Reference health
High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing
26/26 checkable references clean · checked 2026-07-26
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
14 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 26 checked references that resolve
resolves10.1038/s41586-020-2008-3
A new coronavirus associated with human respiratory disease in China
resolves10.2807/1560-7917.ES.2020.25.6.2000094
First cases of coronavirus disease 2019 (COVID-19) in France: surveillance, investigations and control measures, January 2020
resolves10.2196/18606
Emergence of a Novel Coronavirus (COVID-19): Protocol for Extending Surveillance Used by the Royal College of General Practitioners Research and Surveillance Centre and Public Health England
resolves10.15585/mmwr.mm6911e1
Evaluation of the Effectiveness of Surveillance and Containment Measures for the First 100 Patients with COVID-19 in Singapore — January 2–February 29, 2020
resolves10.1016/j.puhe.2020.04.009
Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity
resolves10.1002/jmv.25721
Combination of RT‐qPCR testing and clinical features for diagnosis of COVID‐19 facilitates management of SARS‐CoV‐2 outbreak
resolves10.1016/S0140-6736(20)30251-8
Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
resolves10.1186/s13073-020-00751-4
Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples
resolves10.1038/s41598-020-58356-1
Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life
resolves10.1128/JVI.01234-19
Genome-Scale Phylogeny and Evolutionary Analysis of Ross River Virus Reveals Periodic Sweeps of Lineage Dominance in Western Australia, 1977–2014
resolves10.1371/journal.ppat.1006749
Genome-wide evolutionary dynamics of influenza B viruses on a global scale
resolves10.1128/JVI.02415-07
Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes
resolves10.1093/bioinformatics/btp373
VarScan: variant detection in massively parallel sequencing of individual and pooled samples
resolves10.1371/journal.pone.0163962
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
resolves10.1093/nar/gkq603
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
resolves10.1093/molbev/msu300
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
resolves10.1093/nar/gkw290
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
The 14 references without a DOI — listed, not checked
no DOI — not checkedRapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study
no DOI — not checkedVariation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction-Based SARS-CoV-2 Tests by Time Since Exposure
no DOI — not checkedRevealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling
no DOI — not checkedGISAID: Global initiative on sharing all influenza data—from vision to reality
no DOI — not checkedA distinct phylogenetic cluster of Indian SARS-CoV-2 isolates
no DOI — not checkedSARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission
no DOI — not checkedHigh-coverage SARS-CoV-2 genome sequences acquired by target capture sequencing
no DOI — not checkedpone.0247115.ref020
no DOI — not checkedREMBRANDT: A high-throughput barcoded sequencing approach for COVID-19 screening
no DOI — not checkedLAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding
no DOI — not checkedPoojary M, Shantaraman A, Jolly B, Scaria V. Computational Protocol for Assembly and Analysis of SARS-nCoV-2 Genomes. rr. 2019 [cited 2 Aug 2020]. http://www.companyofscientists.com/index.php/rr/article/view/165
no DOI — not checkedpone.0247115.ref035
no DOI — not checkedJolly B, Scaria V. Computational Analysis and Phylogenetic clustering of SARS-nCov-2 genomes. (Under Review). https://docs.google.com/document/d/1B5NxWFwsRz_vD5Y6EwjKxkRamsPLVfs1MjVoziU1Zq0/edit?usp=embed_facebook
no DOI — not checkedA dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
What this badge says. CiteStamped means the CHECKABLE references of this
work were clean at the dated check: each resolved to a known work in a public registry, and none
carried a retraction notice at that time. It says nothing about the quality, findings,
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