Genomic characterization and phylogenetic analysis of SARS‐COV‐2 in Italy

Zehender, Gianguglielmo; Lai, Alessia; Bergna, Annalisa; Meroni, Luca; Riva, Agostino; Balotta, Claudia; Tarkowski, Maciej; Gabrieli, Arianna; Bernacchia, Dario; Rusconi, Stefano; Rizzardini, Giuliano; Antinori, Spinello; Galli, Massimo

doi:10.1002/jmv.25794

Cited by 116 publications

(142 citation statements)

References 14 publications

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“…1A), leading to the hypothesis that SARS2-S might be less 11 incorporated into lentiviral particles than SARS-S, probably due to reduced compatibility with 12 lentiviral particles. Compared with SARS-S, SARS2-S has one (alanine-to-cysteine at position 13 1247) and two (valine-to-isoleucine at position 1216 and leucine-to-methionine at position 1233) 14 amino acid differences in the cytoplasmic tail (CT) and transmembrane (TM) domain, 15 respectively ( fig. S2A).…”

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confidence: 99%

“…1D) and examined the effects of 11 these mutations on entry into cells expressing ACE2 and TMPRSS2, by comparison with that of 12 wild-type (WT) S protein. These naturally occurring S mutations resulted in reduced (G476S), 13 equal (V483A), or enhanced (D614G, V367F, and H49Y) cell entry. Remarkably, the D614G 14 mutant displayed the highest level of entry activity compared with that of WT S protein ( Fig.…”

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confidence: 99%

“…1E). 13 Given that the D614G S protein is biologically and structurally different from the WT protein, 14 we hypothesized that this mutation might affect the antigenicity of the S protein. To examine this 15 possibility, we performed neutralization assays to compare the neutralizing sensitivity of the WT 16 and D614G S proteins to anti-SARS-CoV-2 sera.…”

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confidence: 99%

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Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry

Ozono

Zhang

Ode

et al. 2020

Preprint

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1The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe 2 acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is steadily mutating during continuous 3 transmission among humans. Such mutations can occur in the spike (S) protein that binds to the 4 angiotensin-converting enzyme-2 (ACE2) receptor and is cleaved by transmembrane protease 5 serine 2 (TMPRSS2). However, whether S mutations affect SARS-CoV-2 infectivity remains 6 unknown. Here, we show that naturally occurring S mutations can reduce or enhance cell entry 7 via ACE2 and TMPRSS2. A SARS-CoV-2 S-pseudotyped lentivirus exhibits substantially lower 8 entry than SARS-CoV S. Among S variants, the D614G mutant shows the highest viral entry, as 9 supported by structural observations. Nevertheless, the D614G mutant remains susceptible to 10 neutralization by antisera against prototypic viruses. Taken together, these data indicate that the 11 D614G mutation enhances viral infectivity while maintaining neutralization susceptibility. 12 13 3

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Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry

Ozono

Zhang

Ode

et al. 2020

Preprint

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“…Neutrality tests, Tajima’s D [18] and Fu’s Fs [19], to evaluate demographic effects were carried out using DnaSP v6.12 [14]. To date changes in the effective population size over time, we used Coalescent Bayesian Skyline Plot (BSP) analysis as implemented in BEAST v. 2.5 [20] with 8 × 10^ −4 subs per site per year substitution rate [8, 21]. Markov chains were run for 2.5 × 10 7 generations and sampled at every 1000 generations, with the first 1000 samples discarded as burn-in.…”

Section: Methodsmentioning

confidence: 99%

“…Study suggests that East Asian populations plausibly contained different susceptibility to coronavirus due to relatively higher ACE2 expression in tissues, a receptor for SARS-CoV-2 [5]. Due to severe havoc caused by coronavirus, scientists across the globe started analyzing viral genomes to address evolutionary history [6], phylogenetic relationship [7, 8], virus evolution [9] and entry routes in different countries [10, 11]. In this context, the Global Initiative on Sharing Avian Influenza Data (GISAID; https://www.gisaid.org/), founded in 2006, developed a dedicated coronavirus repository in December 2019.…”

Section: Introductionmentioning

confidence: 99%

How did SARS-CoV-19 spread in India from Italy, Iran and China? Genetic surveillance of early cases and virus demography

Thakur

Singh

Joshi

et al. 2020

Preprint

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SARS-CoV-19 after emerging from Wuhan, drastically devastated all sectors of human life by crushing down the global economy and increased psychological burden on public, government, and healthcare professionals. We manifested by analyzing 35 early coronavirus cases of India, that virus introduction in India, occurred from Italy, Iran and China and population demography apparently revealed a rapid population expansion after the outbreak with a present steady growth. We depicted nucleotide substitutions in structural genes, drove for the adaptive selection and plead for sequencing more genomes to facilitate identification of new emerged mutants, genetic evolution and disease transmission caused by coronavirus.

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Tuberous sclerosis complex (TSC), lymphangioleiomyomatosis, and COVID‐19: The experience of a TSC clinic in Italy

Peron

Briola

Bruschi

et al. 2020

American J of Med Genetics Pt A

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Individuals with comorbidities are at higher risk of coronavirus disease 2019 (COVID-19) and worse outcome, but little information has been available about patients with genetic diseases and COVID-19. This study aims at evaluating the presence and outcome of COVID-19 in a cohort of Italian patients with tuberous sclerosis complex (TSC) and/or lymphangioleiomyomatosis (LAM), and at reviewing the possible effects of mTOR inhibitors on SARS-CoV-2 infection. We included 102 unselected individuals with a diagnosis of TSC and/or LAM assessed between January 1, 2020 and April 24, 2020 (29% children, 71% adults). Twenty-six patients were on mTOR inhibitors. Demographic data, TSC manifestations, presence, and outcomes in individuals with confirmed or suspected SARS-CoV-2 infection were evaluated. Health status and outcomes of all patients on mTOR inhibitors were assessed. One patient with severe TSC had polymerase chain reaction (PCR)-confirmed SARS-CoV-2 infection, was admitted to ICU, and died. Nine additional patients either met the definition of suspect case or presented with at least two of the most common symptoms of SARS-CoV-2 infection. All recovered fully. None of the patients treated with mTOR inhibitors for their underlying comorbidities was diagnosed with COVID-19, and those who showed suspicious respiratory symptoms recovered fully. This cohort study provides preliminary information on COVID-19 in people with TSC in Italy and suggests feasibility to systematically evaluate the role of mTOR inhibitors in SARS-CoV-2 infection.

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Genomic characterization and phylogenetic analysis of SARS‐COV‐2 in Italy

Cited by 116 publications

References 14 publications

Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry

Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry

How did SARS-CoV-19 spread in India from Italy, Iran and China? Genetic surveillance of early cases and virus demography

Tuberous sclerosis complex (TSC), lymphangioleiomyomatosis, and COVID‐19: The experience of a TSC clinic in Italy

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