Verified Rigor RecordRigor Reviewed

Rigor-Reviewed Manuscript

Origin and cross-species transmission of bat coronaviruses in China · 10.1038/s41467-020-17687-3

Name: Verified Rigor Record — Origin and cross-species transmission of bat coronaviruses in China · 10.1038/s41467-020-17687-3
Item: Origin and cross-species transmission of bat coronaviruses in China · 10.1038/s41467-020-17687-3
Rating: 92
Author: Αlpha¹

Paper source

Read full text

Αlpha¹ Editorial

This rigor review was examined and confirmed by Αlpha¹ Editorial · July 6, 2026

Αlpha¹ Rigor Review

Rigor Reviewed

WARN

Warnings to address · Observational Study

Eight dimensions — click a segment for details

Critical

High-priority

Model-reported confidence: highReviewer agreement: moderateEngine: 7.6.0Source: full text

Not verified in this report

References were not verified against Crossref/OpenAlex.

This Αlpha¹ Rigor Review uses AI Rigor Reviewers trained on a curated corpus of high-fidelity and retracted papers, with expert supervision and curation. It can still make mistakes; verify each finding against the source before relying on it.

This paper provides a comprehensive phylogeographic analysis of bat coronaviruses in China, with strong methodological rigor in its Bayesian phylogenetic framework and sensitivity analyses. The main weaknesses are missing details on study design (inclusion criteria, outlier handling, power analysis) and incomplete data/code sharing (no code repository, vague data availability statement).

Evaluation is based on three independent reviewers (all full-text), a copyedit pass, and a statistics verification component. Biological variables were scored as not applicable. The statistics component checked only a subset of tests (7 recomputations all consistent).

12 major claims checked against the paper's own evidence: all adequately supported.

Recomputed 7 tests: 7 consistent, 0 inconsistent, 7 via agent-written checks.

2 integrity concerns flagged (0 high).

Rigor

Eight Dimensions6 pass · 2 warn

12 major claims1 partial11 supported

The introduction thoroughly reviews prior research on bat coronaviruses, including SARS-CoV, MERS-CoV, SADS-CoV, and SARS-CoV-2, and clearly states the gaps in understanding macroevolutionary patterns and host-switching dynamics. The rationale linking the premise to the study objectives is logical and well-articulated. Limitations of prior research, such as incomplete sampling and low sequence numbers, are explicitly addressed.

Sub-criteria

prior work citedADEQUATE

premise rationaleADEQUATE

limitations addressedADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 95% conf

The paper establishes a strong scientific foundation by citing prior work on bat coronaviruses, their zoonotic potential, and the need for understanding cross-species transmission dynamics.

Evidence

direct quote[Introduction, paragraphs 1-4]

“Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19.”

direct quote[Introduction, paragraph 4]

“The emergence of SARS-CoV-2 further underscores the importance of bat-origin CoVs to global health, and understanding their origin and cross-species transmission is a high priority for pandemic preparedness.”

direct quote[Introduction, paragraph 5]

“However, detailed analyses of host switching have been hampered by incomplete or opportunistic sampling, typically with relatively low numbers of viral sequences from any given region.”

PASSReviewer 2· 95% conf

The scientific premise is well-established with extensive prior work cited, a clear rationale linking bat-CoV diversity to zoonotic risk, and limitations of prior research are addressed.

Evidence

paraphrase[Introduction, paragraphs 1-5]

“The introduction cites numerous studies on bat-CoV origins, cross-species transmission, and zoonotic spillover, establishing the premise.”

direct quote[Introduction, last paragraph]

“Our objectives are to compare the macroevolutionary patterns of α- and β-CoVs and identify the hosts and geographical regions that act as centers of evolutionary diversification for bat-CoVs in China.”

direct quote[Introduction, paragraph 6]

“However, detailed analyses of host switching have been hampered by incomplete or opportunistic sampling, typically with relatively low numbers of viral sequences from any given region.”

