Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants

Massacci, Alice; Sperandio, Eleonora; D’Ambrosio, Lorenzo; Maffei, Mariano; Palombo, Fabio; Aurisicchio, Luigi; Ciliberto, Gennaro; Pallocca, Matteo

doi:10.1186/s12967-020-02675-4

Cited by 17 publications

(11 citation statements)

References 28 publications

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“…The workflow was applied on the multi-FASTA GISAID population available on April 2022. Inter-country resolution bias was smoothed out through use of variation per thousand isolates formula (i.e., VpTI = Mutations * 1e3) available (Massacci et al, 2020 ). Phylogenetic analysis was performed using full FASTA database via the ETE3 web tool (Huerta-Cepas et al, 2016 ) on PhyML default parameters (bootstrap: 100).…”

Section: Methodsmentioning

confidence: 99%

Dynamics of Viral Infection and Evolution of SARS-CoV-2 Variants in the Calabria Area of Southern Italy

Marco

Veneziano

Massacci³

et al. 2022

Front. Microbiol.

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In this study, we report on the results of SARS-CoV-2 surveillance performed in an area of Southern Italy for 12 months (from March 2021 to February 2022). To this study, we have sequenced RNA from 609 isolates. We have identified circulating VOCs by Sanger sequencing of the S gene and defined their genotypes by whole-genome NGS sequencing of 157 representative isolates. Our results indicated that B.1 and Alpha were the only circulating lineages in Calabria in March 2021; while Alpha remained the most common variant between April 2021 and May 2021 (90 and 73%, respectively), we observed a concomitant decrease in B.1 cases and appearance of Gamma cases (6 and 21%, respectively); C.36.3 and Delta appeared in June 2021 (6 and 3%, respectively); Delta became dominant in July 2021 while Alpha continued to reduce (46 and 48%, respectively). In August 2021, Delta became the only circulating variant until the end of December 2021. As of January 2022, Omicron emerged and took over Delta (72 and 28%, respectively). No patient carrying Beta, Iota, Mu, or Eta variants was identified in this survey. Among the genomes identified in this study, some were distributed all over Europe (B1_S477N, Alpha_L5F, Delta_T95, Delta_G181V, and Delta_A222V), some were distributed in the majority of Italian regions (B1_S477N, B1_Q675H, Delta_T95I and Delta_A222V), and some were present mainly in Calabria (B1_S477N_T29I, B1_S477N_T29I_E484Q, Alpha_A67S, Alpha_A701S, and Alpha_T724I). Prediction analysis of the effects of mutations on the immune response (i.e., binding to class I MHC and/or recognition of T cells) indicated that T29I in B.1 variant; A701S in Alpha variant; and T19R in Delta variant were predicted to impair binding to class I MHC whereas the mutations A67S identified in Alpha; E484K identified in Gamma; and E156G and ΔF157/R158 identified in Delta were predicted to impair recognition by T cells. In conclusion, we report on the results of SARS-CoV-2 surveillance in Regione Calabria in the period between March 2021 and February 2022, identified variants that were enriched mainly in Calabria, and predicted the effects of identified mutations on host immune response.

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Section: Methodsmentioning

confidence: 99%

Dynamics of Viral Infection and Evolution of SARS-CoV-2 Variants in the Calabria Area of Southern Italy

Marco

Veneziano

Massacci³

et al. 2022

Front. Microbiol.

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“…SARS-CoV-2 virus is continuing to mutate and evolve [ 36 ] like any other virus. As of August 2021, a total of 32 mutations have been reported on Spike glycoprotein by Covid-Miner [ 37 ] which is enabled by data from the Global Initiative on Sharing Avian Influenza Data [ 38 ]. Out of these 32 mutations, four mutations were found in our three out of final four predicted epitopes ( Supplementary Table 5 , see Supplementary Data available online at http://bib.oxfordjournals.org/ ).…”

Section: Discussionmentioning

confidence: 99%

Immuno-informatics analysis predicts B and T cell consensus epitopes for designing peptide vaccine against SARS-CoV-2 with 99.82% global population coverage

