Nextclade: clade assignment, mutation calling and quality control for viral genomes

Aksamentov, Ivan; Roemer, Cornelius; Hodcroft, Emma B.; Neher, Richard A.

doi:10.5281/zenodo.5607694

Cited by 37 publications

(45 citation statements)

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“…There are no universally recognized or used strategies and criteria to classify viruses below the species level, and only biological classifications and nomenclatures have been proposed (Fauquet et al, 2008; International Committee on Taxonomy of Viruses (ICTV), 2020; Box 1). Classification and naming systems have been specifically proposed for SARS-CoV-2 including those of GISAID (see footnote 3) (Alm et al, 2020), Nextstrain (see footnote 4) (Hadfield et al, 2018;Aksamentov et al, 2021), Pangolin (see footnote 5) (Rambaut et al, 2020), and the WHO (see footnote 6) (Box 2). However, we chose to implement our own classification system and nomenclature and to use names rather than only numbers.…”

Section: The Marseille Ihu Méditerranée Infection Classification Syst...mentioning

confidence: 99%

“…Nomenclature uses actual letters of marker mutations (S, L, V, G, GH, GR, GV, GRY). Nextstrain classification (https://nextstrain.org/blog/2021-01-06updated-SARS-CoV-2-clade-naming) (Hadfield et al, 2018;Aksamentov et al, 2021): Defines major clades that reach ≥ 20% global frequency for ≥ two months, ≥ 30% regional frequency for ≥ two months, or correspond to a 'variant of concern' (VOC). Nomenclature uses a year-letter naming system.…”

Section: Dynamics Of Sars-cov-2 Variants In the Ihu Méditerranée Infe...mentioning

confidence: 99%

“…SARS-CoV-2 is, therefore, currently a rapidly evolving virus with a mutation rate estimated to be 9.8 × 10 −4 substitutions/site/year (van Dorp et al, 2020) and characterized by a high rate of lineage turnover (Rambaut et al, 2020). Several SARS-CoV-2 specific classification and naming systems exist including those of GISAID 3 (Alm et al, 2020), Nextstrain 4 (Hadfield et al, 2018;Aksamentov et al, 2021), Pangolin 5 (Rambaut et al, 2020), or the World Health Organization (WHO) 6 . But, although these are of great interest and usefulness, other classification and naming systems are also valuable, as previously acknowledged (Rambaut et al, 2020), particularly when it comes to better exploring genomic epidemiology on a local scale through real-time nextgeneration sequencing.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics

et al. 2022

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After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.

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Section: The Marseille Ihu Méditerranée Infection Classification Syst...mentioning

confidence: 99%

Section: Dynamics Of Sars-cov-2 Variants In the Ihu Méditerranée Infe...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics

et al. 2022

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“…GridION data was analyzed to get consensus genomes, with the SARS2seq pipeline and additional manual curation 24 . These genomes were analyzed with Pangolin (version 3.1.11) and NextClade (version 1.3.0) to get a final variant call 25,26 .…”

Section: Rt-pcr Amplification and Nanopore Sequencingmentioning

confidence: 99%

Increased risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variant compared to Alpha variant in vaccinated individuals

Andeweg

Vennema

Veldhuijzen

et al. 2021

Preprint

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The extent to which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) break through infection- or vaccine-induced immunity is not well understood. Here, we analyze 28,578 sequenced SARS-CoV-2 samples from individuals with known immune status obtained through national community testing in the Netherlands from March to August 2021. We find evidence for an increased risk of infection by the Beta (B.1.351), Gamma (P.1), or Delta (B.1.617.2) variants compared to the Alpha (B.1.1.7) variant after vaccination. No clear differences were found between vaccines. However, the effect was larger in the first 14-59 days after complete vaccination compared to 60 days and longer. In contrast to vaccine-induced immunity, no increased risk for reinfection with Beta, Gamma or Delta variants relative to Alpha variant was found in individuals with infection-induced immunity.

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“…This strategy allowed assemblying the complete genome from NGS reads obtained within 30 min of run for cycle threshold values (Ct) of qPCR comprised between 15 and 27. SARS-CoV-2 genomes were classified into Nextclade and Pangolin lineages using web applications (https://clades.nextstrain.org/;https://cov-lineages.org/pangolin.html) [10,11,13]. They were deposited in the GISAID sequence database (https://www.gisaid.org/) [14] (Table 1).…”

Section: Textmentioning

confidence: 99%

Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein

Colson

Delerce

Burel

et al. 2021

Preprint

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SARS-CoV-2 variants have become a major virological, epidemiological and clinical concern, particularly with regard to the risk of escape from vaccine-induced immunity. Here we describe the emergence of a new variant. For twelve SARS-CoV-positive patients living in the same geographical area of southeastern France, qPCR testing that screen for variant-associated mutations showed an atypical combination. The index case returned from a travel in Cameroon. The genomes were obtained by next-generation sequencing with Oxford Nanopore Technologies on GridION instruments within approximately 8 h. Their analysis revealed 46 mutations and 37 deletions resulting in 30 amino acid substitutions and 12 deletions. Fourteen amino acid substitutions, including N501Y and E484K, and 9 deletions are located in the spike protein. This genotype pattern led to create a new Pangolin lineage named B.1.640.2, which is a phylogenetic sister group to the old B.1.640 lineage renamed B.1.640.1. Both lineages differ by 25 nucleotide substitutions and 33 deletions. The mutation set and phylogenetic position of the genomes obtained here indicate based on our previous definition a new variant we named 'IHU'. These data are another example of the unpredictability of the emergence of SARS-CoV-2 variants, and of their introduction in a given geographical area from abroad.

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Nextclade: clade assignment, mutation calling and quality control for viral genomes

Cited by 37 publications

References 0 publications

Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics

Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics

Increased risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variant compared to Alpha variant in vaccinated individuals

Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein

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