Rapid Detection of SARS-CoV-2 Variants of Concern, Including B.1.1.28/P.1, British Columbia, Canada

Matic, Nancy; Lowe, Christopher F.; Ritchie, Gordon; Stefanovic, Aleksandra; Lawson, Tanya; Jang, Willson; Young, Matthew; Dong, Winnie; Brumme, Zabrina L.; Brumme, Chanson J.; Leung, Victor; Romney, Marc G.

doi:10.3201/eid2706.210532

Cited by 41 publications

(29 citation statements)

References 5 publications

(5 reference statements)

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“…In the absence of SGTF and presence of 501Y and 484K mutations, the H655Y-specific assay proved to be an excellent discriminator between the Beta and Gamma variant (100% concordance for both). This supports the observations of Matic et al who used a similar set of target-specific RT-PCRs to identify the Alpha, Beta and Gamma variants [ 14 ].…”

Section: Discussionsupporting

confidence: 89%

Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants

Mertens

Coppens

Loens

et al. 2022

Clinical Microbiology and Infection

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Objectives The current study evaluates a testing algorithm for the rapid identification of SARS-CoV-2 variants that includes the use of PCR-based targeted Single Nucleotide Polymorphism (SNP) detection assays preceded by a multiplex PCR sensitive to s -Gene Target Failure (SGTF). Methods PCR SNP assays targeting SARS-CoV-2 s -gene mutations ΔH69-V70, L452R, E484K, N501Y, H655Y, and P681R using melting curve analysis were performed on 567 samples in which SARS-CoV-2 viral RNA was detected by a multiplex PCR. Viral whole genome sequencing (WGS) was performed to confirm the presence of SNPs and to identify the Pangolin lineage. Additionally, 1133 SARS-CoV-2 positive samples with SGTF were further assessed by WGS to determine the presence of ΔH69-V70. Results The N501Y-specific assay (N=567) had an overall percent agreement (OPA) of 98.5%. The ΔH69-V70- (N=178) and E484K-specific (N=401) assays had an OPA of 96.6 and 99.7% respectively. Assessment of H655Y (N=139) yielded a 100.0% concordance when applied in the proposed algorithm. The L452R- (N=67) and P681R-specific (N=62) assays had an OPA of 98.2 and 98.1% respectively. The proposed algorithm identified six variants of concern/interest (VOC/VOI) – Alpha (N=149), Beta (N=65), Gamma (N=86), Delta (N=49), Eta (N=6), Kappa (N=6) – and 205 non-VOC/VOI strains – including the variants under monitoring B.1.214.2 (N=43) and B.1.1.318 (N=18) and Epsilon (N=1). An excellent concordance was observed for the identification of all SARS-CoV-2 lineages evaluated. Conclusions We present a flexible testing algorithm for the rapid detection of current and emerging SARS-CoV-2 VOC/VOIs which can be easily adapted based on the local endemicity of specific variants.

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Section: Discussionsupporting

confidence: 89%

Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants

Mertens

Coppens

Loens

et al. 2022

Clinical Microbiology and Infection

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“…This lineage contains the E484K and N501Y mutations that likely contribute to evasion of vaccine-induced immunity and has been associated with re-infection [ 31 , 41 ]. This variant was recently identified by rapid detection in Canada, highlighting the importance of surveillance testing in identifying variants of concern [ 42 ]. We also identified a variant containing the L452R mutation (S3) that has been reported to contribute to evasion of vaccine-induced immunity [ 30 ].…”

Section: Discussionmentioning

confidence: 99%

Breakthrough Infections with Multiple Lineages of SARS-CoV-2 Variants Reveals Continued Risk of Severe Disease in Immunosuppressed Patients

Deng

Evdokimova

O’Brien

et al. 2021

Viruses

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The pandemic of COVID-19 caused by SARS-CoV-2 infection continues to spread around the world. Vaccines that elicit protective immunity have reduced infection and mortality, however new viral variants are arising that may evade vaccine-induced immunity or cause disease in individuals who are unable to develop robust vaccine-induced responses. Investigating the role of viral variants in causing severe disease, evading vaccine-elicited immunity, and infecting vulnerable individuals is important for developing strategies to control the pandemic. Here, we report fourteen breakthrough infections of SARS-CoV-2 in vaccinated individuals with symptoms ranging from asymptomatic/mild (6/14) to severe disease (8/14). High viral loads with a median Ct value of 19.6 were detected in the nasopharyngeal specimens from subjects regardless of disease severity. Sequence analysis revealed four distinct virus lineages, including alpha and gamma variants of concern. Immunosuppressed individuals were more likely to be hospitalized after infection (p = 0.047), however no specific variant was associated with severe disease. Our results highlight the high viral load that can occur in asymptomatic breakthrough infections and the vulnerability of immunosuppressed individuals to post-vaccination infections by diverse variants of SARS-CoV-2.

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“…The sharp increase in the total COVID-19 infections, followed by an increase in the number of hospital admissions observed in Manaus, indicate the high transmissibility of the variant [ 72 , 73 ]. It has now been detected in more than 200 cases in Canada [ 74 ], Italy [ 75 ], the USA [ 76 ] and Belgium, and the total world infection has now reached 2,300 cases (as of 5 April 2021). Information on the transmissibility of the P.1 variant, however, is scant; it shares several mutations that were acquired independently with the B.1.351 variant- K417T, E484K and N501Y- all of which in the RBD of the S glycoprotein ( Figure 6 a).…”

Section: Lineage P1 (B1128/gamma Variant)mentioning

confidence: 99%

Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion

Salleh

Derrick

Deris

2021

IJMS

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The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents significant social, economic and political challenges worldwide. SARS-CoV-2 has caused over 3.5 million deaths since late 2019. Mutations in the spike (S) glycoprotein are of particular concern because it harbours the domain which recognises the angiotensin-converting enzyme 2 (ACE2) receptor and is the target for neutralising antibodies. Mutations in the S protein may induce alterations in the surface spike structures, changing the conformational B-cell epitopes and leading to a potential reduction in vaccine efficacy. Here, we summarise how the more important variants of SARS-CoV-2, which include cluster 5, lineages B.1.1.7 (Alpha variant), B.1.351 (Beta), P.1 (B.1.1.28/Gamma), B.1.427/B.1.429 (Epsilon), B.1.526 (Iota) and B.1.617.2 (Delta) confer mutations in their respective spike proteins which enhance viral fitness by improving binding affinity to the ACE2 receptor and lead to an increase in infectivity and transmission. We further discuss how these spike protein mutations provide resistance against immune responses, either acquired naturally or induced by vaccination. This information will be valuable in guiding the development of vaccines and other therapeutics for protection against the ongoing coronavirus disease 2019 (COVID-19) pandemic.

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Rapid Detection of SARS-CoV-2 Variants of Concern, Including B.1.1.28/P.1, British Columbia, Canada

Cited by 41 publications

References 5 publications

Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants

Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants

Breakthrough Infections with Multiple Lineages of SARS-CoV-2 Variants Reveals Continued Risk of Severe Disease in Immunosuppressed Patients

Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion

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