Sarbecoviruses of British horseshoe bats; sequence variation and epidemiology.

Horseshoe bats are the natural hosts of the Sarbecovirus subgenus that includes SARS-CoV and SARS-CoV- 2. Despite the devastating impact 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. ferrumequinum 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 to 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.

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

Repeat spillover of severe acute respiratory syndrome coronavirus 2 (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 spillover 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 quantitative PCR and pan coronavirus PCR assays for SARS-CoV-2 using samples collected during the human pandemic to establish if widespread spillover was occurring. Fourteen wildlife species (n=402) were tested, including: two red foxes (Vulpes vulpes), 101 badgers (Meles meles), two wild American mink (Neogale vison), 41 pine marten (Martes martes), two weasels (Mustela nivalis), seven stoats (Mustela erminea), 108 water voles (Arvicola amphibius), 39 bank voles (Myodes glareolous), 10 field voles (Microtus agrestis), 15 wood mice (Apodemus sylvaticus), one common shrew (Sorex aranaeus), two pygmy shrews (Sorex minutus), two hedgehogs (Erinaceus europaeus) and 75 Eurasian otters (Lutra lutra). No cases of SARS-CoV-2 were detected in any animals, but 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.

An investigation into resting behavior in Asian elephants in UK zoos.

Maintaining adequate welfare in captive elephants is challenging. Few studies have investigated overnight rest behavior in zoo elephants, yet time spent resting has been identified as a welfare indicator in some species. We investigated resting behavior in Asian elephants (Elephas maximus) in UK zoos, with the aim of identifying patterns or preferences in lying rest. Details of standing (SR) and lying (LR) rest behavior were identified by observing video footage of inside enclosures collected for 14 elephants (2 male, 12 female) housed at three UK zoos (Zoo A: 18 nights; Zoo B: 27 nights; Zoo C: 46 nights) from 16:00 to 08:30 (approximately). Elephants engaged in a mean of 58-337 min rest per night. Time of night affected mean duration of LR bouts (P < 0.001); longest bouts were observed between 22:01 and 06:00. Elephants showed a substrate preference when lying to rest; LR was not observed on concrete or tiled flooring. Where sand was available (to 11/14 elephants), all elephants engaged in LR on sand flooring. Only two elephants engaged in LR on rubber flooring (available to 7/14 elephants). Mean duration of rest bouts was greater when a conspecific was within two body lengths than when conspecifics were not (P < 0.01). Our study indicated that elephants show substrate preferences when choosing an area for rest and engage in more rest when conspecifics are in close proximity. The results of this study could be used as a basis for future studies investigating the link between rest and welfare in captive elephants.

Understanding Temporal Social Dynamics in Zoo Animal Management: An Elephant Case Study.

Zoo animal management procedures which lead to changes to social groups can cause disruption in social hierarchies and the temporary breakdown of social relationships. Animals have different roles in social networks. Understanding individual positions in social networks is important for effective management and ensuring positive welfare for all animals. Using elephants as a case study, the aim of this research was to investigate temporal social dynamics in zoo animals. Behavioural data were collected between January 2016 and February 2017 from 10 African and 22 Asian elephants housed at seven zoos and safari parks in the UK and Ireland. Social interactions were defined as positive physical, positive non-physical, negative physical or negative non-physical. Social network analysis explored social relationships including the fluidity of networks over time and dyadic reciprocity. Social interaction networks were found to be fluid but did not follow a seasonal pattern. Positive interaction networks tended to include the entire social group whereas negative interactions were restricted to specific individuals. Unbalanced ties were observed within dyads, suggesting potential inequalities in relationships. This could impact on individual experiences and welfare. This research highlights subtle temporal dynamics in zoo elephants with the potential for species-level differences. Similar temporal dynamics may also be present in other socially housed zoo species. This research thus provides evidence for the importance of understanding the social networks of zoo animals over longer periods of time. Understanding social networks enables pro-active and evidence-based management approaches. Further research should seek to identify the minimum sampling efforts for social networks in a range of species, to enable the implementation of regular monitoring of social networks and thus improve the welfare of social species under human care.

Social Interactions in Zoo-Housed Elephants: Factors Affecting Social Relationships.

Elephants have complex social systems that are predominantly driven by ecological factors in situ. Within zoos, elephants are held in relatively static social groups and the factors observed driving social relationships in the wild are largely absent. Little research has investigated the effect of social group factors in zoos on elephant social interactions. The aim of this research was to establish whether there is a relationship between social group factors and social behaviour, in order to identify factors that make elephant herds more or less likely to be compatible. Results will facilitate recommendations for optimum social groupings for zoo elephants. Behavioural data quantifying social interactions were collected between January 2016 and February 2017 at seven UK and Irish zoos and safari parks from 10 African and 22 Asian elephants. Social interactions were split into four categories: positive physical, positive non-physical, negative physical and negative non-physical. Social interactions were related to age (positive physical higher and negative non-physical lower in calves than adults), personality (elephants with higher sociability scores engaged in more positive interactions and less negative interactions), presence of calves in the herd (herds with calves had more positive non-physical), relatedness to other elephants in the herd (positive non-physical were higher when relatives were in the group and negative non-physical were higher between unrelated elephants) and species (Asian elephants engaged in more positive non-physical than African elephants). A greater understanding of factors that may contribute to the success of zoo-elephant social groups is important for individual and herd welfare as it will enable evidence-based decisions which have minimal impact on social structures to be executed. This knowledge will enable proactive management approaches to be undertaken and will thus be paramount in ensuring optimal welfare for elephant herds moving forwards.

Assessing personality in San Joaquin kit fox in situ: efficacy of field-based experimental methods and implications for conservation management.

Utilisation of animal personality has potential benefit for conservation management. Due to logistics of robust behavioural evaluation in situ, the majority of studies on wild animals involve taking animals into captivity for testing, potentially compromising results. Three in situ tests for evaluation of boldness in San Joaquin kit fox (Vulpes macrotis mutica) were developed (ENOT: extended novel object test; RNOT: rapid novel object test; TH: trap/handling test). Each test successfully identified variation in boldness within its target age class(es). The TH test was suitable for use across all age classes. Tests were assessed for in situ suitability and for quantity/quality of data yielded. ENOT was rated as requiring high levels of time, cost and labour with greater likelihood of failure. However, it was rated highly for data quantity/quality. The TH test was rated as requiring little time, labour and cost, but yielding lower quality data. RNOT was rated in the middle. Each test had merit and could be adapted to suit project or species constraints. We recommend field-based evaluation of personality, reducing removal of animals from the wild and facilitating routine incorporation of personality assessment into conservation projects.