Implementation of an in-house real-time reverse transcription-PCR assay to detect the emerging SARS-CoV-2 N501Y variants

Bedotto, Marielle; Fournier, Pierre‐Edouard; Houhamdi, Linda; Colson, Philippe; Raoult, Didier

doi:10.1101/2021.02.03.21250661

Cited by 6 publications

(6 citation statements)

References 4 publications

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“…Since the summer of 2020, we intensified our activity of SARS-CoV-2 genotyping using next-generation sequencing and also through performing partial spike gene sequencing and implementing variant-specific qPCR ( 17, 18 ). To characterise the increasing SARS-CoV-2 genome diversity observed during the summer of 2020, we promptly implemented a viral genome classification system and a nomenclature of SARS-CoV-2 variants.…”

Section: Resultsmentioning

confidence: 99%

“…SARS-CoV-2 genotyping was performed by genome sequencing in our institute for at least 12% of positive diagnoses of SARS-CoV-2 infection monthly, and for at least one fifth and one third of positive diagnoses monthly for 14 and 7 of the 18 months from February 2020 to July 2021, respectively (Table S2). Genotype was obtained primarily by whole genome next-generation sequencing in 11,387 (47%) cases and by partial genome next-generation sequencing (spike fragment) in 2,621 (11%) cases, and retrospectively or prospectively (since January 2021) by in house variant-specific qPCR assays gradually designed and implemented subsequent to the detection of new variants ( 17, 18 ) in 10,173 (42%) cases. The most frequently detected variants were, in decreasing order, the Alpha (a.k.a.…”

Section: Resultsmentioning

confidence: 99%

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Analysis of SARS-CoV-2 variants from 24,181 patients exemplifies the role of globalisation and zoonosis in pandemics

Colson

Fournier

Chaudet

et al. 2021

Preprint

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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 Mediterranee 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 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 analysing 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 mink farms. 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: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Analysis of SARS-CoV-2 variants from 24,181 patients exemplifies the role of globalisation and zoonosis in pandemics

Colson

Fournier

Chaudet

et al. 2021

Preprint

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“…On December 2020, a different mutation, N501T was reported in Brescia (Lombardy) in a single immunocompromised patient (MB61): the same N501T mutation was observed in mustelids (minks 101,123 and ferrets 119 ). An N501Y‐specific one‐step, real‐time RT‐PCR has been recently developed 124 …”

Section: Spike Protein Mutations Detected In Currently Circulating Strainsmentioning

confidence: 99%

Neutralising antibody escape of SARS‐CoV‐2 spike protein: Risk assessment for antibody‐based Covid‐19 therapeutics and vaccines

Focosi¹,

Maggi

2021

Reviews in Medical Virology

150

170

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Summary The Spike protein is the target of both antibody‐based therapeutics (convalescent plasma, polyclonal serum, monoclonal antibodies) and vaccines. Mutations in Spike could affect efficacy of those treatments. Hence, monitoring of mutations is necessary to forecast and readapt the inventory of therapeutics. Different phylogenetic nomenclatures have been used for the currently circulating SARS‐CoV‐2 clades. The Spike protein has different hotspots of mutation and deletion, the most dangerous for immune escape being the ones within the receptor binding domain (RBD), such as K417N/T, N439K, L452R, Y453F, S477N, E484K, and N501Y. Convergent evolution has led to different combinations of mutations among different clades. In this review we focus on the main variants of concern, that is, the so‐called UK (B.1.1.7), South African (B.1.351) and Brazilian (P.1) strains.

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“…In-housespecific RT-qPCR allowed us to determine that the SARS-CoV-2 genotype was 20H/501Y. V2 (B1.351, Beta) variant (9).…”

Section: Foetal Examination and Results Of Sars-cov-2 Testingmentioning

confidence: 99%

Congenital Infection of Severe Acute Respiratory Syndrome Coronavirus 2 With Intrauterine Fetal Death: A Clinicopathological Study With Molecular Analysis

Lesieur

Torrents

Fina

et al. 2021

Clinical Infectious Diseases

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Observations of vertical transmission of SARS-CoV-2 infection from mother to foetus have recently been described in the literature. However, the consequences of such transmission, whether foetal or neonatal, are poorly understood. From a case of in utero foetal death at 24 +2 weeks of gestation that occurred seven days after the diagnosis of symptomatic SARS-CoV-2 infection in the mother, we isolated the incriminating virus by immunochemistry and molecular techniques in several foetal tissues, with a variant analysis of the SARS-CoV-2 genome. Moreover, the foetal demise could be explained by the presence of placental histological lesions, such as histiocytic intervillositis and trophoblastic necrosis, in addition to foetal tissue damage. We observed mild foetal growth retardation and visceral damage to the liver, causing hepatocellular damage and haemosiderosis. To the best of our knowledge, this is the first report in the literature of foetal demise secondary to maternal-foetal transmission of SARS-CoV-2 with a congenital infection and a pathological description of placental and foetal tissue damage. SARS-CoV-2 was identified in both specimens by three independent techniques (immunochemistry, RT-qPCR and RT-dPCR). Furthermore, the incriminating variant has been identified.

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Implementation of an in-house real-time reverse transcription-PCR assay to detect the emerging SARS-CoV-2 N501Y variants

Cited by 6 publications

References 4 publications

Analysis of SARS-CoV-2 variants from 24,181 patients exemplifies the role of globalisation and zoonosis in pandemics

Analysis of SARS-CoV-2 variants from 24,181 patients exemplifies the role of globalisation and zoonosis in pandemics

Neutralising antibody escape of SARS‐CoV‐2 spike protein: Risk assessment for antibody‐based Covid‐19 therapeutics and vaccines

Congenital Infection of Severe Acute Respiratory Syndrome Coronavirus 2 With Intrauterine Fetal Death: A Clinicopathological Study With Molecular Analysis

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