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3.
Viruses ; 14(6)2022 06 07.
Article in English | MEDLINE | ID: covidwho-1884389

ABSTRACT

Recombination is a common evolutionary tool for RNA viruses, and coronaviruses are no exception. We review here the evidence for recombination in SARS-CoV-2 and reconcile nomenclature for recombinants, discuss their origin and fitness, and speculate how recombinants could make a difference in the future of the COVID-19 pandemics.


Subject(s)
COVID-19 , Chiroptera , Animals , Phylogeny , Recombination, Genetic , SARS-CoV-2/genetics
4.
J Clin Virol Plus ; 2(3): 100084, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1851466
5.
Virol J ; 19(1): 79, 2022 05 13.
Article in English | MEDLINE | ID: covidwho-1846849

ABSTRACT

BACKGROUND: Torquetenovirus (TTV), a widespread anellovirus recognized as the main component of the healthy human virome, displays viremia that is highly susceptible to variations in immune competence. TTV possesses microRNA (miRNA)-coding sequences that might be involved in viral immune evasion. Among TTV-encoded miRNAs, miRNA t1a, t3b, and tth8 have been found in biological fluids. Here, the presence of TTV DNA and TTV miRNAs in the plasma of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected subjects was investigated to monitor the possible association with coronavirus disease 2019 (COVID-19) severity. METHODS: Detection of TTV DNA and miRNA t1a, t3b, and tth8 was investigated in plasma samples of 56 SARS-CoV-2-infected subjects with a spectrum of different COVID-19 outcomes. TTV DNA and TTV miRNAs were assessed with a universal single step real-time TaqMan PCR assay and miRNA quantitative RT-PCR miRNA assay, respectively. RESULTS: The TTV DNA prevalence was 59%, whereas at least one TTV miRNA was found in 94% of the patients tested. miRNA tth8 was detected in 91% of subjects, followed by miRNAs t3b (64%) and miRNAt1a (30%). Remarkably, although TTV DNA was unrelated to COVID-19 severity, miRNA tth8 was significantly associated with the degree of disease (adjusted incidence rate ratio (IRR) 2.04, 95% CI 1.14-3.63, for the subjects in the high severity group compared to those in the low severity group). CONCLUSIONS: Our findings encourage further investigation to understand the potential role of TTV miRNAs in the different outcomes of COVID-19 at early and late stages.


Subject(s)
COVID-19 , MicroRNAs , Torque teno virus , DNA, Viral/genetics , Humans , MicroRNAs/genetics , SARS-CoV-2/genetics , Torque teno virus/genetics
6.
J Clin Virol Plus ; 2(3): 100082, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1821341

ABSTRACT

Given the ongoing COVID19 pandemic, the decline in serological response since dose 2, and the upcoming flu season, COVID19 vaccines will increasingly be administered in combination with vaccines against seasonal pathogens. It is of interest to confirm that concurrent vaccination against influenzavirus has no negative impact on serological response to SARS CoV-2. Anti-Spike IgG and Anti-Receptor Binding Domain (RBD) Neutralizing Antibodies (NAb) in serum  was assessed in 64 immunocompetent healthcare workers (HCW) before and 14 days post the third dose of BNT162b2 vaccine (Comirnaty®, Pfizer/BioNTech) or BNT162b2 plus quadrivalent flu vaccine (Vaxigript Tetra ®Sanofi Pasteur) on the same day. We report here safety and efficacy of combined BNT162b2 and flu vaccine in 64 healthcare workers at a single institution. No differences were found in adverse events or anti-Spike antibody levels.

7.
Emerg Infect Dis ; 28(6): 1301-1302, 2022 06.
Article in English | MEDLINE | ID: covidwho-1789326

ABSTRACT

We report 25 cases of infection with SARS-CoV-2 Omicron variant containing spike protein L452R mutation in northern Lombardy, Italy. Prevalence of this variant was >30% in this region, compared with <0.5% worldwide. Many laboratories are using previously developed L452R-specific PCRs to discriminate Omicron from Delta mutations, but these tests may be unreliable.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Humans , Mutation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism
8.
Rev Med Virol ; : e2351, 2022 Apr 05.
Article in English | MEDLINE | ID: covidwho-1772841
9.
Vaccines (Basel) ; 10(3)2022 Mar 08.
Article in English | MEDLINE | ID: covidwho-1732278

ABSTRACT

During the ongoing COVID-19 pandemic, serology has suffered several manufacturing and budget bottlenecks. Kode technology exposes exogenous antigens on the surface of cells; in the case of red blood cells, modified cells are called kodecytes, making antibody-antigen reactions detectable by the old-fashioned hemagglutination test. In this commentary, we review evidence supporting the utility of SARS-CoV-2 Spike kodecytes for clinical diagnostic purposes and serosurveys in resource-poor settings.

