Severe acute respiratory syndrome coronavirus 2 escape mutants and protective immunity from natural infections or immunizations

Di, Antonino; Cunha, Flávia; Petrosillo, Nicola; Beeching, Nicholas; Ergonul, Oner; Petersen, Eskild; Koopmans, Marion

doi:10.1016/j.cmi.2021.03.011

Cited by 23 publications

(19 citation statements)

References 17 publications

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“…This evolution may notably hinder efforts in the combat of SARS-CoV-2 pandemics [ 8 ]. Furthermore, expanding population immunity exerts novel selection pressures on the virus, further underscoring the importance of monitoring the vaccine, convalescent plasma, and immunoglobulin escape variants [ 9 ]. Novel virus strains are also classified as variants of interest and variants under monitoring, with preliminary data suggesting an increase in transmission risk or disease severity.…”

Section: Introductionmentioning

confidence: 99%

Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland

Serwin

Ossowski

Szargut

et al. 2021

Viruses

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The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolved into a worldwide outbreak, with the first Polish cases in February/March 2020. This study aimed to investigate the molecular epidemiology of the circulating virus lineages between March 2020 and February 2021. We performed variant identification, spike mutation pattern analysis, and phylogenetic and evolutionary analyses for 1106 high-coverage whole-genome sequences, implementing maximum likelihood, multiple continuous-time Markov chain, and Bayesian birth–death skyline models. For time trends, logistic regression was used. In the dataset, virus B.1.221 lineage was predominant (15.37%), followed by B.1.258 (15.01%) and B.1.1.29 (11.48%) strains. Three clades were identified, being responsible for 74.41% of infections over the analyzed period. Expansion in variant diversity was observed since September 2020 with increasing frequency of the number in spike substitutions, mainly H69V70 deletion, P681H, N439K, and S98F. In population dynamics inferences, three periods with exponential increase in infection were observed, beginning in March, July, and September 2020, respectively, and were driven by different virus clades. Additionally, a notable increase in infections caused by the B.1.1.7 lineage since February 2021 was noted. Over time, the virus accumulated mutations related to optimized transmissibility; therefore, faster dissemination is reflected by the second wave of epidemics in Poland.

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Section: Introductionmentioning

confidence: 99%

Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland

Serwin

Ossowski

Szargut

et al. 2021

Viruses

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“…SARS-CoV-2 undergoes inherent gene mutation during the worldwide spread [ 5 ] and the global pandemic promotes the emergence of variants [ 6 ]. In particular, the rapid emergence of variants of concerns (VOCs), including B.1.351 [ 7 ], P.1 [ 8 ], B.1.1.7 [ 9 ] and B.1.617.2 [ 10 ], and variants of interest (VOIs) [ 11 ], has attracted persistent public attention due to their unusual divergence and potential impact on biological importance [ 12 , 13 ]. The variation resulting from virus adaptive evolution endows the virus with the ability to escape the detection of the developed PCR methods by the current primer/probe sets if mutations happen within the primers and the probes in term of diagnosis, thus resulting in false negative results [ 9 , 14 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

A Reverse Transcription Recombinase-Aided Amplification Method for Rapid and Point-of-Care Detection of SARS-CoV-2, including Variants

Xiong

et al. 2021

Viruses

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The worldwide pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its emergence of variants needs rapid and point-of-care testing methods for a broad diagnosis. The regular RT-qPCR is time-consuming and limited in central laboratories, so a broad and large-scale screening requirement calls for rapid and in situ methods. In this regard, a reverse transcription recombinase-aided amplification (RT-RAA) is proposed here for the rapid and point-of-care detection of SARS-CoV-2. A set of highly conserved primers and probes targeting more than 98% of SARS-CoV-2 strains, including currently circulating variants (four variants of concerns (VOCs) and three variants of interest (VOIs)), was used in this study. With the preferred primers, the RT-RAA assay showed a 100% specificity to SARS-CoV-2 from eight other respiratory RNA viruses. Moreover, the assay here is of a high sensitivity and 0.48 copies/μL can be detected within 25 min at a constant temperature (42 °C), which can be realized on portable equipment. Furthermore, the RT-RAA assay demonstrated its high agreement for the detection of SARS-CoV-2 in clinical specimens compared with RT-qPCR. The rapid, simple and point-of-care RT-RAA method is expected to be an appealing detection tool to detect SARS-CoV-2, including variants, in clinical diagnostic applications.

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“…The continuous emergence of mutations resulting to amino-acid substitutions in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of Life 2021, 11, 1015 2 of 12 major importance. This is due to the fact that some of them are associated with alterations in host cell receptor binding leading to increased infectivity and transmissibility, as well as in poor antigen/antibody interactions, reduced neutralization and consequently, immune escape [1]. The S:D614G (aspartic acid to glycine) amino-acid substitution emerged early in the SARS-CoV-2 evolutionary history and has been associated with higher virus infectivity [2].…”

Section: Introductionmentioning

confidence: 99%

A Novel Real-Time RT-PCR-Based Methodology for the Preliminary Typing of SARS-CoV-2 Variants, Employing Non-Extendable LNA Oligonucleotides and Three Signature Mutations at the Spike Protein Receptor-Binding Domain

Chaintoutis

Chassalevris

Balaska

et al. 2021

Life

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Mutations resulting in amino-acid substitutions of the SARS-CoV-2 spike protein receptor-binding domain (RBD) have been associated with enhanced transmissibility and immune escape of the respective variants, namely Alpha, Beta, Gamma or Delta. Rapid identification of the aforementioned variants of concern and their discrimination of other variants is thus of importance for public health interventions. For this reason, a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed, to target signature mutations associated with amino-acid substitutions at positions 478, 484 and 501 present in the receptor-binding motif (RBM) of the spike protein RBD. This region contains most contacting residues of SARS-CoV-2 that bind to ACE2. A novel strategy employing the use of non-extendable LNA oligonucleotide blockers that can reduce non-specific hybridization of probes increased the number of different mutated sites examined in a multiplex PCR. The combinatory analysis of the different fluorescence signals obtained enabled the preliminary differentiation of SARS-CoV-2 variants of concern. The assay is sensitive with a LOD of 263 copies/reaction for the Delta variant, 170 copies/reaction for the Beta variant, amplification efficiencies > 91% and a linear range of >5 log10 copies/reaction against all targets. Validation of the assay using known SARS-CoV-2-positive and negative samples from humans and animals revealed its ability to correctly identify the targeted mutations and preliminary characterize the SARS-CoV-2 variants. The novel approach for mutation typing using LNA oligonucleotide blockers can be modified to target signature mutations at four different sites in the RBM and further expand the range of variants detected.

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Severe acute respiratory syndrome coronavirus 2 escape mutants and protective immunity from natural infections or immunizations

Cited by 23 publications

References 17 publications

Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland

Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland

A Reverse Transcription Recombinase-Aided Amplification Method for Rapid and Point-of-Care Detection of SARS-CoV-2, including Variants

A Novel Real-Time RT-PCR-Based Methodology for the Preliminary Typing of SARS-CoV-2 Variants, Employing Non-Extendable LNA Oligonucleotides and Three Signature Mutations at the Spike Protein Receptor-Binding Domain

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