The evidence remains clear: SARS-CoV-2 emerged via the wildlife trade.
Ontology highlight
ABSTRACT:
SUBMITTER: Garry RF
PROVIDER: S-EPMC9704731 | biostudies-literature | 2022 Nov
REPOSITORIES: biostudies-literature
Publications
The evidence remains clear: SARS-CoV-2 emerged via the wildlife trade.
Proceedings of the National Academy of Sciences of the United States of America 20221110 47
Similar Datasets
Project description:Despite the discovery of several closely related viruses in bats, the direct evolutionary progenitor of SARS-CoV-2 has not yet been identified. In this study, we investigated potential animal sources of SARS-related coronaviruses using archived specimens from Sunda pangolins (Manis javanica) and Chinese pangolins (Manis pentadactyla) confiscated from the illegal wildlife trade, and from common palm civets (Paradoxurus hermaphroditus) raised on wildlife farms in Viet Nam. A total of 696 pangolin and civet specimens were screened for the presence of viral RNA from five zoonotic viral families and from Sarbecoviruses using primers specifically designed for pangolin coronaviruses. We also performed a curated data collection of media reports of wildlife confiscation events involving pangolins in Viet Nam between January 2016 and December 2020, to illustrate the global pangolin supply chain in the context of Viet Nam where the trade confiscated pangolins were sampled for this study. All specimens from pangolins and civets sampled along the wildlife supply chains between February 2017 and July 2018, in Viet Nam and tested with conventional PCR assays designed to detect flavivirus, paramyxovirus, filovirus, coronavirus, and orthomyxovirus RNA were negative. Civet samples were also negative for Sarbecoviruses, but 12 specimens from seven live pangolins confiscated in Hung Yen province, northern Viet Nam, in 2018 were positive for Sarbecoviruses. Our phylogenetic trees based on two fragments of the RdRp gene revealed that the Sarbecoviruses identified in these pangolins were closely related to pangolin coronaviruses detected in pangolins confiscated from the illegal wildlife trade in Yunnan and Guangxi provinces, China. Our curated data collection of media reports of wildlife confiscation events involving pangolins in Viet Nam between January 2016 and December 2020, reflected what is known about pangolin trafficking globally. Pangolins confiscated in Viet Nam were largely in transit, moving toward downstream consumers in China. Confiscations included pangolin scales sourced originally from Africa (and African species of pangolins), or pangolin carcasses and live pangolins native to Southeast Asia (predominately the Sunda pangolin) sourced from neighboring range countries and moving through Viet Nam toward provinces bordering China.
| S-EPMC8959545 | biostudies-literature
Project description:The link between unsustainable harvest of species for the wildlife trade and extinction is clear in some cases, but little is known about the number of species across taxonomic groups that have gone extinct because of trade-related factors, or future risks for traded species. We conducted a rapid review of published articles and species assessments on the IUCN Red List of Threatened Species with the aim of recording examples of extinctions that were attributed to trade. We found reports of extinctions linked, at least in part, to wildlife trade for 511 unique taxa. These include 294 reports of global extinctions, 25 extinctions in the wild, and 192 local extinctions. The majority of global/in the wild extinctions linked to trade (230) involved ray-finned fishes, primarily due to predation by introduced commercial species. Seventy-one of the 175 reported local extinctions of animal taxa linked to trade were mammals. Twenty-two global/in the wild extinctions and 16 local extinctions of plants were reportedly linked to trade. One fungal species was reported locally extinct due to over-harvesting for trade. Furthermore, 340 species were reported to be near-extinct linked to trade, 269 of which were animals, including several high-profile megafauna. Extinctions were linked to direct harvesting and/or indirect threats such as bycatch or invasive species introduced for trade, but often it was not possible to determine the relative role of trade-related threats in extinctions. Our results highlight the need for better data collection on trade-related extinction risk to understand its impacts and to inform more effective wildlife trade policy.
| S-EPMC11895731 | biostudies-literature
Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the pandemic of the coronavirus disease 2019 (COVID-19), resulting in a global lockdown in 2020. This stagnation in human activities ('anthropause') has been reported to affect the behaviour of wildlife in various ways. The sika deer Cervus nippon in Nara Park, central Japan, has had a unique relationship with humans, especially tourists, in which the deer bow to receive food and sometimes attack if they do not receive it. We investigated how a decrease and subsequent increase in the number of tourists visiting Nara Park affects the number of deer observed in the park and their behaviour (bows and attacks against humans). Compared with the pre-pandemic years, the number of deer in the study site decreased from an average of 167 deer in 2019 to 65 (39%) in 2020 during the pandemic period. Likewise, the number of deer bows decreased from 10.2 per deer in 2016-2017 to 6.4 (62%) in 2020-2021, whereas the proportion of deer showing aggressive behaviour did not change significantly. Moreover, the monthly numbers of deer and their bows both corresponded with the fluctuation in the number of tourists during the pandemic period of 2020 and 2021, whereas the number of attacks did not. Thus, the anthropause caused by the coronavirus altered the habitat use and behaviour of deer that have continuous interactions with humans.