10.
The New Microbiologica ; 44(4):205, 2021.
Article in English | ProQuest Central | ID: covidwho-1696320

ABSTRACT

The SARS-CoV-2 pandemic is ongoing worldwide, causing prolonged pressure on molecular diagnostics. Viral antigen (Ag) assays have several advantages, ranging from lower cost to shorter turnaround time to detection. Given the rare occurrence of low-load viremia, antigen assays for SARSCoV-2 have focused on nasopharyngeal swab and saliva as biological matrices, but their effectiveness must be validated. We assayed here the performances of the novel quantitative Liaison® SARSCoV-2 Ag assay on 119 nasopharyngeal swabs and obtained results were compared with Hologic Panther and Abbott m2000 RT-qPCR. The Ag assay demonstrated a good correlation with viral load, shorter turnaround time, and favorable economics. The best performance was obtained in the acute phase of disease.

12.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315957

ABSTRACT

(1) Background: Nicotine is implicated in the SARS-COV-2 infection through activation of the α7-nAChR and over-expression of ACE2. Our objective is to clarify the role of nicotine in SARS-CoV-2 infection exploring its molecular and cellular activity. (2) Methods: HBEpC or si-mRNA-α7-HBEpC were treated for 1, 48 h or continuously with 10-7 M Nicotine, a concentration mimicking human exposure to a cigarette. Cell viability and proliferation were evaluated by trypan blue dye exclusion and cell counting, migration by cell migration assay, senescence by SA-beta-Gal activity, and anchorage-independent growth by cloning in soft agar. Expression of Ki67, p53/phospho-p53, VEGF, EGFR/pEGFR, phospho-p38, intracellular Ca+2, ATP and EMT were evaluated by ELISA and/or western blotting. (3) Results: Nicotine induced through α7-nAChR (i) increase in cell viability (ii) cell proliferation;(iii) Ki67 over-expression, (iv) phospho-p38 up-regulation (v) EGFR/pEGFR over-expression;(vi) increase in basal Ca+2 concentration, (vii) reduction of ATP production;(viii) decreased level of p53/phospho-p53, (ix) delayed senescence, (x) VEGF increase, (xi) EMT and consequent (xii) enhanced migration, and (xiii) ability to grow independently of the substrate. (4) Conclusions: Based on our results and on evidence showing that Nicotine potentiates viral infection it is likely that Nicotine is involved in SARS-CoV-2 infection and severity

13.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-315452

ABSTRACT

BNT162b2 vaccine was introduced in Italy on 27th December 2020 and healthcare workers were rapidly vaccinated. In this study, we demonstrated that one vaccine dose was sufficient for eliciting a sustained humoral and cell-mediated response in SARS-CoV-2 experienced healthcare workers but had a lower effect in SARS-CoV-2 naïve subjects. However, 98% naïve subjects developed both neutralizing antibodies and Spike-specific T-cells after the second dose. Moreover, the antibody and T-cell responses were effective against viral variants since a partial reduction in antibody response was observed only against the South-African variant in SARS-CoV-2 naïve individuals, while the T-cell response was less affected.

14.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-314808

ABSTRACT

A growing number of emerging SARS-CoV-2 variants is being identified worldwide, potentially impacting the effectiveness of current vaccines. We report the data obtained in several Italian regions involved in the SARS-CoV-2 variant monitoring from the beginning of the epidemic and spanning the period from October 2020 to March 2021.

15.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-310568

ABSTRACT

Human respiratory beta coronavirus are emerging causes for Public Health Emergencies of International Concern (PHEIC). SARS-CoV2 is circulating worldwide since November 2019. We review here the cardiovascular morbidity and mortality in COVID-19, and data supporting the role for dysregulation of the RAS counterregulatory axis due to binding of SARS-CoV2 S protein to ACE2 receptor. Since this counterregulatory axis provides benefits not only on the cardiovascular front but also in acute lung injury, we speculate on potential use of ACE inhibitors and AT1R blockers in critically ill COVID-19 patients, and report current evidences.

16.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-310566

ABSTRACT

We report here the first in vivo selection of a Spike mutation (Q493R) conferring simultaneoius full resistance to both bamlanivimab and etesivimab.

