A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43

Maurier, Florence; Beury, Delphine; Fléchon, Léa; Varré, Jean Stéphane; Touzet, Hélène; Goffard, Anne; Hot, David; Caboche, Ségolène

doi:10.1016/j.virol.2019.03.006

Cited by 34 publications

(32 citation statements)

References 18 publications

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“…Viral genome sequencing was performed as described by Maurier et al [15]. Briefly, extracted viral RNA was reverse transcribed, PCR amplified using multiple primer pairs and pooled before preparing sequencing libraries using NxSeq AmpFREE LowDNA (Lucigen) library kit and barcoded with Illumina-compatible adaptors.…”

Section: Sequencingmentioning

confidence: 99%

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Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit

Beury

Fléchon

Maurier

et al. 2020

Journal of Clinical Virology

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A B S T R A C TBackground: While respiratory viral infections are recognized as a frequent cause of illness in hematopoietic stem cell transplantation (HSCT) recipients, HCoV−OC43 infections have rarely been investigated as healthcareassociated infections in this population. Objectives: In this report, HCoV−OC43 isolates collected from HSCT patients were retrospectively characterized to identify potential clusters of infection that may stand for a hospital transmission. Study design: Whole-genome and S gene sequences were obtained from nasal swabs using next-generation sequencing and phylogenetic trees were constructed. Similar identity matrix and determination of the most common ancestor were used to compare clusters of patient's sequences. Amino acids substitutions were analysed. Results: Genotypes B, E, F and G were identified. Two clusters of patients were defined from chronological data and phylogenetic trees. Analyses of amino acids substitutions of the S protein sequences identified substitutions specific for genotype F strains circulating among European people. Conclusions: HCoV−OC43 may be implicated in healthcare-associated infections.

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Section: Sequencingmentioning

confidence: 99%

“…Libraries were paired-end sequenced in 2 × 300 cycles on Illumina MiSeq. Sequencing analysis and genome assembly was performed as described by Maurier et al [15]…”

Section: Sequencingmentioning

confidence: 99%

Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit

Beury

Fléchon

Maurier

et al. 2020

Journal of Clinical Virology

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“…Detection of SARS-CoV-2 IgM and IgG antibody in vivo as a supplement to molecular diagnostic methods [8]. Genomic sequencing has been playing an irreplaceable role in the identification of emerging viruses [9]. In this review, we describe the current laboratory diagnosis of SARS-CoV-2 infection.…”

Section: Introductionmentioning

confidence: 99%

Laboratory diagnosis of coronavirus disease-2019 (COVID-19)

Zhao

Bao

et al. 2020

Clinica Chimica Acta

132

116

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The outbreak of Coronavirus Disease-2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has threatened health worldwide. As of the end of 2020, there were nearly 10 million confirmed cases and nearly 5 million deaths associated with COVID-19. Rapid and early laboratory diagnosis of COVID-19 is the main focus of treatment and control. Molecular tests are the basis for confirmation of COVID-19, but serological tests for SARS-CoV-2 are widely available and play an increasingly important role in understanding the epidemiology of the virus and in identifying populations at higher risk for infection. Pointof-care tests have the advantage of rapid, accurate, portable, low cost and non-specific device requirements, which provide great help for disease diagnosis and detection. This review will discuss the performance of different laboratory diagnostic tests and platforms, as well as suitable clinical samples for testing, and related biosafety protection. This review shall guide for the diagnosis of COVID-19 caused by SARS-CoV-2.

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“…Localized outbreaks are common when SARS-CoV-2 is introduced in a new geographic area. These outbreaks require urgent testing and tracing, identification of the causative agent, and epidemiological investigations to allow for appropriate infection control and for clusters of patients to be identified [ 3 ]. Genomic sequencing can be used to rapidly and accurately identify the transmission routes of the pathogen [ 4 , 5 ].…”

Section: Introductionmentioning

confidence: 99%

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic

Pillay

Giandhari

Tegally

et al. 2020

Genes

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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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A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43

Cited by 34 publications

References 18 publications

Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit

Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit

Laboratory diagnosis of coronavirus disease-2019 (COVID-19)

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic

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