Overview of Bat and Wildlife Coronavirus Surveillance in Africa: A Framework for Global Investigations

Geldenhuys, Marike; Mortlock, Marinda; Epstein, Jonathan H.; Pawęska, Janusz T.; Weyer, Jacqueline; Markotter, Wanda

doi:10.3390/v13050936

Cited by 26 publications

(51 citation statements)

References 149 publications

(417 reference statements)

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“…We should also consider targeted risk assessment and screening of different wild mustelids, bats, wild canids, and felids in the different zoo and safari parks. Moreover, all animal caretakers should take precautions to prevent viral exposure to wild animal species and vice versa [ 21 , 80 , 81 ].…”

Section: Discussionmentioning

confidence: 99%

Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals

et al. 2021

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The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed susceptibility to diverse animal species. We conducted this study to understand the spatial epidemiology, genetic diversity, and statistically significant genetic similarity along with per-gene recombination events of SARS-CoV-2 and related viruses (SC2r-CoVs) in animals globally. We collected a number of different animal species infected with SARS-CoV-2 and its related viruses. Then, we retrieved genome sequences of SARS-CoV-2 and SC2r-CoVs from GISAID and NCBI GenBank for genomic and mutational analysis. Although the evolutionary origin of SARS-CoV-2 remains elusive, the diverse SC2r-CoV have been detected in multiple Rhinolophus bat species and in Malayan pangolin. To date, human-to-animal spillover events have been reported in cat, dog, tiger, lion, gorilla, leopard, ferret, puma, cougar, otter, and mink in 25 countries. Phylogeny and genetic recombination events of SC2r-CoVs showed higher similarity to the bat coronavirus RaTG13 and BANAL-103 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the N protein from bats and pangolin showed close resemblance to SARS-CoV-2. The clustering of animal and human strains from the same geographical area has proved human-to-animal transmission of the virus. The Alpha, Delta and Mu-variant of SARS-CoV-2 was detected in dog, gorilla, lion, tiger, otter, and cat in the USA, India, Czech Republic, Belgium, and France with momentous genetic similarity with human SARS-CoV-2 sequences. The mink variant mutation (spike_Y453F) was detected in both humans and domestic cats. Moreover, the dog was affected mostly by clade O (66.7%), whereas cat and American mink were affected by clade GR (31.6 and 49.7%, respectively). The α-variant was detected as 2.6% in cat, 4.8% in dog, 14.3% in tiger, 66.7% in gorilla, and 77.3% in lion. The highest mutations observed in mink where the substitution of D614G in spike (95.2%) and P323L in NSP12 (95.2%) protein. In dog, cat, gorilla, lion, and tiger, Y505H and Y453F were the common mutations followed by Y145del, Y144del, and V70I in S protein. We recommend vaccine provision for pet and zoo animals to reduce the chance of transmission in animals. Besides, continuous epidemiological and genomic surveillance of coronaviruses in animal host is crucial to find out the immediate ancestor of SARS-CoV-2 and to prevent future CoVs threats to humans.

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Section: Discussionmentioning

confidence: 99%

Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals

et al. 2021

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“…This is especially crucial as the worldwide encroachment of growing human populations into wildlife habitats, along with an increase in agriculture and livestock density in areas adjacent to fragmented forests, increases the risk of zoonotic virus transmission from bats to humans [ 73 ]. Bats, along with domesticated species, primates and rodents, are a large and diverse order that host a variety of viruses with zoonotic potential [ 38 , 57 ], with several bat species (including M. natalensis and R. aegyptiacus ) in South Africa earmarked for ongoing monitoring for potentially zoonotic viruses [ 30 , 31 , 51 ]. Our research has highlighted important roost localities for M. natalensis and R. aegyptiacus that are under pressure from land-cover changes, particularly increasing urbanisation and agricultural activities and the loss of trees.…”

Section: Discussionmentioning

confidence: 99%

“…Both M. natalensis and R. aegyptiacus are species of interest as transmission hosts for potential zoonotic viruses [ 51 ], specifically, various potentially zoonotic coronaviruses [ 30 , 31 ]. The two bat species are characterised by large population sizes and may often be found co-roosting, which increases the chance of cross-species viral sharing and infection [ 20 , 61 ].…”

