRxiv2017

Differential and defective expression of Koala Retrovirus reveal complexity of host and virus evolution

Koala retrovirus (KoRV) is unique amongst endogenous (inherited) retroviruses in that its incorporation to the host genome is still active, providing an opportunity to study what drives this fundamental process in vertebrate genome evolution. Animals in the southern part of the natural range of koalas were previously thought to be either virus free or to have only exogenous variants of KoRV with low rates of KoRV induced disease. In contrast, animals in the northern part of their range universally have both endogenous and exogenous KoRV with very high rates of KoRV induced disease such as lymphoma. This paper uses a combination of sequencing technologies, Illumina RNA sequencing of "southern" (south Australian) and "northern" (SE QLD) koalas and CRISPR enrichment and nanopore sequencing of DNA of "southern" (South Australian and Victorian animals) to retrieve full length loci and intregration sites of KoRV variants. We demonstrate that koalas that tested negative to the KoRV pol gene qPCR, used to detect replication competent KoRV, are not in fact KoRV free but harbour defective, presumably endogenous, "RecKoRV" variants that are not fixed between animals. This indicates that these populations have historically been exposed to KoRV and raises questions as to whether these variants have arisen by chance or whether they provide a protective effect from the infectious forms of KoRV. This latter explanation would offer the intriguing prospect of being able to monitor and selectively breed for disease resistance to protect the wild koala population from KoRV induced disease.

microbiology↗