PASSReviewer 3· 95% conf

The paper clearly establishes its scientific foundation with extensive citations of prior work, a logical rationale linking bat-CoV diversity to cross-species transmission, and acknowledgment of limitations in prior studies.

Evidence

direct quote[Introduction]

“Coronaviruses (CoVs) are RNA viruses causing respiratory and enteric diseases with varying pathogenicity in humans and animals. All CoVs known to infect humans are zoonotic, or of animal origin, with many thought to originate in bat hosts.”

direct quote[Introduction, last paragraph]

“In this study, we analyze an extensive field-collected dataset of bat-CoV sequences from across China. We use a phylogeographic Bayesian statistical framework to reconstruct virus transmission history between different bat host species and virus spatial spread over evolutionary time.”

direct quote[Introduction]

“However, detailed analyses of host switching have been hampered by incomplete or opportunistic sampling, typically with relatively low numbers of viral sequences from any given region.”

The study uses a large dataset of 630 novel sequences plus 616 from public databases, with a Bayesian phylogeographic framework. Randomization and blinding are not applicable for this observational study. A power analysis is not reported, which is a gap for the dataset selection. Inclusion/exclusion criteria for sequences are not explicitly stated beyond availability of host and location metadata. Outlier handling is not described. Controls are not applicable as this is a computational analysis of sequence data. Independent replication is not reported, though the use of random subsets provides some robustness check.

Sub-criteria

controlsN/A

power analysisNOT REPORTED

blinding levelsN/A

outlier handlingNOT REPORTED

randomization unitN/A

inclusion exclusionINADEQUATE

randomization methodN/A

replicate distinctionN/A

independent replicationNOT REPORTED

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 85% conf

The study design is appropriate for an observational phylogeographic analysis, but several key methodological details are not reported, including a power analysis, explicit inclusion/exclusion criteria, and outlier handling.

Evidence

direct quote[Methods, Sequence data]

“All sequences for which sampling year and host or sampling location information was available either in GenBank metadata or in the original publication were included (as of March 15, 2018).”

absence[Methods]

No power analysis or sample size justification is provided for the dataset.

absence[Methods]

Outlier handling is not described.

WARNReviewer 2· 85% conf

The study design is observational and computational (phylodynamics) with strong sequence data collection and phylogenetic methods, but lacks explicit details on pre-specified inclusion/exclusion criteria, power analysis, and control for sampling bias beyond random subsetting.

Evidence

absence[Methods]

No a priori sample-size or power calculation is reported.

direct quote[Methods, Sequence data]

“All sequences for which sampling year and host or sampling location information was available either in GenBank metadata or in the original publication were included (as of March 15, 2018).”

direct quote[Results, Taxonomic and geographic sampling]

“As some regions or hosts were overrepresented in our datasets, we also created and ran our analyses using a more uniform subset of our sequence data that included ~30 randomly selected sequences per host family or region to mitigate sampling and surveillance intensity bias.”

PASSReviewer 3· 85% conf

The study design is appropriate for a computational phylogenetics study, with clear data curation, sensitivity analyses (random subsets), and a robust analytical framework.

Evidence

direct quote[Methods, Sequence data]

“All sequences for which sampling year and host or sampling location information was available either in GenBank metadata or in the original publication were included (as of March 15, 2018).”

direct quote[Methods, Ancestral state reconstruction and transition rates]

“These analyses were performed for each trait on the complete dataset and random subsets.”

direct quote[Results, Taxonomic and geographic sampling]

Each viral sequence is linked to a bat host identified to species level via morphological and DNA barcoding methods. Host family, genus, and species are reported. Sex and age of individual bats are not reported, but these are not typical variables in viral macroevolution studies where host taxonomy is the key biological variable. Geographic location (province, zoogeographic region) is reported for each sequence. Health status is not reported, but rectal swabs from apparently free-ranging bats are collected.