Section: Introductionmentioning

confidence: 99%

Assessing the extent of land-use change around important bat-inhabited caves

Pretorius¹,

Markotter²,

Keith³

2021

BMC Zool

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Background Modification and destruction of natural habitats are bringing previously unencountered animal populations into contact with humans, with bats considered important zoonotic transmission vectors. Caves and cave-dwelling bats are under-represented in conservation plans. In South Africa, at least two cavernicolous species are of interest as potential zoonotic hosts: the Natal long-fingered bat Miniopterus natalensis and the Egyptian fruit bat Rousettus aegyptiacus. Little information is available about the anthropogenic pressures these species face around important roost sites. Both bats are numerous and widespread throughout the country; land-use changes and urban expansions are a rising concern for both conservation and increased bat-human contact. Results Our study addressed this shortfall by determining the extent of land-cover change around 47 roosts between 2014 and 2018 using existing land cover datasets. We determined the land-cover composition around important roost sites (including maternity, hibernacula and co-roosts), distances to urban settlements and assessed the current protection levels of roost localities. We detected an overall 4% decrease in natural woody vegetation (trees) within 5 km buffer zones of all roost sites, with a 10% decrease detected at co-roost sites alone. Agricultural land cover increased the most near roost sites, followed by plantations and urban land-cover. Overall, roosts were located 4.15 ± 0.91 km from urban settlements in 2018, the distances decreasing as urban areas expand. According to the South African National Biodiversity Institute Ecosystem Threat Status assessment, 72% of roosts fall outside of well-protected ecosystems. Conclusions The current lack of regulatory protection of cavernicolous bats and their roosts, increasing anthropogenic expansions and proximity to human settlements raises concerns about increased human-bat contact. Furthermore, uncontrolled roost visitation and vandalism are increasing, contributing to bat health risks and population declines, though the extent of roosts affected is yet to be quantified. In an era where pandemics are predicted to become more frequent and severe due to land-use change, our research is an urgent call for the formal protection of bat-inhabited caves to safeguard both bats and humans.

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“…In this context, it is crucial to mention how previously established panCoV RT-PCR assays have failed to detect the newly emerged PDCoV in diarrheic pig feces subsequently found to be positive using probe-based assays [32]. Thus, as underlined elsewhere [33], there is a critical need to improve available pan-coronavirus methods for the survey of these viruses that might be currently vastly under-detected in mammals.…”

Section: How Diagnostic Failure Can Affect Animal Surveillancementioning

confidence: 99%

Best Molecular Tools to Investigate Coronavirus Diversity in Mammals: A Comparison

Drzewnioková

Festa

Panzarin

et al. 2021

Viruses

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Coronaviruses (CoVs) are widespread and highly diversified in wildlife and domestic mammals and can emerge as zoonotic or epizootic pathogens and consequently host shift from these reservoirs, highlighting the importance of veterinary surveillance. All genera can be found in mammals, with α and β showing the highest frequency and diversification. The aims of this study were to review the literature for features of CoV surveillance in animals, to test widely used molecular protocols, and to identify the most effective one in terms of spectrum and sensitivity. We combined a literature review with analyses in silico and in vitro using viral strains and archive field samples. We found that most protocols defined as pan-coronavirus are strongly biased towards α- and β-CoVs and show medium-low sensitivity. The best results were observed using our new protocol, showing LoD 100 PFU/mL for SARS-CoV-2, 50 TCID50/mL for CaCoV, 0.39 TCID50/mL for BoCoV, and 9 ± 1 log2 ×10−5 HA for IBV. The protocol successfully confirmed the positivity for a broad range of CoVs in 30/30 field samples. Our study points out that pan-CoV surveillance in mammals could be strongly improved in sensitivity and spectrum and propose the application of a new RT-PCR assay, which is able to detect CoVs from all four genera, with an optimal sensitivity for α-, β-, and γ-.

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Overview of Bat and Wildlife Coronavirus Surveillance in Africa: A Framework for Global Investigations

Cited by 26 publications

References 149 publications

Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals

Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals

Assessing the extent of land-use change around important bat-inhabited caves

Best Molecular Tools to Investigate Coronavirus Diversity in Mammals: A Comparison

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