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1.
Sci Rep ; 12(1): 5736, 2022 Apr 06.
Article in English | MEDLINE | ID: covidwho-1778634

ABSTRACT

The aims of this study were to characterize new SARS-CoV-2 genomes sampled all over Italy and to reconstruct the origin and the evolutionary dynamics in Italy and Europe between February and June 2020. The cluster analysis showed only small clusters including < 80 Italian isolates, while most of the Italian strains were intermixed in the whole tree. Pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 (20B) most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 (20D) developed most probably in other European countries entering Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, within the limitations of phylogeographical reconstruction, the estimated ancestral scenario suggests an important role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Communicable Disease Control , Europe/epidemiology , Genome, Viral/genetics , Humans , Italy/epidemiology , Phylogeography , SARS-CoV-2/genetics
2.
Vaccines (Basel) ; 10(3)2022 Mar 14.
Article in English | MEDLINE | ID: covidwho-1742765

ABSTRACT

Residents of long-term care facilities (LTCFs) have been dramatically hit by the COVID-19 pandemic on a global scale as older age and comorbidities pose an increased risk of severe disease and death. The aim of the study was to assess the quantity and durability of specific antibody responses to SARS-CoV-2 after the first cycle (two doses) of BNT162b2 vaccine. To achieve this, SARS-CoV-2 Spike-specific IgG (S-IgG) titers was evaluated in 432 residents of the largest Italian LTCF at months 2 and 6 after vaccination. By stratifying levels of humoral responses as high, medium, low and null, we did not find any difference when comparing the two time points; however, the median levels of antibodies halved overtime. As positive nucleocapsid serology was associated with a reduced risk of a suboptimal response at both time points, we conducted separate analyses accordingly. In subjects with positive serology, the median level of anti-S IgG slightly increased at the second time point, while a significant reduction was observed in patients without previous exposure to the virus. At month 6, diabetes alone was associated with an increased risk of impaired response. Our data provide additional insights into the longitudinal dynamics of the immune response to BNT162b2 vaccination in the elderly, highlighting the need for SARS-CoV-2 antibody monitoring following third-dose administration.

3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-314810

ABSTRACT

The aim of this study was the reconstruction of SARS-CoV-2 evolutionary dynamics in time and space in Italy and Europe between February and June 2020. The cluster analysis showed that pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 entered Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, the reconstructed ancestral scenario suggests a central role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.

4.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-314809

ABSTRACT

The aims of this study were to characterize new SARS-CoV-2 genomes sampled all over Italy and to reconstruct the origin and the evolutionary dynamics in Italy and Europe between February and June 2020. The cluster analysis showed only small clusters including <80 Italian isolates, while most of the Italian strains were intermixed in the whole tree. Pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 developed most probably in other European countries entering Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, the reconstructed ancestral scenario suggests a central role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.

5.
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.

6.
Front Immunol ; 12: 793191, 2021.
Article in English | MEDLINE | ID: covidwho-1608200

ABSTRACT

Purpose: To compare SARS-CoV-2 antigen-specific antibody production and plasma neutralizing capacity against B.1 wild-type-like strain, and Gamma/P.1 and Delta/B.1.617.2 variants-of-concern, in subjects with different Covid-19 disease and vaccination histories. Methods: Adult subjects were: 1) Unvaccinated/hospitalized for Covid-19; 2) Covid-19-recovered followed by one BNT162b2 vaccine dose; and 3) Covid-19-naïve/2-dose BNT162b2 vaccinated. Multiplex Luminex® immunoassays measured IgG, IgA, and IgM plasma levels against SARS-CoV-2 receptor-binding domain (RBD), spike-1 (S), and nucleocapsid proteins. Neutralizing activity was determined in Vero E6 cytopathic assays. Results: Maximum anti-RBD IgG levels were similar in Covid-19­recovered individuals 8‒10 days after single-dose vaccination and in Covid-19-naïve subjects 7 days after 2nd vaccine dosing; both groups had ≈2­fold higher anti-RBD IgG levels than Unvaccinated/Covid-19 subjects tracked through 2 weeks post-symptom onset. Anti-S IgG expression patterns were similar to RBD within each group, but with lower signal strengths. Viral antigen-specific IgA and IgM levels were more variable than IgG patterns. Anti-nucleocapsid immunoglobulins were not detected in Covid-19-naïve subjects. Neutralizing activity against the B.1 strain, and Gamma/P.1 and Delta/B.1.617.2 variants, was highest in Covid­19-recovered/single-dose vaccinated subjects; although neutralization against the Delta variant in this group was only 26% compared to B.1 neutralization, absolute anti-Delta titers suggested maintained protection. Neutralizing titers against the Gamma and Delta variants were 33‒77% and 26‒67%, respectively, versus neutralization against the B.1 strain (100%) in the three groups. Conclusion: These findings support SARS-CoV-2 mRNA vaccine usefulness regardless of Covid-19 history, and confirm remarkable protection provided by a single vaccine dose in people who have recovered from Covid-19.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/immunology , Immunoglobulin Isotypes/immunology , SARS-CoV-2/immunology , Adult , Aged , Aged, 80 and over , Animals , COVID-19/virology , Chlorocebus aethiops , Female , Humans , Immunoassay/methods , Immunoglobulin A/blood , Immunoglobulin A/immunology , Immunoglobulin G/blood , Immunoglobulin G/immunology , Immunoglobulin Isotypes/blood , Immunoglobulin M/blood , Immunoglobulin M/immunology , Male , Middle Aged , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/metabolism , Vaccination/methods , Vero Cells
7.
Open Forum Infect Dis ; 8(11): ofab217, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1526175