Sub-criteria

demographicsN/A

sex reportedN/A

sex justifiedN/A

age weight healthN/A

housing conditionsN/A

species strain sourceADEQUATE

Per reviewer (3) — the votes behind the verdict

N/AReviewer 1· 95% conf

This is a computational analysis of viral sequences, not a biological experiment on organisms, so biological variables such as sex, age, and housing conditions are not applicable.

Evidence

direct quote[Results, Taxonomic and geographic sampling]

“Our host datasets included 701 α-CoV sequences (353 new sequences, including 102 new SADSr-CoV sequences (Rhinacovirus)) from 41 bat species (14 genera, five families) and 528 β-CoV sequences (273 new sequences, including 97 new SARSr-CoV sequences (Sarbecovirus)) from 31 bat species (15 genera, four families).”

PASSReviewer 2· 95% conf

Biological variables (host species, family, genus) are comprehensively reported for all sequences, with host identification confirmed by DNA barcoding.

Evidence

direct quote[Methods, Bat sampling and Species identifications]

“Species identifications from the field were also confirmed and re-confirmed by cytochrome (cytb) DNA barcoding using DNA extracted from the feces or swabs.”

direct quote[Results, Taxonomic and geographic sampling; Supplementary Table]

“Our host datasets included 701 α-CoV sequences ... from 41 bat species (14 genera, five families) and 528 β-CoV sequences ... from 31 bat species (15 genera, four families) (Supplementary Table).”

absence[Methods, Bat sampling]

Sex, age, weight, health status, and housing conditions of individual bats are not reported.

PASSReviewer 3· 70% conf

The paper reports host species identities and geographic origins, which are the key biological variables for this study; sex, age, and health status are not reported but are not critical for the viral sequence analysis.

Evidence

direct quote[Methods, Bat sampling]

“Species identifications from the field were also confirmed and re-confirmed by cytochrome (cytb) DNA barcoding using DNA extracted from the feces or swabs.”

direct quote[Results, Taxonomic and geographic sampling]

“Our host datasets included 701 α-CoV sequences... from 41 bat species (14 genera, five families) and 528 β-CoV sequences... from 31 bat species (15 genera, four families).”

The methods section explicitly states that bat-handling methods were approved by two named IACUC committees (Tufts University and Wuhan Institute of Virology) with protocol numbers. This satisfies the requirement for animal research ethics. Regulatory compliance is not further detailed but is implied through the IACUC approval. The study uses non-human animal subjects, so human ethics criteria are not applicable.

Sub-criteria

iacuc statementADEQUATE

informed consentN/A

irb ethics statementN/A

regulatory complianceINADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 90% conf

Ethical approvals for animal handling are reported with named IACUC committees and protocol numbers, and regulatory compliance is stated.

Evidence

direct quote[Methods, Bat sampling]

“Bat-handling methods were approved by Tufts University IACUC committee (proposal #G2017-32) and Wuhan Institute of Virology Chinese Academy of Sciences IACUC committee (proposal WIVA05201705).”

PASSReviewer 2· 95% conf

Ethical approvals for animal handling are clearly stated with named IACUC committees and protocol numbers; regulatory compliance is implied.

Evidence

direct quote[Methods, Bat sampling]

“Bat-handling methods were approved by Tufts University IACUC committee (proposal #G2017-32) and Wuhan Institute of Virology Chinese Academy of Sciences IACUC committee (proposal WIVA05201705).”

absence[Methods, Bat sampling]

No explicit statement of compliance with a specific animal welfare regulation or directive is given.

PASSReviewer 3· 90% conf

The study provides explicit IACUC approvals for bat-handling methods, which is appropriate for non-human animal research, and regulatory compliance is implicit.

Evidence

direct quote[Methods, Bat sampling]

“Bat-handling methods were approved by Tufts University IACUC committee (proposal #G2017-32) and Wuhan Institute of Virology Chinese Academy of Sciences IACUC committee (proposal WIVA05201705).”

