ArticleGenes2020
Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic.
Article in Genes, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
58 citing papers in PubMed, 1 synthesis or guideline pooled it, 95 citations in OpenAlex.
- Technological Barriers to Routine Genomic Surveillance for Vaccine Development Against SARS-CoV-2 in Africa: A Systematic Review.Influenza and other respiratory viruses · 2024Pooled it
- Trial
- Whole genome sequencing of hepatitis A virus: adapting Illumina protocols for foodborne investigation.NPJ science of food · 2025Article
- Validation of polyester nasal swabs for post-mortem SARS-CoV-2 diagnosis in Karachi, Pakistan: a prospective surveillance analysis.Journal of global health · 2025Observational
- Monitoring SARS-CoV-2 variants in wastewater during periods of low clinical case surveillance in Ethiopia.mSphere · 2025Article
- Enhancing public health surveillance: a comparative study of platform-specific and hybrid assembly approaches in SARS-CoV-2 genome sequencing.Microbial genomics · 2025Article
- Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification.Viruses · 2025Article
- Building Pathogen Genomic Sequencing Capacity in Africa: Centre for Epidemic Response and Innovation Fellowship.Tropical medicine and infectious disease · 2025Article
- Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant.OBM genetics · 2025Article
- A novel fast hybrid capture sequencing method for high-efficiency common human coronavirus whole-genome acquisition.mSystems · 2024Article
- Whole genome sequencing and phylogenetic analysis of SARS-CoV-2 strains isolated during the COVID-19 pandemic in Nigeria.IJID regions · 2024Article
- Epidemiologic investigation and genetic characterization of canine respiratory coronavirus in the Southeastern United States.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2024Article
- SARS-CoV-2 Nucleocapsid Protein Mutations Found in Switzerland Disrupt N-Gene Amplification in Commonly Used Multiplex RT-PCR Assay.Pathogens (Basel, Switzerland) · 2023Article
- Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice.Epidemiology and infection · 2023Article
- Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications.Diseases (Basel, Switzerland) · 2023Article
- Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique.PLOS global public health · 2023Article
- Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing.PloS one · 2023Article
- The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.Science (New York, N.Y.) · 2022Article
- Transcriptomics and RNA-Based Therapeutics as Potential Approaches to Manage SARS-CoV-2 Infection.International journal of molecular sciences · 2022Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 5 institutions in 3 countries.
Funding
Abstract
The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.