| S-EPMC10187922 | biostudies-literature
Project description:BackgroundBats have been considered natural reservoirs for several pathogenic human coronaviruses (CoVs) in the last two decades. Recently, a bat CoV was detected in the Republic of Korea; its entire genome was sequenced and reported to be genetically similar to that of the severe acute respiratory syndrome CoV (SARS-CoV).ObjectivesThe objective of this study was to compare the genetic sequences of SARS-CoV, SARS-CoV-2, and the two Korean bat CoV strains 16BO133 and B15-21, to estimate the likelihood of an interaction between the Korean bat CoVs and the human angiotensin-converting enzyme 2 (ACE2) receptor.MethodsThe phylogenetic analysis was conducted with the maximum-likelihood (ML) method using MEGA 7 software. The Korean bat CoVs receptor binding domain (RBD) of the spike protein was analyzed by comparative homology modeling using the SWISS-MODEL server. The binding energies of the complexes were calculated using PRODIGY and MM/GBGA.ResultsPhylogenetic analyses of the entire RNA-dependent RNA polymerase, spike regions, and the complete genome revealed that the Korean CoVs, along with SARS-CoV and SARS-CoV-2, belong to the subgenus Sarbecovirus, within BetaCoVs. However, the two Korean CoVs were distinct from SARS-CoV-2. Specifically, the spike gene of the Korean CoVs, which is involved in host infection, differed from that of SARS-CoV-2, showing only 66.8%-67.0% nucleotide homology and presented deletions within the RBD, particularly within regions critical for cross-species transmission and that mediate interaction with ACE2. Binding free energy calculation revealed that the binding affinity of Korean bat CoV RBD to hACE2 was drastically lower than that of SARS-CoV and SARS-CoV-2.ConclusionsThese results suggest that Korean bat CoVs are unlikely to bind to the human ACE2 receptor.
| S-EPMC7850784 | biostudies-literature
Project description:Spillover of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) to North American white-tailed deer (Odocoileus virginianus) has been documented. However, it is unclear if this is a phenomenon specific to North American deer or is a broader problem. We evaluated pre and pandemic exposure of German and Austrian deer species using a SARS-CoV-2 pseudoneutralization assay. In stark contrast to North American white-tailed deer, we found no evidence of SARS-CoV-2 exposure.
| S-EPMC9031146 | biostudies-literature
Project description:Pervasive SARS-CoV-2 infections in humans have led to multiple transmission events to animals. While SARS-CoV-2 has a potential broad wildlife host range, most documented infections have been in captive animals and a single wildlife species, the white-tailed deer. The full extent of SARS-CoV-2 exposure among wildlife communities and the factors that influence wildlife transmission risk remain unknown. We sampled 23 species of wildlife for SARS-CoV-2 and examined the effects of urbanization and human use on seropositivity. Here, we document positive detections of SARS-CoV-2 RNA in six species, including the deer mouse, Virginia opossum, raccoon, groundhog, Eastern cottontail, and Eastern red bat between May 2022-September 2023 across Virginia and Washington, D.C., USA. In addition, we found that sites with high human activity had three times higher seroprevalence than low human-use areas. We obtained SARS-CoV-2 genomic sequences from nine individuals of six species which were assigned to seven Pango lineages of the Omicron variant. The close match to variants circulating in humans at the time suggests at least seven recent human-to-animal transmission events. Our data support that exposure to SARS-CoV-2 has been widespread in wildlife communities and suggests that areas with high human activity may serve as points of contact for cross-species transmission.
| S-EPMC11286844 | biostudies-literature
Project description:The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This pathogen has spread rapidly across the world, causing high numbers of deaths and significant social and economic impacts. SARS-CoV-2 is a novel coronavirus with a suggested zoonotic origin with the potential for cross-species transmission among animals. Antarctica can be considered the only continent free of SARS-CoV-2. Therefore, concerns have been expressed regarding the potential human introduction of this virus to the continent through the activities of research or tourism to minimise the effects on human health, and the potential for virus transmission to Antarctic wildlife. We assess the reverse-zoonotic transmission risk to Antarctic wildlife by considering the available information on host susceptibility, dynamics of the infection in humans, and contact interactions between humans and Antarctic wildlife. The environmental conditions in Antarctica seem to be favourable for the virus stability. Indoor spaces such as those at research stations, research vessels or tourist cruise ships could allow for more transmission among humans and depending on their movements between different locations the virus could be spread across the continent. Among Antarctic wildlife previous in silico analyses suggested that cetaceans are at greater risk of infection whereas seals and birds appear to be at a low infection risk. However, caution needed until further research is carried out and consequently, the precautionary principle should be applied. Field researchers handling animals are identified as the human group posing the highest risk of transmission to animals while tourists and other personnel pose a significant risk only when in close proximity (< 5 m) to Antarctic fauna. We highlight measures to reduce the risk as well as identify of knowledge gaps related to this issue.
