Will the emergent SARS‐CoV2 B.1.1.7 lineage affect molecular diagnosis of COVID‐19?

Ramírez, Juan David; Muñoz, Marina; Patiño, Luz Helena; Ballesteros, Nathalia; Paniz‐Mondolfi, Alberto

doi:10.1002/jmv.26823

Cited by 31 publications

(31 citation statements)

References 8 publications

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“…N501Y, E69/70, P681H, 144Y, A570D, E484K, K417N, K417T), which could impact transmission, and raises concern about immunological escape (Rambaut et al, 2020a). The broad SARS-CoV-2 lineage diversity circulating in South America could exacerbate the impact of the pandemic in the region, affecting the reliability of molecular diagnosis schemes (Ramirez et al, 2021b) and even the efficacy of vaccines since the polymorphisms in the spike gene could promote immune evasion (Bouayad, 2020, McCarthy et al, 2021.…”

Section: Discussionmentioning

confidence: 99%

Characterizing SARS-CoV-2 genome diversity circulating in South American countries: Signatures of potentially emergent lineages?

Muñoz¹,

Patiño²,

Ballesteros³

et al. 2021

International Journal of Infectious Diseases

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Objectives To evaluate the genomic diversity and geographic distribution of SARS-CoV-2 lineages currently circulating in South America (SA). Methods SARS-CoV-2 lineages reported from South American countries were analyzed from a public dataset of 5597 genome assemblies. Polymorphisms in the main open reading frames were identified and compared to those present in the main lineages of epidemiology concern: B.1.1.7 (from UK) and B.1.351 (from South Africa). Results A total of 169 circulating lineages across 16 South American countries were identified, revealing a predominant circulation of the major lineage B, the one with the greatest diversity and broadest geographic distribution. Sixteen lineages were selected to be comprehensively analyzed because are predominant in the region. Two lineages of concern report were remarkably identified: P.1 recognized as the Brazilian variant (with 94 genomes) and B.1.1.7 the UK variant (with 28 genomes), both displayed 33 polymorphisms compared to the reference genome, the highest number among analyzed genomes. While the most of other lineages circulating in SA displayed 24 or less polymorphisms compared to the reference strain. A high number of polymorphisms were detected in the evaluated lineages with a limited number of common variable positions amongst them, in agreement with the profiles identified in the main lineages of epidemiology concern. Conclusions The ever-increasing genetic diversity of SARS-CoV-2 continues to lead to the emergence of novel lineages. Different variants and lineages are now present across SA with the presence of major lineage B mostly. The circulation of variants as P.1 and B.1.1.7 in different countries as well as the elevated number of polymorphisms highlighted the importance of continuing with the genomic surveillance to determine introduction events, identify transmission chains, trace emergence and help to implement successful prevention, vaccination and control strategies.

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Section: Discussionmentioning

confidence: 99%

Characterizing SARS-CoV-2 genome diversity circulating in South American countries: Signatures of potentially emergent lineages?

Muñoz¹,

Patiño²,

Ballesteros³

et al. 2021

International Journal of Infectious Diseases

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“…SARS-CoV-2 genomes [46]. The Alpha lineage was shown to have higher false-negative results when using specific commercial kits directed to the spike (S) gene but not when using standard protocols such as Berlin-Cherite protocol since it does not involve the S protein-encoding gene as target [47]. Another concern is a variant detected in France of a S deletion (ΔH69-V70) which has shown to be associated with S-gene target gene detection failure in three-target RT-PCR [48].…”

Section: Decreased Diagnostic Sensitivitymentioning

confidence: 99%

Emerging SARS-CoV-2 variants of concern and potential intervention approaches

2021

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The major variant of concerns (VOCs) have shared mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike proteins, mostly on the S1 unit and resulted in higher transmissibility rate and affect viral virulence and clinical outcome. The spike protein mutations and other non-structural protein mutations in the VOCs may lead to escape approved vaccinations in certain extend. We will discuss these VOC mutations and discuss the need for combination therapeutic strategies targeting viral cycle and immune host responses.

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“…The clade S, a subtype of SARS-CoV-2, was identified to possess the mutation L84S in the ORF8 protein sequence [25,26,27]. Presently, among many variants of SARS-CoV-2, the lineage B.1.1.7 carries a larger than usual number of genetic changes [28,29,30]. Among many non-synonymous mutations, Q27STOP in the ORF8 protein contributed to deduce the branch leading to lineage B.1.1.7 [31,32].…”

Section: Introductionmentioning

confidence: 99%

An Issue of Concern: Unique Truncated ORF8 Protein Variants of SARS-CoV-2

Hassan¹,

Kodakandla

et al. 2021

Preprint

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Open reading frame 8 (ORF8) protein is one of the most evolving accessory proteins in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits presentation of viral antigens by the major histocompatibility complex class I (MHC-I) and interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 to evade immunity and replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein defines the B.1.1.7 lineage of SARS-CoV-2, which is engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) due to the Q27STOP mutations were identified among 49055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents which includes Africa, Asia, Europe and South America. Based on various quantitative features such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, a collection of nine possible T-ORF8 unique variants were defined. The question of whether T-ORF8 variants work similarly to ORF8 has yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.

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Will the emergent SARS‐CoV2 B.1.1.7 lineage affect molecular diagnosis of COVID‐19?

Cited by 31 publications

References 8 publications

Characterizing SARS-CoV-2 genome diversity circulating in South American countries: Signatures of potentially emergent lineages?

Characterizing SARS-CoV-2 genome diversity circulating in South American countries: Signatures of potentially emergent lineages?

Emerging SARS-CoV-2 variants of concern and potential intervention approaches

An Issue of Concern: Unique Truncated ORF8 Protein Variants of SARS-CoV-2

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