18.
Free Radic Biol Med ; 180: 236-243, 2022 02 20.
Article in English | MEDLINE | ID: covidwho-1649942

ABSTRACT

The key role of inflammation in COVID-19 induced many authors to study the cytokine storm, whereas the role of other inflammatory mediators such as oxylipins is still poorly understood. IMPRECOVID was a monocentric retrospective observational pilot study with COVID-19 related pneumonia patients (n = 52) admitted to Pisa University Hospital between March and April 2020. Our MS-based analytical platform permitted the simultaneous determination of sixty plasma oxylipins in a single run at ppt levels for a comprehensive characterisation of the inflammatory cascade in COVID-19 patients. The datasets containing oxylipin and cytokine plasma levels were analysed by principal component analysis (PCA), computation of Fisher's canonical variable, and a multivariate receiver operating characteristic (ROC) curve. Differently from cytokines, the panel of oxylipins clearly differentiated samples collected in COVID-19 wards (n = 43) and Intensive Care Units (ICUs) (n = 27), as shown by the PCA and the multivariate ROC curve with a resulting AUC equal to 0.92. ICU patients showed lower (down to two orders of magnitude) plasma concentrations of anti-inflammatory and pro-resolving lipid mediators, suggesting an impaired inflammation response as part of a prolonged and unsolvable pro-inflammatory status. In conclusion, our targeted oxylipidomics platform helped shedding new light in this field. Targeting the lipid mediator class switching is extremely important for a timely picture of a patient's ability to respond to the viral attack. A prediction model exploiting selected lipid mediators as biomarkers seems to have good chances to classify patients at risk of severe COVID-19.


Subject(s)
COVID-19 , Oxylipins , Humans , Inflammation , Retrospective Studies , SARS-CoV-2
19.
Antiviral Res ; 198: 105247, 2022 02.
Article in English | MEDLINE | ID: covidwho-1632314

ABSTRACT

Massive usage of antiviral compounds during a pandemic creates an ideal ground for emergence of resistant strains. Remdesivir, a broad-spectrum inhibitor of the viral RNA-dependent RNA polymerase (RdRp), was extensively prescribed under emergency use authorization during the first 18 months of the COVID19 pandemic, before randomized controlled trials showed poor efficacy in hospitalized patients. RdRp mutations conferring resistance to remdesivir are well known from in vitro studies, and the huge SARS-CoV-2 sequencing effort during the ongoing COVID19 pandemic represents an unprecedented opportunity to assess emergence and fitness of antiviral resistance in vivo. We mined the GISAID database to extrapolate the frequency of remdesivir escape mutations. Our analysis reveals very low levels of remdesivir resistance worldwide despite massive usage.


Subject(s)
Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , Antiviral Agents/therapeutic use , COVID-19/drug therapy , Drug Resistance, Viral/genetics , SARS-CoV-2/genetics , Adenosine Monophosphate/therapeutic use , Alanine/therapeutic use , Drug Repositioning , Genome, Viral/genetics , Humans , Polyproteins/genetics , RNA-Dependent RNA Polymerase/antagonists & inhibitors , SARS-CoV-2/drug effects , Viral Proteins/genetics
20.
Viruses ; 14(2)2022 01 19.
Article in English | MEDLINE | ID: covidwho-1625188

ABSTRACT

Sterilizing immunity after vaccination is desirable to prevent the spread of infection from vaccinees, which can be especially dangerous in hospital settings while managing frail patients. Sterilizing immunity requires neutralizing antibodies at the site of infection, which for respiratory viruses such as SARS-CoV-2 implies the occurrence of neutralizing IgA in mucosal secretions. Systemic vaccination by intramuscular delivery induces no or low-titer neutralizing IgA against vaccine antigens. Mucosal priming or boosting, is needed to provide sterilizing immunity. On the other side of the coin, sterilizing immunity, by zeroing interhuman transmission, could confine SARS-CoV-2 in animal reservoirs, preventing spontaneous attenuation of virulence in humans as presumably happened with the endemic coronaviruses. We review here the pros and cons of each vaccination strategy, the current mucosal SARS-CoV-2 vaccines under development, and their implications for public health.


Subject(s)
COVID-19 Vaccines/immunology , COVID-19/prevention & control , Immunity, Mucosal/immunology , Mucous Membrane/immunology , SARS-CoV-2/immunology , SARS-CoV-2/pathogenicity , Animals , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , Disease Models, Animal , Humans , Immunoglobulin G/immunology , Mice , Spike Glycoprotein, Coronavirus/immunology , Virulence
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