The study uses standard PCR reagents (Roche kit, Promega vector) and primer sequences are given in full. Software (BEAST, Tracer, R, ARLEQUIN) is identified with version numbers. However, catalog numbers or RRIDs for the RNA extraction kit, cloning vector, or other reagents are not provided. For a computational phylogenetic study, the software identification is adequate. Reagent identification is reported but incomplete.

Sub-criteria

mycoplasma testingN/A

reagents identifiedINADEQUATE

organisms identifiedADEQUATE

antibodies identifiedN/A

cell line authenticationN/A

software tools identifiedADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 80% conf

Key resources are partially identified: software tools are named with versions, and reagents are mentioned, but primer sequences are not fully provided in the main text, and no RRIDs or catalog numbers are given for key reagents.

Evidence

direct quote[Methods, RNA extraction and PCR screening]

“CoV-FWD3: GGTTGGGAYTAYCCHAARTGTGA; CoV-RVS3: CCATCATCASWYRAATCATCATA; CoV-FWD4/Bat: GAYTAYCCHAARTGTGAYAGAGC”

direct quote[Methods, Model selection and phylogenetic analysis]

“Bayesian phylogenetic analysis was performed in BEAST 1.8.4.”

direct quote[Methods, RNA extraction and PCR screening]

“RNA was extracted from 200 μl swab rectal samples or fecal pellets with the High Pure Viral RNA Kit (Roche) following the manufacturer’s instructions.”

WARNReviewer 2· 85% conf

Key resources such as PCR primers, sequencing vector, and software are identified, but reagent details (e.g., catalog numbers, RRIDs) are largely absent; the study is primarily computational, so the missing catalog numbers for basic molecular reagents are not critical but reduce score.

Evidence

direct quote[Methods, RNA extraction and PCR screening]

“CoV-FWD3: GGTTGGGAYTAYCCHAARTGTGA; CoV-RVS3: CCATCATCASWYRAATCATCATA; CoV-FWD4/Bat: GAYTAYCCHAARTGTGAYAGAGC”

direct quote[Methods, Model selection and phylogenetic analysis; Mantel tests]

“Bayesian phylogenetic analysis was performed in BEAST 1.8.4.”

absence[Methods, RNA extraction and PCR screening]

No catalog numbers or RRIDs are provided for the RNA extraction kit, cloning vector, or other reagents.

PASSReviewer 3· 80% conf

Key resources (organisms, reagents, software) are identified, though reagent catalog numbers are missing, and no custom code repository is provided.

Evidence

direct quote[Methods, Bat sampling]

“Species identifications from the field were also confirmed and re-confirmed by cytochrome (cytb) DNA barcoding using DNA extracted from the feces or swabs.”

direct quote[Methods, RNA extraction and PCR screening]

“RNA was extracted from 200 μl swab rectal samples or fecal pellets with the High Pure Viral RNA Kit (Roche)... PCR products were cloned into pGEM-T Easy Vector (Promega) for sequencing.”

direct quote[Methods, Model selection and phylogenetic analysis]

“Bayesian phylogenetic analysis was performed in BEAST 1.8.4.”

All statistical tests are named (e.g., Mantel tests, linear regression, BF, Markov jumps), with exact p-values and test statistics reported in text and tables. Software (R, ARLEQUIN, BEAST) and versions are identified. Data is presented via phylogenetic trees, figures with individual data points, and tables. Error bars are defined (95% CI). Assumptions for phylogeographic models are not explicitly verified with sensitivity analyses beyond using random subsets. Effect sizes (r for Mantel, rate ratios) are reported. Mathematical plausibility is not applicable as data are continuous sequence distances.

Sub-criteria

tests namedADEQUATE

exact p valuesADEQUATE

effect sizes ciADEQUATE

data presentationADEQUATE

software identifiedADEQUATE

assumptions verifiedINADEQUATE

mathematical plausibilityN/A

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 85% conf

Statistical methods are well-described and appropriate for the study, with named tests, software identified, and data presentation including phylogenetic trees and diversity metrics.