Shukla

Pandey

Prasad

et al. 2021

Briefings in Bioinformatics

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The current global pandemic due to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has taken a substantial number of lives across the world. Although few vaccines have been rolled-out, a number of vaccine candidates are still under clinical trials at various pharmaceutical companies and laboratories around the world. Considering the intrinsic nature of viruses in mutating and evolving over time, persistent efforts are needed to develop better vaccine candidates. In this study, various immuno-informatics tools and bioinformatics databases were deployed to derive consensus B-cell and T-cell epitope sequences of SARS-CoV-2 spike glycoprotein. This approach has identified four potential epitopes which have the capability to initiate both antibody and cell-mediated immune responses, are non-allergenic and do not trigger autoimmunity. These peptide sequences were also evaluated to show 99.82% of global population coverage based on the genotypic frequencies of HLA binding alleles for both MHC class-I and class-II and are unique for SARS-CoV-2 isolated from human as a host species. Epitope number 2 alone had a global population coverage of 98.2%. Therefore, we further validated binding and interaction of its constituent T-cell epitopes with their corresponding HLA proteins using molecular docking and molecular dynamics simulation experiments, followed by binding free energy calculations with molecular mechanics Poisson–Boltzmann surface area, essential dynamics analysis and free energy landscape analysis. The immuno-informatics pipeline described and the candidate epitopes discovered herein could have significant impact upon efforts to develop globally effective SARS-CoV-2 vaccines.

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“…Whole genome genetic variations, including single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs), were determined and annotated using a bioinformatic framework proposed by Massacci et al (2020) with Wuhan-Hu-1 (GenBank NC_045512.2) ( Wu et al, 2020 ) as the reference. In summary, the viral sequences were first aligned against the reference using the nucmer command with default settings except requiring only the forward matching of the query sequences (–forward), provided by the MUMmer package (version 3.23) ( Marcais et al, 2018 ).…”

Section: Methodsmentioning

confidence: 99%

A New Way to Trace SARS-CoV-2 Variants Through Weighted Network Analysis of Frequency Trajectories of Mutations

et al. 2022

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Early detection of SARS-CoV-2 variants enables timely tracking of clinically important strains in order to inform the public health response. Current subtype-based variant surveillance depending on prior subtype assignment according to lag features and their continuous risk assessment may delay this process. We proposed a weighted network framework to model the frequency trajectories of mutations (FTMs) for SARS-CoV-2 variant tracing, without requiring prior subtype assignment. This framework modularizes the FTMs and conglomerates synchronous FTMs together to represent the variants. It also generates module clusters to unveil the epidemic stages and their contemporaneous variants. Eventually, the module-based variants are assessed by phylogenetic tree through sub-sampling to facilitate communication and control of the epidemic. This process was benchmarked using worldwide GISAID data, which not only demonstrated all the methodology features but also showed the module-based variant identification had highly specific and sensitive mapping with the global phylogenetic tree. When applying this process to regional data like India and South Africa for SARS-CoV-2 variant surveillance, the approach clearly elucidated the national dispersal history of the viral variants and their co-circulation pattern, and provided much earlier warning of Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529). In summary, our work showed that the weighted network modeling of FTMs enables us to rapidly and easily track down SARS-CoV-2 variants overcoming prior viral subtyping with lag features, accelerating the understanding and surveillance of COVID-19.

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Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants

Cited by 17 publications

References 28 publications

Dynamics of Viral Infection and Evolution of SARS-CoV-2 Variants in the Calabria Area of Southern Italy

Dynamics of Viral Infection and Evolution of SARS-CoV-2 Variants in the Calabria Area of Southern Italy

Immuno-informatics analysis predicts B and T cell consensus epitopes for designing peptide vaccine against SARS-CoV-2 with 99.82% global population coverage

A New Way to Trace SARS-CoV-2 Variants Through Weighted Network Analysis of Frequency Trajectories of Mutations

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