Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014
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SciScore for 10.1101/2020.06.05.098590: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: The study was approved by the Department of Animal Health of the Ministry of Agriculture and Rural Development and protocols were reviewed by the Institutional Animal Care and Use Committee at the University of California at Davis (protocol number 16048). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Alignments were performed using MUSCLE, and trees were constructed using Maximum likelihood and the Tamura 3-parameter model in MEGA7 [31]. MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)MEGA7suggested: NoneStatistical analyses: … SciScore for 10.1101/2020.06.05.098590: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: The study was approved by the Department of Animal Health of the Ministry of Agriculture and Rural Development and protocols were reviewed by the Institutional Animal Care and Use Committee at the University of California at Davis (protocol number 16048). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Alignments were performed using MUSCLE, and trees were constructed using Maximum likelihood and the Tamura 3-parameter model in MEGA7 [31]. MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)MEGA7suggested: NoneStatistical analyses: Visualization of sampling locations in provinces in Viet Nam, along with the distribution by species and interface was constructed with the ggmap, ggplot2, and sp packages [34]. ggplot2suggested: (ggplot2, RRID:SCR_014601)All analyses were done using R version 3.5.0 or higher (R Development Core Team, Vienna, Austria). R Development Coresuggested: (R Project for Statistical Computing, RRID:SCR_001905)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:These limitations mean we are not able to make inferences about larger spatial patterns or the inter-annual variability of coronavirus prevalence in wildlife populations found in this interface, which spans into neighboring Cambodia. However, from a mechanistic perspective as animals progress along the wildlife supply chain, opportunity for human contact increases, including close direct contact with traders, butchers, cooks, and consumers [40]. The combination of increased coronavirus prevalence in traded wildlife and greater opportunity for human-wildlife contact as well as intra- and inter-species contact in trade systems is likely to increase the risk of zoonotic transmission of coronaviruses in wildlife markets, restaurants, and other trade interfaces. Viral sharing or environmental mixing: We detected avian and bat coronaviruses in wildlife farm rodents, including Malayan porcupines and bamboo rats, but we did not detect rodent-associated coronaviruses. The only previously published coronavirus testing of Malayan porcupine samples carried out in China were negative [41]. It is unclear if the Malayan porcupine samples from animals screened in this study were infected with the avian or bat viruses or if environmental contamination or mixing occurred with avian and bat guano. Chickens were present at the two sites where the IBV-positive rodents were detected, and bats fly and potentially roost overhead at most farms. ‘Artificial market’ studies of influenza A viruses have ...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
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SciScore for 10.1101/2020.06.05.098590: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement The study was approved by the Department of Animal Health of the Ministry of Agriculture and Rural Development and protocols were reviewed by the Institutional Animal Care and Use Committee at the University of California at Davis ( protocol number 16048) . Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Alignments were performed using MUSCLE , and trees were constructed using Maximum likelihood and the Tamura 3-parameter model in MEGA7 [ 31] . MUSCLEsuggested: (MUSCLE, SCR_011812)…SciScore for 10.1101/2020.06.05.098590: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement The study was approved by the Department of Animal Health of the Ministry of Agriculture and Rural Development and protocols were reviewed by the Institutional Animal Care and Use Committee at the University of California at Davis ( protocol number 16048) . Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Alignments were performed using MUSCLE , and trees were constructed using Maximum likelihood and the Tamura 3-parameter model in MEGA7 [ 31] . MUSCLEsuggested: (MUSCLE, SCR_011812)<div style="margin-bottom:8px"> <div><b>MEGA7</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses Visualization of sampling locations in provinces in Viet Nam , along with the distribution by species and interface was constructed with the ggmap , ggplot2 , and sp packages [ 34] .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>ggplot2</b></div> <div>suggested: (ggplot2, <a href="https://scicrunch.org/resources/Any/search?q=SCR_014601">SCR_014601</a>)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All analyses were done using R version 3.5.0 or higher ( R Development Core Team , Vienna , Austria) .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>R Development Core</b></div> <div>suggested: (R Project for Statistical Computing, <a href="https://scicrunch.org/resources/Any/search?q=SCR_001905">SCR_001905</a>)</div> </div> </td></tr></table>Results from OddPub: Thank you for sharing your code and data.
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