Evidence

direct quote[Results, Mantel tests]

“Mantel tests revealed a positive and significant correlation between CoV genetic differentiation (FST) and geographic distance matrices, both with and without provinces, including fewer than four viral sequences, for α-CoVs (r = 0.25, p = 0.0097; r = 0.32, p = 0.0196; respectively) and β-CoVs (r = 0.22, p = 0.0095; r = 0.23, p = 0.0336; respectively).”

direct quote[Methods, Model selection and phylogenetic analysis]

“Model combinations were compared and the best-fitting model was selected using a modified Akaike information criterion implemented in Tracer 1.6.”

direct quote[Methods, Model selection and phylogenetic analysis]

“Bayesian phylogenetic analysis was performed in BEAST 1.8.4.”

PASSReviewer 2· 90% conf

Statistical tests are named, software identified, exact p-values and CIs reported for key analyses, and data presentation is adequate for a phylogenetic study; mathematical plausibility checks are not applicable due to continuous data.

Evidence

direct quote[Results, Mantel tests]

“Mantel tests revealed a positive and significant correlation between CoV genetic differentiation (FST) and geographic distance matrices ... for α-CoVs (r = 0.25, p = 0.0097; ...) and β-CoVs (r = 0.22, p = 0.0095; ...).”

direct quote[Results, Ancestral hosts and cross-species transmission]

“We identified nine highly supported (BF > 10) inter-family host switches for α-CoVs and three for β-CoVs.”

direct quote[Methods, Model selection and phylogenetic analysis]

“Preliminary analysis were run to select the best-fitting combination of substitution models ... molecular clock ... and coalescent models.”

PASSReviewer 3· 85% conf

Statistical methods are named, assumptions are verified through model selection and MCMC diagnostics, exact p-values are reported, and data presentation is clear, though effect sizes lack confidence intervals.

Evidence

direct quote[Results, Mantel tests]

“Mantel tests revealed a positive and significant correlation between CoV genetic differentiation (FST) and geographic distance matrices... for α-CoVs (r = 0.25, p = 0.0097; r = 0.32, p = 0.0196; respectively) and β-CoVs (r = 0.22, p = 0.0095; r = 0.23, p = 0.0336; respectively).”

direct quote[Methods, Model selection and phylogenetic analysis]

“Convergence of the chain was assessed in Tracer so that the effective sample size (ESS) of all parameters was >200 after removing at least 10% of the chain as burn-in.”

direct quote[Results, Host switching rates]

“The rate of inter-family host-switching events was five times higher in the evolutionary history of α-CoVs (0.010 host switches/unit time) than β-CoVs (0.002 host switches/unit time) in China.”

The paper explicitly states that all GenBank, China National Genomics Data Center, and GISAID accession numbers are listed in the Supplementary Note and tables. This constitutes a concrete data availability statement with a verifiable route to the data. The primary data are sequences, which are deposited in public repositories. No custom code is shared, but the paper describes all analysis methods and uses standard, versioned software. Code sharing is not applicable as the analyses used standard packages.

Sub-criteria

code sharingN/A

accession numbersADEQUATE

repository depositADEQUATE

data availability statementADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 80% conf

A data availability statement is present, and accession numbers for sequences are provided in a supplementary note, but no code sharing is mentioned, and the data statement is vague about the repository.

Evidence

direct quote[Data availability]

“GenBank, China National Genomics Data Center and GISAID accession numbers of sequences generated in this study and previously published sequences included in our analysis are available in the Supplementary Note and Supplementary Tables 1, 2, and 3.”

direct quote[Data availability]

absence[Data availability]

Code sharing is not mentioned.

PASSReviewer 2· 90% conf

Data availability is strong: sequence accession numbers are provided in supplementary material for both novel and previously published sequences.

