SARS-CoV-2 spike protein displays sequence similarities with paramyxovirus surface proteins; a bioinformatics study

Ahmadi, Ehsan; Zabihi, Mohammad Reza; Hosseinzadeh, Reza; Khosroshahi, Leila Mohamed; Noorbakhsh, Farshid

doi:10.1371/journal.pone.0260360

Cited by 12 publications

(6 citation statements)

References 28 publications

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“…Evolutionary conservation of the SARS-CoV-2 spike protein with other single-stranded RNA viruses has also been described, and computational analysis has shown genetic sequence similarities between regions of SARS-CoV-2 and paramyxoviruses including mumps, measles and Nipah viruses 48 . Interestingly, within the spike protein, the region of highest sequence similarity between SARS-CoV-2 and paramyxoviruses corresponds with the SARS-CoV-2 S2 fusion protein domain, which is also highly conserved among HCoVs 48 . The high sequence homology between these viruses and SARS-CoV-2 suggests that viruses other than HCoV may also contribute to SARS-CoV-2 immune cross-reactivity and impact on infection and vaccine outcomes.…”

Section: Sars-cov-2 Sequence Homology With Other Virusesmentioning

confidence: 99%

The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses

et al. 2022

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Pre-existing cross-reactive immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins in infection-naive subjects have been described by several studies. In particular, regions of high homology between SARS-CoV-2 and common cold coronaviruses have been highlighted as a likely source of this cross-reactivity. However, the role of such cross-reactive responses in the outcome of SARS-CoV-2 infection and vaccination is currently unclear. Here, we review evidence regarding the impact of pre-existing humoral and T cell immune responses to outcomes of SARS-CoV-2 infection and vaccination. Furthermore, we discuss the importance of conserved coronavirus epitopes for the rational design of pan-coronavirus vaccines and consider cross-reactivity of immune responses to ancestral SARS-CoV-2 and SARS-CoV-2 variants, as well as their impact on COVID-19 vaccination.

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Section: Sars-cov-2 Sequence Homology With Other Virusesmentioning

confidence: 99%

The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses

et al. 2022

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“…It is crucial for tracking the transmission dynamics of the SARS-CoV-2 variants between Taiyuan and Wuhan. Our results provide valuable data for researchers and healthcare departments to carefully monitor the evolution of SARS-CoV-2, which can help in controlling the spread of SARS-CoV-2 in particular and other viruses in general [ 35 , 36 ].…”

Section: Discussionmentioning

confidence: 99%

Evolutionary and Phylogenetic Dynamics of SARS-CoV-2 Variants: A Genetic Comparative Study of Taiyuan and Wuhan Cities of China

Hussain,

2024

Viruses

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA genome-containing virus which has infected millions of people all over the world. The virus has been mutating rapidly enough, resulting in the emergence of new variants and sub-variants which have reportedly been spread from Wuhan city in China, the epicenter of the virus, to the rest of China and all over the world. The occurrence of mutations in the viral genome, especially in the viral spike protein region, has resulted in the evolution of multiple variants and sub-variants which gives the virus the benefit of host immune evasion and thus renders modern-day vaccines and therapeutics ineffective. Therefore, there is a continuous need to study the genetic characteristics and evolutionary dynamics of the SARS-CoV-2 variants. Hence, in this study, a total of 832 complete genomes of SARS-CoV-2 variants from the cities of Taiyuan and Wuhan in China was genetically characterized and their phylogenetic and evolutionary dynamics studied using phylogenetics, genetic similarity, and phylogenetic network analyses. This study shows that the four most prevalent lineages in Taiyuan and Wuhan are as follows: the Omicron lineages EG.5.1.1, followed by HK.3, FY.3, and XBB.1.16 (Pangolin classification), and clades 23F (EG.5.1), followed by 23H (HK.3), 22F (XBB), and 23D (XBB.1.9) (Nextclade classification), and lineage B followed by the Omicron FY.3, lineage A, and Omicron FL.2.3 (Pangolin classification), and the clades 19A, followed by 22F (XBB), 23F (EG.5.1), and 23H (HK.3) (Nextclade classification), respectively. Furthermore, our genetic similarity analysis show that the SARS-CoV-2 clade 19A-B.4 from Wuhan (name starting with 412981) has the least genetic similarity of about 95.5% in the spike region of the genome as compared to the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234), followed by the Omicron FR.1.4 from Taiyuan (name starting with 18495199) with ~97.2% similarity and Omicron DY.3 (name starting with 17485740) with ~97.9% similarity. The rest of the variants showed ≥98% similarity with the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234). In addition, our recombination analysis results show that the SARS-CoV-2 variants have three statistically significant recombinant events which could have possibly resulted in the emergence of Omicron XBB.1.16 (recombination event 3), FY.3 (recombination event 5), and FL.2.4 (recombination event 7), suggesting some very important information regarding viral evolution. Also, our phylogenetic tree and network analyses show that there are a total of 14 clusters and more than 10,000 mutations which may have probably resulted in the emergence of cluster-I, followed by 47 mutations resulting in the emergence of cluster-II and so on. The clustering of the viral variants of both cities reveals significant information regarding the phylodynamics of the virus among them. The results of our temporal phylogenetic analysis suggest that the variants of Taiyuan have likely emerged as independent variants separate from the variants of Wuhan. This study, to the best of our knowledge, is the first ever genetic comparative study between Taiyuan and Wuhan cities in China. This study will help us better understand the virus and cope with the emergence and spread of new variants at a local as well as an international level, and keep the public health authorities informed for them to make better decisions in designing new viral vaccines and therapeutics. It will also help the outbreak investigators to better examine any future outbreak.

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“…Insights into the mechanism behind such cross-protection revealed that individuals vaccinated with the MMR or tetanus, diphtheria and pertussis (Tdap) vaccine shared TCR clonotypes with individuals who were convalescent or vaccinated against SARS-CoV-2 [ 36 ]. Furthermore, sequence homologies between MMR surface proteins and SARS-CoV-2 spike have been identified that may give rise to cross-reactive T cells [ 136 , 137 ]. This suggests that T cell cross-reactivity between MMR or Tdap and SARS-CoV-2 may result in a cross-protective effect against COVID-19.…”

Section: T Cell Cross-reactivity From the Measles Mumps And Rubella V...mentioning

confidence: 99%

The Influence of Cross-Reactive T Cells in COVID-19

Eggenhuizen,

Ooi

2024

Biomedicines

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Memory T cells form from the adaptive immune response to historic infections or vaccinations. Some memory T cells have the potential to recognise unrelated pathogens like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and generate cross-reactive immune responses. Notably, such T cell cross-reactivity has been observed between SARS-CoV-2 and other human coronaviruses. T cell cross-reactivity has also been observed between SARS-CoV-2 variants from unrelated microbes and unrelated vaccinations against influenza A, tuberculosis and measles, mumps and rubella. Extensive research and debate is underway to understand the mechanism and role of T cell cross-reactivity and how it relates to Coronavirus disease 2019 (COVID-19) outcomes. Here, we review the evidence for the ability of pre-existing memory T cells to cross-react with SARS-CoV-2. We discuss the latest findings on the impact of T cell cross-reactivity and the extent to which it can cross-protect from COVID-19.

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SARS-CoV-2 spike protein displays sequence similarities with paramyxovirus surface proteins; a bioinformatics study

Cited by 12 publications

References 28 publications

The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses

The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses

Evolutionary and Phylogenetic Dynamics of SARS-CoV-2 Variants: A Genetic Comparative Study of Taiyuan and Wuhan Cities of China

The Influence of Cross-Reactive T Cells in COVID-19

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