A Parvovirus B19 synthetic genome: sequence features and functional competence

Manaresi, Elisabetta; Conti, Ilaria; Bua, Gloria; Bonvicini, Francesca; Gallinella, Giorgio

doi:10.1016/j.virol.2017.05.006

Cited by 18 publications

(25 citation statements)

References 24 publications

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“…For each position of the multi-aligned 54 2019-nCoV, we calculated Shannon Entropy as a measure of the position variability [12]. Apart from the 5’ and 3’ ends, likely non-protein coding and less homogeneous, we identified two hot spots of hyper variability at positions 8789 and 28151 (Figures 3B and C).…”

Section: Resultsmentioning

confidence: 99%

Genomic variance of the 2019-nCoV coronavirus

Ceraolo

Giorgi

2020

Preprint

170

199

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There is rising global concern for the recently emerged novel Coronavirus (2019-nCov). Full genomic sequences have been released by the worldwide scientific community in the last few weeks in order to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and SARS. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hyper-variable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.

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Section: Resultsmentioning

confidence: 99%

Genomic variance of the 2019-nCoV coronavirus

Ceraolo

Giorgi

2020

Preprint

170

199

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“…For infection experiments, both viremic plasma I700 and recombinant virus B19V-EC [ 10 ] were used at a multiplicity of infection (moi) 10 000 geq/cell. As controls (mock infected cells) B19V negative plasma or M199 alone were used.…”

Section: Methodsmentioning

confidence: 99%

Parvovirus B19 activates in vitro normal human dermal fibroblasts: a possible implication in skin fibrosis and systemic sclerosis

Arvia¹,

Margheri

Stincarelli³

et al. 2020

Rheumatology

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Objective Fibrosis is the most characteristic pathological hallmark of SSc, a connective tissue disease characterized by vascular and immunological abnormalities, inflammation and enhanced extracellular matrix production, leading to progressive fibrosis of skin and internal organs. We previously demonstrated that parvovirus B19 (B19V) can infect normal human dermal fibroblasts (NHDFs) and that B19V persists in SSc fibroblasts. In this study, we investigated whether parvovirus B19V is able to activate in vitro NHDFs and to induce in these cells some phenotypic features similar to that observed in the SSc fibroblasts. Methods We preliminarily analysed the time course of B19V infection in cultured NHDFs, then we investigated the ability of B19V to induce cell migration, invasive phenotype and mRNA expression of some profibrotic and/or proinflammatory genes. Results We confirmed our previous findings that B19V infects NHDFs, but the infection is not productive. After incubation with B19V, NHDFs showed a significant increase of both migration and invasiveness, along with mRNA expression of different profibrotic genes (α-SMA, EDN-1, IL-6, TGF-β1 receptors 1 and 2, Col1α2), some genes associated with inflammasome platform (AIM2, IFI16, IL-1β, CASP-1) and genes for metalloprotease (MMP 2, 9 and 12). Conclusion These data suggest that B19V can activate dermal fibroblasts and may have a role in the pathogenesis of fibrosis. B19V-induced fibroblast migration and invasiveness could be due to the B19V-associated MMP9 overexpression and activation. Moreover, the up-regulation of MMP12, typical of SSc, could link the B19V infection of fibroblasts to the anti-angiogenic process.

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“…1). Positional variability of the SARS-CoV-2 genomes was calculated from the MSA of 320 SARS-CoV-2 whole genomes as a measure of Entropy value (H(x)) (Manaresi et al, 2017). Excluding 5′ and 3′ UTR, ten hotspots of hypervariable positions were identified, of which seven were located at ORF1ab (1059C > T, 3037C > T, 8782C > T, 14408C > T, 17747C > T, 17858A > G, 18060C > T), and one at ORF S (23403A > G), ORF3a (25563G > T), and ORF8 (28,144 T > C), respectively.…”

Section: Genomic Variations Of Sars-cov-2mentioning

confidence: 99%

Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach

Lokman

Rasheduzzaman

Salauddin

et al. 2020

Infection, Genetics and Evolution

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The newly identified SARS-CoV-2 has now been reported from around 185 countries with more than a million confirmed human cases including more than 120,000 deaths. The genomes of SARS-COV-2 strains isolated from different parts of the world are now available and the unique features of constituent genes and proteins need to be explored to understand the biology of the virus. Spike glycoprotein is one of the major targets to be explored because of its role during the entry of coronaviruses into host cells. We analyzed 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 using multiple sequence alignment. In this study, 483 unique variations have been identified among the genomes of SARS-CoV-2 including 25 nonsynonymous mutations and one deletion in the spike (S) protein. Among the 26 variations detected in S, 12 variations were located at the Nterminal domain (NTD) and 6 variations at the receptor-binding domain (RBD) which might alter the interaction of S protein with the host receptor angiotensin-converting enzyme 2 (ACE2). Besides, 22 amino acid insertions were identified in the spike protein of SARS-CoV-2 in comparison with that of SARS-CoV. Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis. Based on results reported herein, potential inhibitors against S protein can be designed by considering these variations and their impact on protein structure.

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A Parvovirus B19 synthetic genome: sequence features and functional competence

Cited by 18 publications

References 24 publications

Genomic variance of the 2019-nCoV coronavirus

Genomic variance of the 2019-nCoV coronavirus

Parvovirus B19 activates in vitro normal human dermal fibroblasts: a possible implication in skin fibrosis and systemic sclerosis

Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach

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