Evidence

direct quote[Abstract and Data availability section]

direct quote[Abstract]

“...including 630 novel CoV sequences”

absence[Methods]

No custom code is shared; analysis software is named.

PASSReviewer 3· 80% conf

A data availability statement is present, and sequences are deposited in public repositories with accession numbers provided in the supplementary; custom code is not shared, but the study uses standard software.

Evidence

direct quote[Data availability]

direct quote[Methods, Sequence data]

“Our final datasets include 630 sequences generated for this study and 616 sequences from GenBank or GISAID (list of GenBank, China National Genomics Data Center and GISAID accession numbers available in Supplementary Note).”

Methods are thoroughly described, allowing replication. Limitations are explicitly discussed in the final section of the Discussion, including the use of partial RdRp sequences, potential PCR detection bias, and geographic scope. Conclusions are proportional, clearly distinguishing between association and causation, and noting the study cannot rule out origins outside China. Trial registration is not applicable. Reporting guidelines are implied (journal requirement) but not explicitly named. All outcomes appear to be reported. Funding sources and grant numbers are listed, and author contributions are transparent. Conflicts of interest are not explicitly stated but can be inferred from author affiliations.

Sub-criteria

funding coiADEQUATE

trial registrationN/A

reporting guidelineNOT REPORTED

methods completenessADEQUATE

all outcomes reportedADEQUATE

limitations discussedADEQUATE

conclusions proportionalADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 90% conf

The paper is well-reported with detailed methods, a discussion of limitations, proportional conclusions, and funding/COI statements. Trial registration and reporting guidelines are not applicable for this observational study.

Evidence

direct quote[Discussion, paragraph 8]

“Despite being an exhaustive study of bat-CoVs in China, this study had several limitations that must be taken into consideration when interpreting our results.”

direct quote[Acknowledgements]

“This study was funded by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (Award Number R01AI110964) and the United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICT project (cooperative agreement number GHN-A-OO-09-00010-00)...”

direct quote[Discussion, paragraph 1]

“However, it is important to note that: (1) our study collected and analyzed samples solely from China; (2) many sampling sites were close to the borders of Myanmar and Lao PDR; and (3) most of the bats sampled in Yunnan also occur in these countries... we cannot rule out an origin for the clade of viruses that are progenitors of SARS-CoV-2 that is outside China.”

PASSReviewer 2· 95% conf

Reporting is transparent: methods are detailed, limitations are discussed, conclusions are proportional, and funding/COI are disclosed.

Evidence

direct quote[Discussion, paragraph 10]

“Despite being an exhaustive study of bat-CoVs in China, this study had several limitations that must be taken into consideration when interpreting our results.”

direct quote[Discussion, paragraph 1]

“For these reasons, we cannot rule out an origin for the clade of viruses that are progenitors of SARS-CoV-2 that is outside China, and within Myanmar, Lao PDR, Vietnam, or another Southeast Asian country.”

direct quote[Acknowledgements]

PASSReviewer 3· 85% conf

Methods are detailed, all outcomes are reported, limitations are discussed, conclusions are proportional, and funding is acknowledged, but a conflict-of-interest statement is missing.

Evidence

paraphrase[Methods, entire section]

“The Methods section comprehensively describes bat sampling, RNA extraction, PCR, sequencing, phylogenetic analysis, model selection, ancestral state reconstruction, and statistical tests.”

direct quote[Discussion, paragraph 5]

“Despite being an exhaustive study of bat-CoVs in China, this study had several limitations that must be taken into consideration when interpreting our results.”

direct quote[Discussion, paragraph 1]

“We cannot rule out an origin for the clade of viruses that are progenitors of SARS-CoV-2 that is outside China, and within Myanmar, Lao PDR, Vietnam, or another Southeast Asian country.”

10 copyedit issues flagged: mostly clarity, typo, consistency.

Reproducibility

3 data/code links checked; 3 live.

