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

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This paper/research report evaluated whether SARS-CoV-2 could be detected in wildlife sampled from Kerala, India during 2020–2021, using field sampling under ethics approval from the University of Nottingham School of Veterinary Medicine and Science Committee for Animal Research and Ethics and a Kerala wildlife permit for forest-area sampling. The key reported outcome was that SARS-CoV-2 was not detected in the wildlife samples, with SciScore noting “not detected” for several study-reporting elements such as attrition, randomization, blinding, and other demographic/study-design descriptors, and it did not find detailed statistical methods or data/code availability statements. Limitations highlighted by the SciScore material include missing reporting for key rigor criteria (e.g., power analysis and replication) as presented in the automated check. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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Abstract

Spillover 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).
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Materials

Design Analysis Reporting (MDAR) Checklist for Authors The MDAR framework establishes a minimum set of requirements in transparent reporting applicable to studies in the life sciences (see Statement of Task: doi:10.31222/osf.oio/9sm4x.). The MDAR checklist is a tool for authors, editors and others seeking to adopt the MDAR framework for transparent reporting in manuscripts and other outputs. Please refer to the MDAR Elaboration Document for additional context for the MDAR framework. Report provided by SciScore | August 01, 2023 | Based on DocumentID 2277_64c8ce2fb91d65.94943320

Materials

Antibodies Yes (indicate where provided: page no/section/legend) n/a For commercial reagents, provide supplier name, catalogue number and RRID, if available No antibodes detected. Please add identifiers for all resources where possible Cell Materials Yes (indicate where provided: page no/section/legend) n/a Cell lines: Provide species information, strain. Provide accession number in repository OR supplier name, catalog number, clone number, OR RRID No cell lines detected Please add identifiers for all resources where possible Primary cultures: Provide species, strain, sex of origin, genetic modification status. Not currently checked by SciScore Experimental Animals Yes (indicate where provided: page no/section/legend) n/a Laboratory animals: Provide species, strain, sex, age, genetic modification status. Provide accession number in repository OR supplier name, catalog number, clone number, OR RRID No organisms detected Please add identifiers for all resources where possible Animal observed in or captured from the field: Provide species, sex and age where possible Not currently checked by SciScore Model organisms: Provide Accession number in repository (where relevant) OR RRID See laboratory animals section for information. Plants and microbes Yes (indicate where provided: page no/section/legend) n/a Plants: provide species and strain, unique accession number if available, and source (including location for collected wild specimens) Not currently checked by SciScore Microbes: provide species and strain, unique accession number if available, and source Not currently checked by SciScore Human research participants Yes (indicate where provided: page no/section/legend) n/a Identify authority granting ethics approval (IRB or equivalent committee(s), provide reference number for approval. Not detected. Provide statement confirming informed consent obtained from study participants. Not detected. Report on age and sex for all study participants. Age:not detected. Sex:not detected. Report provided by SciScore | August 01, 2023 | Based on DocumentID 2277_64c8ce2fb91d65.94943320 Design Study protocol Yes (indicate where provided: page no/section/legend) n/a For clinical trials, provide the trial registration number OR cite DOI in manuscript. Not detected. Laboratory protocol Yes (indicate where provided: page no/section/legend) n/a Provide DOI or other citation details if detailed step- by-step protocols are available. Not detected. Experimental study design (statistics details) Yes (indicate where provided: page no/section/legend) n/a State whether and how the following have been done, or if they were not carried out Sample size determination not detected. Randomization not detected. Blinding not detected. inclusion/exclusion criteria not detected. Sample definition and in-laboratory replication Yes (indicate where provided: page no/section/legend) n/a State number of times the experiment was replicated in laboratory Not detected. Define whether data describe technical or biological replicates Not detected. Ethics Yes (indicate where provided: page no/section/legend) n/a Studies involving human participants: State details of authority granting ethics approval (IRB or equivalent committee(s), provide reference number for approval. Not detected. Studies involving experimental animals: State details of authority granting ethics approval (IRB or equivalent committee(s), provide reference number for approval. Ethical approval was granted by the University of Nottingham School of Veterinary Medicine and Science Committee for Animal Research and Ethics (CARE). Studies involving specimen and field samples: State if relevant permits obtained, provide details of authority approving study; if none were required, explain why. Permission for Field work in Forest Areas for Scientific Research and sample collection was as per the permit number KFDHQ- 1979/ 2021-CWW / WL 10 issued by the Chief Wildlife Warden, Kerala state, India. Dual Use Research of Concern (DURC) Yes (indicate where provided: page no/section/legend) n/a If study is subject to dual use research of concern, state the authority granting approval and reference number for the regulatory approval Not currently checked by SciScore Report provided by SciScore | August 01, 2023 | Based on DocumentID 2277_64c8ce2fb91d65.94943320 Analysis Attrition Yes (indicate where provided: page no/section/legend) n/a State if sample or data point from the analysis is excluded, and whether the criteria for exclusion were determined and specified in advance. not detected. Statistics Yes (indicate where provided: page no/section/legend) n/a Describe statistical tests used and justify choice of tests. Not detected. Data availability Yes (indicate where provided: page no/section/legend) n/a State whether newly created datasets are available, including protocols for access or restriction on access. Not detected. If data are publicly available, provide accession number in repository or DOI or URL. Not detected. If publicly available data are reused, provide accession number in repository or DOI or URL, where possible. Not detected. Code availability Yes (indicate where provided: page no/section/legend) n/a For all newly generated code and software essential for replicating the main findings of the study: State whether the code or software is available. Not detected. If code is publicly available, provide accession number in repository, or DOI or URL. Not detected. Report provided by SciScore | August 01, 2023 | Based on DocumentID 2277_64c8ce2fb91d65.94943320 Analysis Adherence to community standards Yes (indicate where provided: page no/section/legend) n/a MDAR framework recommends adoption of discipline-specific guidelines, established and endorsed through community initiatives. Journals have their own policy about requiring specific guidelines and recommendations to complement MDAR. State if relevant guidelines (eg., ICMJE, MIBBI, ARRIVE) have been followed, and whether a checklist (eg., CONSORT, PRISMA, ARRIVE) is provided with the manuscript. Not currently checked by SciScore Report provided by SciScore | August 01, 2023 | Based on DocumentID 2277_64c8ce2fb91d65.94943320 ACMI-S-23-00251.pdf By Rachael Tarlinton WORD COUNT 5819 TIME SUBMITTED 31-JUL-2023 12:41PM PAPER ID 101649106 7 7 1 0 1 2 1 9 1 1 1 1 1 2 2 4 4 5 5 5 6 6 9 1 4 1 5 1 7 2 1 2 3 1 2 4 1 3 1 2 8 1 1 2 2 2 2 0 1 3 3 3 8 1 8 2 2 2 4 1 1 2 1 1 1 6 1 18% SIMILARITY INDEX 1 2 3 4 5 6 ACMI-S-23-00251.pdf ORIGINALITY REPORT PRIMARY SOURCES Ternenge Apaa, Amy J. Withers, Laura McKenzie, Ceri Staley et al. " Lack of detection of SARS-CoV-2 in British wildlife 2020-21 and first description of a stoat ( ", Cold Spring Harbor Laboratory, 2023 Crossref Posted Content orca.cardiff.ac.uk Internet Wendy Puryear, Kaitlin Sawatzki, Nichola Hill, Alexa Foss et al. 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