A SARS-CoV-2 mutant from B.1.258 lineage with ∆H69/∆V70 deletion in the Spike protein circulating in Central Europe in the fall 2020

Brejová, Broňa; Boršová, Kristína; Hodorová, Viktória; Čabanová, Viktória; Reizigová, Lenka; Paul, Evan D.; Čekan, Pavol; Klempa, Boris; Nosek, Jozef; Vinař, Tomáš

doi:10.1007/s11262-021-01866-5

Cited by 32 publications

(27 citation statements)

References 16 publications

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“…Analysis of the results obtained with specimens of the B.1.1.7 lineage always revealed a notable difference between the Cq values for the N and S genes (mean, + 11 ±2; range, + 8/ + 15), while such a difference was not observed with specimens of the other lineages ( Table 1 ). The Taq-Path COVID-19 RT-PCR assay revealed a missing S-gene target amplification with all specimens of VOC-UK, but also with B.1.258 ( Table 1 ), as expected from the presence of the HV69-70 spike deletion also in members of this lineage ( Brejová et al ., 2021 ).…”

supporting

confidence: 52%

Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay

Giovacchini

Coppi

Aiezza

et al. 2021

International Journal of Infectious Diseases

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Background: The emergence of SARS-CoV-2 variants of concern (VOCs) for increased transmissibility and being potentially capable of immune-escape mandates for epidemiological surveillance. Genomic alterations present in VOCs can affect the results of RT-qPCR assays for routine diagnostic purposes, leading to peculiar profiles that can be used for rapid screening of variants. This study reports a peculiar profile observed with the Allplex TM SARS-CoV-2/FluA/FluB/RSV assay and VOC-Alpha (202012/01, lineage B.1.1.7, also named VOC-UK), which was the first identified SARS-CoV-2 VOC. Methods: Samples were analyzed by two RT-qPCR assays: the Allplex TM SARS-CoV-2/FluA/FluB/RSV assay (ASFR, Seegene Technologies Inc; Seoul, South Korea) and the TaqPath COVID-19 RT-PCR (Thermo Fisher Scientific, USA). Definition of the SARS-CoV-2 variant was carried out by Sanger sequencing of the relevant S-gene regions and, in some cases, by whole genome sequencing (WGS) using the ARTIC-nCoV workflow on a MiniION (Oxford Nanopore Technologies, Oxford, UK) or a Illumina MiSeq platform (San Diego, California, USA). Results: Of the 173 SARS-CoV-2-positive specimens, all those of lineage B.1.1.7 (N = 71) showed an average Cq difference between the N and S genes of + 11 ±2 (range, + 8/ + 15). None of the other specimens, including several different lineages (Wild-type for the analyzed regions, N = 22; Gamma, N = 63; Delta, N = 9; B.1.258 , N = 3; B.1.160, N = 3; B.1.177.7, N = 1; B.1.1.420, N = 1), exhibited a similar difference in Cq values. Conclusions:The peculiar pattern of delayed N gene positivity could constitute a convenient method for VOC-Alpha screening, simultaneous to viral detection, when using the Allplex TM SARS-CoV-2/FluA/FluB/RSV assay.

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supporting

confidence: 52%

Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay

Giovacchini

Coppi

Aiezza

et al. 2021

International Journal of Infectious Diseases

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“…This variant was identified in the Czech Republic and Slovakia in late 2020, within the clade B.1.258 (Brejováet al, 2021). It has been observed to escape the immune response and increase the severity of infection.…”

Section: Lineage B1258dmentioning

confidence: 99%

SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines

Singh

Parveen

Yadav

2021

Front. Cell. Infect. Microbiol.

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The emergence of SARS-CoV-2 variants may cause resistance at the immunity level against current vaccines. Some emergent new variants have increased transmissibility, infectivity, hospitalization, and mortality. Since the administration of the first SARS-CoV-2 vaccine to a human in March 2020, there is an ongoing global race against SARS-CoV-2 to control the current pandemic situation. Spike (S) glycoprotein of SARS-CoV-2 is the main target for current vaccine development, which can neutralize the infection. Companies and academic institutions have developed vaccines based on the S glycoprotein, as well as its antigenic domains and epitopes, which have been proven effective in generating neutralizing antibodies. The effectiveness of SARS-CoV-2 vaccines and other therapeutics developments are limited by the new emergent variants at the global level. We have discussed the emergent variants of SARS-CoV-2 on the efficacy of developed vaccines. Presently, most of the vaccines have been tremendously effective in severe diseases. However, there are still noteworthy challenges in certifying impartial vaccines; the stories of re-infections are generating more stressful conditions, and this needs further clinical evaluation.

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“…A study in Slovakia found that samples with spike target failure were assigned as B.1.258. The B.1.258 lineage with the deletion had a higher viral load and became one of the dominant variants found in Slovakia [6]. The higher infectivity of variant harboring Δ69-70 mutation may be explained by the increased cleavage on S2 domain of spike protein with the mutation [7].…”

Section: Discussionmentioning

confidence: 99%

Optimization of multiplex PCR composition to screen for SARS-CoV-2 variants of concern

2021

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Background: The ongoing COVID-19 pandemic has led to the emergence of several variants of concern. To rapidly identify those variants, screening samples for whole-genome sequencing (WGS) prioritization could be performed. Objective: We optimized the polymerase chain reaction (PCR) screening method to identify the mutation in spike and ORF1a regions. Methods: We adopted primers targeting mutation in spike and ORF1a region from another study. We optimized the PCR screening method using kits readily available in Indonesia. Firstly, we compared N1 and N2 primers as internal positive control. We also compared GoTaq® 1-Step RT-qPCR System and Indonesia TFRIC-19 BioCOV-19 for the multiplex reaction. We used the optimized composition to screen SARS-CoV-2 positive samples from April – June 2021. Samples with spike and/or ORF1a target failure were subjected to whole genome sequencing (WGS). Results: The results demonstrated the N2 BioCOV-19 reaction as the optimized multiplex PCR composition for spike and ORF1a mutations screening. Whole-genome sequencing has shown that a sample with spike and ORF1a targets failure to be Alpha variant, while other samples with single target failure as non-variants of concern. Therefore, a multiplex RT-PCR composition has been optimized to detect mutation in spike and ORF1a regions. Conclusion: We have optimized a multiplex RT-PCR composition to detect mutation in spike and ORF1a regions.

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A SARS-CoV-2 mutant from B.1.258 lineage with ∆H69/∆V70 deletion in the Spike protein circulating in Central Europe in the fall 2020

Cited by 32 publications

References 16 publications

Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay

Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay

SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines

Optimization of multiplex PCR composition to screen for SARS-CoV-2 variants of concern

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