Αlpha¹ Rigor Action ItemsFinal pass before journal submission

Post-publication assessment: The published paper is broadly robust in its key conclusions, but an informed reader should weigh the lack of explicit sample-size justification and the absence of code sharing as limiting reproducibility. The minor copyedit issues (typos, missing hyphen in beta-CoVs) are not validity threats but should be corrected in a revision. No erratum is warranted at this stage.

1.
HIGHrigor
Add an explicit statement of inclusion/exclusion criteria for sequences (e.g., minimum sequence length, quality filters, ambiguous host identification handling) in the Methods (Sequence data section).
Currently the criteria are vague (only 'availability of host/location metadata'), which limits reproducibility and clarity.
2.
HIGHrigor
Describe criteria and methods for handling outliers or low-quality sequences in the Methods.
Outlier handling is not mentioned; this is a standard requirement for transparent data curation.
3.
HIGHdata code
Provide a direct link (DOI) to a repository containing the analysis alignment files, BEAST XML files, and any custom R/Python scripts in the Data Availability section.
The current data availability statement is vague; code sharing is absent, which hinders reproducibility of a computational study.
4.
HIGHdata code
Add a code availability statement that either deposits custom scripts in a public repository (GitHub/Zenodo) or explicitly states that all analyses used standard software with versioned commands available in the Methods.
No code sharing is mentioned; for a computational phylogenetics paper, readers should be able to replicate the analyses.
5.
MEDIUMreporting
Add catalog numbers or RRIDs for the High Pure Viral RNA Kit (Roche) and pGEM-T Easy Vector (Promega) in the Methods (RNA extraction and PCR screening).
Catalog numbers improve reproducibility by enabling precise identification of reagents.
6.
MEDIUMrigor
Add a sample size/power justification for the sequence dataset (e.g., statement that the dataset size is consistent with or exceeds that used in comparable published studies).
No power analysis is reported; a brief justification would strengthen the study design.
7.
MEDIUMreporting
Include confidence intervals (e.g., 95% HPD intervals for Bayes factors, 95% CIs for Mantel correlations) alongside effect sizes in the Results.
Reviewers noted that effect sizes are reported without confidence intervals; CIs provide essential uncertainty quantification.
8.
MEDIUMreporting
Add a separate 'Competing interests' statement (or declare 'The authors declare no competing interests') in the Acknowledgements or a dedicated section.
A transparent conflict-of-interest statement is a standard reporting requirement.
9.
MEDIUMreporting
Add a sentence describing sensitivity/assumption checks for the Bayesian phylogeographic models (e.g., prior sensitivity analysis, model misspecification tests) in the Methods or Supplementary Information.
Model assumptions are not explicitly verified beyond MCMC convergence; adding sensitivity checks would strengthen the statistical analysis.
10.
LOWcopyedit
Fix typo in Methods: change 'Hierachical clustering' to 'Hierarchical clustering' (Defining zoogeographic regions in China).
Copyedit issue flagged by the copyedit pass.
11.
LOWcopyedit
Fix typo in Abstract: change 'betaCoVs' to 'beta-CoVs' for consistency.
Inconsistent hyphenation between alpha- and beta-CoVs noted by copyedit pass.
12.
LOWcopyedit
Remove the PMC ID ('PMC7302205') from the Abstract text, as it appears out of context.
Copyedit pass flagged this as an out-of-place identifier in the Abstract.
13.
LOWcopyedit
Insert missing article in Results: change 'calculated Bayesian factor (BF)' to 'calculated a Bayesian factor (BF)' or 'calculated Bayesian factors (BFs)'.
Grammar fix flagged by copyedit pass.
14.
LOWcopyedit
Fix verb missing in Discussion: change 'their topology consistent' to 'their topology is consistent' (Discussion, paragraph 10).
Grammar correction flagged by copyedit pass.

Full text (57,806 chars)Analyzed: Jul 6, 2026

Αlpha¹ assesses methodological rigor, not the importance of the findings. See how we calibrate →