{"doi":"10.1016/j.ijid.2020.11.128","title":"Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report","abstract":"OBJECTIVES: The Network for Genomic Surveillance in South Africa (NGS-SA) was formed to investigate the introduction and understand the early transmission dynamics of the SARS-CoV-2 epidemic in South-Africa. DESIGN: This paper presents the first results from this group, which is a molecular epidemiological study of the first 21 SARS-CoV-2 whole genomes sampled in the first port of entry - KwaZulu-Natal (KZN) - during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), it aimed to shed light on the patterns of infections in South Africa. RESULTS: Two of the largest provinces - Gauteng and KZN - had a slow growth rate for the number of detected cases, while the epidemic spread faster in the Western Cape and Eastern Cape. The estimates of transmission potential suggested a decrease towards R = 1 since the first cases and deaths, but a subsequent estimated R average of 1.39 between 6-18 May 2020. It was also demonstrated that early transmission in KZN was associated with multiple international introductions and dominated by lineages B1 and B. Evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic was also provided. CONCLUSION: The COVID-19 pandemic in South Africa was very heterogeneous in its spatial dimension, with many distinct introductions of SARS-CoV2 in KZN and evidence of nosocomial transmission, which inflated early mortality in KZN. The epidemic at the local level was still developing and NGS-SA aimed to clarify the dynamics in South Africa and devise the most effective measures as the outbreak evolved.","journal":"International Journal of Infectious Diseases","year":2020,"id":54795,"datarank":4.788499731043058,"base_score":4.61512051684126,"endowment":4.61512051684126,"self_citation_contribution":0.692268077526189,"citation_network_contribution":4.096231653516869,"self_endowment_contribution":0.692268077526189,"citer_contribution":4.096231653516869,"corpus_percentile":95.49005956525103,"corpus_rank":584,"citation_count":100,"citer_count":84,"citers_with_citation_signal":70,"citers_with_endowment":70,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7349,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":58.3333,"fair_percentile":72.8829104249465,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":282132,"name":"Sureshnee Pillay","orcid":"0000-0001-9288-7996","position":1,"is_corresponding":false},{"id":282133,"name":"Eduan Wilkinson","orcid":"0000-0002-2503-9441","position":2,"is_corresponding":false},{"id":282134,"name":"Houriiyah Tegally","orcid":"0000-0002-7102-8540","position":3,"is_corresponding":false},{"id":282135,"name":"Ilya Sinayskiy","orcid":"0000-0002-3040-0051","position":4,"is_corresponding":false},{"id":282136,"name":"Maria Schuld","orcid":"0000-0001-8626-168X","position":5,"is_corresponding":false},{"id":282137,"name":"José Lourenço","orcid":"0000-0002-9318-2581","position":6,"is_corresponding":false},{"id":282138,"name":"Benjamin Chimukangara","orcid":"0000-0002-8391-4531","position":7,"is_corresponding":false},{"id":69666,"name":"Richard Lessells","orcid":"0000-0003-0926-710X","position":8,"is_corresponding":false},{"id":282139,"name":"Mahomed‐Yunus S. Moosa","orcid":"0000-0001-6191-4023","position":9,"is_corresponding":false},{"id":282140,"name":"Inbal Gazy","orcid":"0000-0003-3944-6977","position":10,"is_corresponding":false},{"id":282141,"name":"Maryam Fish","orcid":"0000-0003-0255-7286","position":11,"is_corresponding":false},{"id":282142,"name":"Lavanya Singh","orcid":"0000-0002-1726-4454","position":12,"is_corresponding":false},{"id":282143,"name":"Khulekani Sedwell Khanyile","orcid":"0000-0001-8632-6025","position":13,"is_corresponding":false},{"id":282144,"name":"Vagner Fonseca","orcid":"0000-0001-5521-6448","position":14,"is_corresponding":false},{"id":282145,"name":"Marta Giovanetti","orcid":"0000-0002-5849-7326","position":15,"is_corresponding":false},{"id":283627,"name":"Luiz Carlos Junior Alcantara","orcid":null,"position":16,"is_corresponding":false},{"id":282146,"name":"Francesco Petruccione","orcid":"0000-0002-8604-0913","position":17,"is_corresponding":false},{"id":279259,"name":"Túlio de Oliveira","orcid":"0000-0002-3027-5254","position":18,"is_corresponding":false},{"id":282131,"name":"Jennifer Giandhari","orcid":"0000-0002-2944-4583","position":0,"is_corresponding":true}],"reference_count":52,"raw_metadata":null,"created_at":"2026-07-18T21:04:14.743014Z","pmid":"33189939","pmcid":"PMC7658561","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":72.2222,"fair_a":50.0,"fair_i":20.0,"fair_r":33.3333,"fair_zscore":0.9454,"fair_rationale":{"fair_score":58.33,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":72.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The SARS-CoV-2 genome sequences generated in this study were deposited in the GISAID database ( https://www.gisaid.org/ ) under the following accession IDs: EPI_ISL_421572, EPI_ISL_421573, EPI_ISL_421574, EPI_ISL_421575 EPI_ISL_421576 EPI_ISL_436684 EPI_ISL_436685 EPI_ISL_436686 EPI_ISL_436687 . In addition, raw short and long reads were submitted to the Short Read Archive (SRA) and can be accessed under BioProject Accession: PRJNA636748 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA636748 ).","grounded":true,"rationale":"The paper provides persistent identifiers (GISAID EPI_ISL accessions and BioProject PRJNA636748) for the study's own data. