Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

Tyson, John R.; James, Phillip; Stoddart, David; Sparks, Natalie; Wickenhagen, Arthur; Hall, Grant; Choi, Jane Ru; Lapointe, Hope R.; Kamelian, Kimia; Smith, Andrew D.; Prystajecky, Natalie; Goodfellow, Ian; Wilson, Sam J.; Harrigan, Richard; Snutch, Terrance P.; Loman, Nicholas J.; Quick, Joshua

doi:10.1101/2020.09.04.283077

Cited by 356 publications

(404 citation statements)

References 34 publications

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“…The authors of the preprint, Vanaerschot et al noted that SNVs could impact assay accuracy if diagnostic primers and probes are also being used to quantify viral loads in patients. We found that at least 10 other primer pairs could potentially be at risk in different geographical regions due to SNVs that appear proximal to the 3’ ends of primers ( Figure 3B–K ): China-CDC-N-F and R; NIH, Thailand, WH-NIC N-F; US CDC 2019-nCoV-N1-R; US CDC 2019-nCoV-N2-F; ARTIC-V3_nCoV-2019_11_RIGHT; ARTIC-V3_nCoV-2019_13_LEFT; ARTIC-V3_nCoV-2019_34_LEFT; ARTIC-V3_nCoV-2019_39_LEFT (note that the ARTIC primers are used for nanopore sequencing; Tyson et al, 2020 ); WHO N_Sarbarco_R1; and Institut Pasteur, Paris 12759Rv. Labs and clinics can use COVID-19 CG ( https://covidcg.org ) to check their most commonly used primers and probes against the SARS-CoV-2 sequences that are prevalent in their geographical regions.…”

Section: Resultsmentioning

confidence: 99%

COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest

Chen

Altschuler

Zhan

et al. 2021

eLife

108

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COVID-19 CG (covidcg.org) is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs), lineages, and clades using the virus genomes on the GISAID database while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to projects on SARS-CoV-2 transmission, evolution, diagnostics, therapeutics, vaccines, and intervention tracking. Here, we describe case studies in which users can interrogate (1) SNVs in the SARS-CoV-2 spike receptor binding domain (RBD) across different geographical regions to inform the design and testing of therapeutics, (2) SNVs that may impact the sensitivity of commonly used diagnostic primers, and (3) the emergence of a dominant lineage harboring an S477N RBD mutation in Australia in 2020. To accelerate COVID-19 efforts, COVID-19 CG will be upgraded with new features for users to rapidly pinpoint mutations as the virus evolves throughout the pandemic and in response to therapeutic and public health interventions.

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Section: Resultsmentioning

confidence: 99%

COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest

Chen

Altschuler

Zhan

et al. 2021

eLife

108

View full text Add to dashboard Cite

show abstract

“…30 RNA samples from nasal swabs and bronchoalveolar lavage at day 3 and 5 were selected for sequencing. cDNA and multiplex PCR reactions were prepared following the ARTIC SARS-CoV-2 sequencing protocol v2 (Tyson et al, 2020). The inoculum was also sequenced.…”

Section: Methodsmentioning

confidence: 99%

Two-component spike nanoparticle vaccine protects macaques from SARS-CoV-2 infection

Brouwer

Brinkkemper

Maisonnasse

et al. 2020

Preprint

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The SARS-CoV-2 pandemic is continuing to disrupt personal lives, global healthcare systems and economies. Hence, there is an urgent need for a vaccine that prevents viral infection, transmission and disease. Here, we present a two-component protein-based nanoparticle vaccine that displays multiple copies of the SARS-CoV-2 spike protein. Immunization studies show that this vaccine induces potent neutralizing antibody responses in mice, rabbits and cynomolgus macaques. The vaccine-induced immunity protected macaques against a high dose challenge, resulting in strongly reduced viral infection and replication in upper and lower airways. These nanoparticles are a promising vaccine candidate to curtail the SARS-CoV-2 pandemic.

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“…10 RNA samples from nasopharyngeal swabs at day 3 post-exposure were selected for sequencing along with the inoculum. cDNA and multiplex PCR reactions were prepared following the ARTIC SARS-CoV-2 sequencing protocol v2 49 . V3 primer scheme Ther., therapeutic.…”

Section: Viral Sequencingmentioning

confidence: 99%

COVA1-18 neutralizing antibody protects against SARS-CoV-2 in three preclinical models

Grand

Maisonnasse

Aldon

et al. 2021

Preprint

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One year into the Coronavirus Disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), effective treatments are still needed1–3. Monoclonal antibodies, given alone or as part of a therapeutic cocktail, have shown promising results in patients, raising the hope that they could play an important role in preventing clinical deterioration in severely ill or in exposed, high risk individuals4–6. Here, we evaluated the prophylactic and therapeutic effect of COVA1-18 in vivo, a neutralizing antibody isolated from a convalescent patient7 and highly potent against the B.1.1.7. isolate8,9. In both prophylactic and therapeutic settings, SARS-CoV-2 remained undetectable in the lungs of COVA1-18 treated hACE2 mice. Therapeutic treatment also caused a dramatic reduction in viral loads in the lungs of Syrian hamsters. When administered at 10 mg kg− 1 one day prior to a high dose SARS-CoV-2 challenge in cynomolgus macaques, COVA1-18 had a very strong antiviral activity in the upper respiratory compartments with an estimated reduction in viral infectivity of more than 95%, and prevented lymphopenia and extensive lung lesions. Modelling and experimental findings demonstrate that COVA1-18 has a strong antiviral activity in three different preclinical models and could be a valuable candidate for further clinical evaluation.

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Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

Cited by 356 publications

References 34 publications

COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest

COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest

Two-component spike nanoparticle vaccine protects macaques from SARS-CoV-2 infection

COVA1-18 neutralizing antibody protects against SARS-CoV-2 in three preclinical models

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