| S-EPMC7598351 | biostudies-literature
Project description:The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a key role in viral infectivity. It is also the major antigen stimulating the host's protective immune response, specifically, the production of neutralizing antibodies. Recently, a new variant of SARS-CoV-2 possessing multiple mutations in the S protein, designated P.1, emerged in Brazil. Here, we characterized a P.1 variant isolated in Japan by using Syrian hamsters, a well-established small animal model for the study of SARS-CoV-2 disease (COVID-19). In hamsters, the variant showed replicative abilities and pathogenicity similar to those of early and contemporary strains (i.e., SARS-CoV-2 bearing aspartic acid [D] or glycine [G] at position 614 of the S protein). Sera and/or plasma from convalescent patients and BNT162b2 messenger RNA vaccinees showed comparable neutralization titers across the P.1 variant, S-614D, and S-614G strains. In contrast, the S-614D and S-614G strains were less well recognized than the P.1 variant by serum from a P.1-infected patient. Prior infection with S-614D or S-614G strains efficiently prevented the replication of the P.1 variant in the lower respiratory tract of hamsters upon reinfection. In addition, passive transfer of neutralizing antibodies to hamsters infected with the P.1 variant or the S-614G strain led to reduced virus replication in the lower respiratory tract. However, the effect was less pronounced against the P.1 variant than the S-614G strain. These findings suggest that the P.1 variant may be somewhat antigenically different from the early and contemporary strains of SARS-CoV-2.
| S-EPMC8271735 | biostudies-literature
Project description:Ongoing emergence of SARS-CoV-2 Omicron subvariants and their rapid worldwide spread pose a threat to public health. From November 2022 to February 2023, newly emerged Omicron subvariants, including BQ.1.1, BF.7, BA.5.2, XBB.1, XBB.1.5, and BN.1.9, became prevalent global strains (>5% global prevalence). These Omicron subvariants are resistant to several therapeutic antibodies. Thus, the antiviral activity of current drugs such as remdesivir, molnupiravir, and nirmatrelvir, which target highly conserved regions of SARS-CoV-2, against newly emerged Omicron subvariants need to be evaluated. We assessed the antiviral efficacy of the drugs using the half-maximal inhibitory concentration (IC50) against human isolates of 23 Omicron subvariants and four former SARS-CoV-2 variants of concern (VOCs) and compared it with the antiviral efficacy of these drugs against the SARS-CoV-2 reference strain (hCoV/Korea/KCDC03/2020). Maximal IC50-fold changes of remdesivir, molnupiravir, and nirmatrelvir were 1.9 (BA.2.75.2), 1.2 (B.1.627.2), and 1.4 (BA.2.3), respectively, compared to median IC50 values of the reference strain. Moreover, median IC50-fold changes of remdesivir, molnupiravir, and nirmatrelvir against the Omicron variants were 0.96, 0.4, and 0.62, respectively, similar to the 1.02, 0.88, and 0.67, respectively, median IC50-fold changes for previous VOCs. Although K90R and P132H in Nsp 5, and P323L, A529V, G671S, V405F, and ins823D in Nsp 12 mutations were identified, these amino acid substitutions did not affect drug antiviral activity. These results indicate that current antivirals retain antiviral efficacy against newly emerged Omicron subvariants. It is important to continue active surveillance and testing of new variants for drug resistance to enable early identification of drug-resistant strains.
| S-EPMC10118056 | biostudies-literature
Project description:Interventions: Group 1: A qualitative interview study as well as a cross-sectional questionnaire survey is conducted with patients, oncologists and nurses working in the field of oncology (subproject 1). This is complemented by retrospective analysis of quantitative data derived from the registry of colon cancer centres (subproject 2) and data from the statutory health insurance (subproject 3).
Primary outcome(s): Aim: Assessment of ethical and psychosocial challenges in cancer care via semi-structured interviews with stakeholders (oncologists, nurses, patients) between January and July 2021. Assessment of psychosocial burden of oncologists, nurses and patients between February and July 2021 via questionnaires.
patients: Mini-SCL, EORTC QLQ-C30, NCCN Distress Thermometer, FACT-19
oncologists: PHQ-9, PHQ-15, GAD-7, Maslach Burnout Inventory, Moral Distress Thermometer, FACT-19, sociodemographic questionnaire
nurses: PHQ-9, PHQ-15, GAD-7, Maslach Burnout Inventory, Moral Distress Thermometer, FACT-19, BERNCA, sociodemographic questionnaire
Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: other
| 2439669 | ecrin-mdr-crc