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The SARS-CoV-2 genome sequences generated in this study were deposited in the GISAID database ( https://www.gisaid.org/ ) under the following accession IDs: EPI_ISL_421572, EPI_ISL_421573, EPI_ISL_421574, EPI_ISL_421575 EPI_ISL_421576 EPI_ISL_436684 EPI_ISL_436685 EPI_ISL_436686 EPI_ISL_436687 . In addition, raw short and long reads were submitted to the Short Read Archive (SRA) and can be accessed under BioProject Accession: PRJNA636748 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA636748 ).","grounded":true,"rationale":"The paper names GISAID and SRA (via BioProject) as repositories holding the data. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The SARS-CoV-2 genome sequences generated in this study were deposited in the GISAID database ( https://www.gisaid.org/ ) under the following accession IDs: EPI_ISL_421572, EPI_ISL_421573, EPI_ISL_421574, EPI_ISL_421575 EPI_ISL_421576 EPI_ISL_436684 EPI_ISL_436685 EPI_ISL_436686 EPI_ISL_436687 . In addition, raw short and long reads were submitted to the Short Read Archive (SRA) and can be accessed under BioProject Accession: PRJNA636748 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA636748 ).","grounded":true,"rationale":"The data availability statement points to repositories with accessions, satisfying Colavizza category 3. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"It managed to produce 20 near-whole genome sequences (>90% coverage) from these samples, and six partial genomes.","grounded":false,"rationale":"The dataset's content is described in running prose (number of sequences and coverage) without an itemised inventory or section. [downgraded to 'no' — no verifiable quote from the paper]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The SARS-CoV-2 genome sequences generated in this study were deposited in the GISAID database ( https://www.gisaid.org/ ) under the following accession IDs: EPI_ISL_421572, EPI_ISL_421573, EPI_ISL_421574, EPI_ISL_421575 EPI_ISL_421576 EPI_ISL_436684 EPI_ISL_436685 EPI_ISL_436686 EPI_ISL_436687 . In addition, raw short and long reads were submitted to the Short Read Archive (SRA) and can be accessed under BioProject Accession: PRJNA636748 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA636748 ).","grounded":true,"rationale":"The dataset's identifiers appear only in the body text (data availability section), not in the reference list. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":50.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The SARS-CoV-2 genome sequences generated in this study were deposited in the GISAID database ( https://www.gisaid.org/ ) under the following accession IDs: EPI_ISL_421572, EPI_ISL_421573, EPI_ISL_421574, EPI_ISL_421575 EPI_ISL_421576 EPI_ISL_436684 EPI_ISL_436685 EPI_ISL_436686 EPI_ISL_436687 . In addition, raw short and long reads were submitted to the Short Read Archive (SRA) and can be accessed under BioProject Accession: PRJNA636748 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA636748 ).","grounded":true,"rationale":"The data are deposited in public repositories (GISAID and SRA) with no stated precondition; the text does not mention registration, embargo, or application. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"The SARS-CoV-2 genome sequences generated in this study were deposited in the GISAID database (https://www.gisaid.org/) under the following accession IDs: EPI_ISL_421572, EPI_ISL_421573, EPI_ISL_421574, EPI_ISL_421575 EPI_ISL_421576 EPI_ISL_436684 EPI_ISL_436685 EPI_ISL_436686 EPI_ISL_436687. In addition, raw short and long reads were submitted to the Short Read Archive (SRA) and can be accessed under BioProject Accession: PRJNA636748 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA636748).","grounded":false,"rationale":"The data availability statement describes the action of deposition but does not explicitly label the access level (e.g., 'open access' or 'restricted'). [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"The project was approved by University of KwaZulu-Natal Biomedical Research Ethics Committee. Protocol reference number: BREC/00,001,195/2020.","grounded":true,"rationale":"The data are human-subject derived but deposited in public repositories with no named gatekeeper; the ethics approval is for the study, not an access gatekeeper.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No sentence states when the data become available or how long they persist; only the act of deposit is mentioned.","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format is named for the released data; the text mentions 'sequences' and 'reads' but not a specific format like FASTA or FASTQ.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No data or metadata community standard (e.g., MIAME, FAIRsharing-registered ontology) is named for the data. [majority verdict 'no' (4/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"The dataset also contained one additional KZN sequence ( EPI_ISL_417186 ) that was generated by the National Institute for Communicable Diseases (NICD) and represented a distant contact of the first diagnosed case in South Africa.","grounded":true,"rationale":"The paper references an identifier for a third-party dataset (EPI_ISL_417186) and also a GenBank accession (MN908947) for Wuhan-Hu1. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":33.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No licence or terms-of-use document is named for the data; the article's CC-BY footer applies to the paper, not the data.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Illumina MiSeq sequencing PCR products for samples yielding sufficient material were included in this sequencing platform.","grounded":true,"rationale":"The paper names specific instruments, kits, and software (e.g., Illumina MiSeq, QIAGEN Viral RNA Mini Kit, Genome Detective) used to produce the data. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Supplementary Table S2, Table S3","grounded":true,"rationale":"Variable/field definitions are provided in supplementary tables within the article, not in a separate documentation file shipped with the data. [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No version token or date is stated for the data; the accession IDs are persistent identifiers, not version indicators.","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not provide a locator for the study's own code; only third-party tools are mentioned.","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"by the National Human Genome Research Institute of the National Institutes of Health under Award Number U24HG006941.","grounded":true,"rationale":"A specific grant number (U24HG006941) is attached to a named funder. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No licence or terms-of-use document is named for the data; the article's CC-BY footer applies to the paper, not the data.","gain":16.67,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format is named for the released data; the text mentions 'sequences' and 'reads' but not a specific format like FASTA or FASTQ.","gain":8.33,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not provide a locator for the study's own code; only third-party tools are mentioned.","gain":8.33,"priority":"important","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The SARS-CoV-2 genome sequences generated in this study were deposited in the GISAID database ( https://www.gisaid.org/ ) under the following accession IDs: EPI_ISL_421572, EPI_ISL_421573, EPI_ISL_421574, EPI_ISL_421575 EPI_ISL_421576 EPI_ISL_436684 EPI_ISL_436685 EPI_ISL_436686 EPI_ISL_436687 . In addition, raw short and long reads were submitted to the Short Read Archive (SRA) and can be accessed under BioProject Accession: PRJNA636748 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA636748 ).","why":"The dataset's identifiers appear only in the body text (data availability section), not in the reference list. [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No version token or date is stated for the data; the accession IDs are persistent identifiers, not version indicators.","gain":4.17,"priority":"useful","scored":true},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"It managed to produce 20 near-whole genome sequences (>90% coverage) from these samples, and six partial genomes.","why":"The dataset's content is described in running prose (number of sequences and coverage) without an itemised inventory or section. [downgraded to 'no' — no verifiable quote from the paper]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. 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[downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In clinical / human-subjects, describe the data with OMOP CDM, CDISC SDTM or HL7 FHIR.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No data or metadata community standard (e.g., MIAME, FAIRsharing-registered ontology) is named for the data. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Supplementary Table S2, Table S3","why":"Variable/field definitions are provided in supplementary tables within the article, not in a separate documentation file shipped with the data. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human clinical / human-subjects data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The project was approved by University of KwaZulu-Natal Biomedical Research Ethics Committee. Protocol reference number: BREC/00,001,195/2020.","why":"The data are human-subject derived but deposited in public repositories with no named gatekeeper; the ethics approval is for the study, not an access gatekeeper.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No sentence states when the data become available or how long they persist; only the act of deposit is mentioned.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:04:25.716813Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}