ABSTRACT

BACKGROUND: Immunocompromised patients show prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal swabs. We report a case of prolonged persistence of viable SARS-CoV-2 associated with clinical relapses of coronavirus disease 2019 (COVID-19) in a patient with mantle cell lymphoma who underwent treatment with rituximab, bendamustine, cytarabine with consequent lymphopenia and hypogammaglobulinemia. METHODS: Nasopharyngeal swabs and blood samples were tested for SARS-CoV-2 by real-time polymerase chain reaction (RT-PCR). On 5 positive nasopharyngeal swabs, we performed viral culture and next-generation sequencing. We analyzed the patient's adaptive and innate immunity to characterize T- and NK-cell subsets. RESULTS: SARS-CoV-2 RT-PCR on nasopharyngeal swabs samples remained positive for 268 days. All 5 performed viral cultures were positive, and genomic analysis confirmed a persistent infection with the same strain. Viremia resulted positive in 3 out of 4 COVID-19 clinical relapses and cleared each time after remdesivir treatment. The T- and NK-cell dynamic was different in aviremic and viremic samples, and no SARS-CoV-2-specific antibodies were detected throughout the disease course. CONCLUSIONS: In our patient, SARS-CoV-2 persisted with proven infectivity for >8 months. Viremia was associated with COVID-19 relapses, and remdesivir treatment was effective in viremia clearance and symptom remission, although it was unable to clear the virus from the upper respiratory airways. During the viremic phase, we observed a low frequency of terminal effector CD8+ T lymphocytes in peripheral blood; these are probably recruited in inflammatory tissue for viral eradication. In addition, we found a high level of NK-cell repertoire perturbation with relevant involvement during SARS-CoV-2 viremia.

8.
Acta Biomed ; 92(S6): e2021445, 2021 10 07.
Article in English | MEDLINE | ID: covidwho-1478882

ABSTRACT

INTRODUCTION: Nursing home residents were the most vulnerable population to be affected by Coronavirus disease 2019 (COVID-19) in Italy. The Italian vaccination strategy decided to indicate them as the target population in the first phase of the massive vaccination campaign. We carried out an analysis on an outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection which occurred in a nursing home in northern Italy (Cremona) after the administration of the complete vaccination cycle affecting most of the guests of the structure. METHODS: Data relating to the outbreak were obtained through the Regional Surveillance System for Infectious Diseases of Lombardia Region. RESULTS: During the outbreak, among the 61 guests, 56 were vaccinated. Thirty four were found positive for COVID-19: 22 were asymptomatic, 12 were symptomatic and 4 died. The observed difference in the number of deaths between vaccinated and non-vaccinated subjects was significant. During the outbreak 104 healthcare workers (HCWs) were employed in the nursing home, only 66 were vaccinated. Eight HCWs were found COVID-19 positive, 4 of them were vaccinated and of female gender. CONCLUSIONS: Similarly to data reported in literature for described outbreaks, we observed that the vaccine is able to protect from the symptomatic form and a valid antibody response protect from a symptomatic disease. The low number of HCWs found positive indicates a correct use of individual protective devices.


Subject(s)
COVID-19 , Disease Outbreaks , Female , Health Personnel , Humans , Nursing Homes , SARS-CoV-2
10.
Virol J ; 18(1): 168, 2021 08 14.
Article in English | MEDLINE | ID: covidwho-1359000

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.


Subject(s)
COVID-19/epidemiology , Epidemics , SARS-CoV-2/genetics , COVID-19/virology , Humans , Italy/epidemiology , Prevalence
12.
Pathogens ; 10(2)2021 Feb 23.
Article in English | MEDLINE | ID: covidwho-1100145

ABSTRACT

There have been previous reports of the human-to-cat transmission of SARS-CoV-2, but there are only a few molecular studies that have compared the whole genome of the virus in cats and their owners. We here describe a case of domestic SARS-CoV-2 transmission from a healthcare worker to his cat for which nasopharyngeal swabs of both the cat and its owner were used for full-genome analysis. The results indicate that quarantine measures should be extended to pets living in SARS-CoV-2-infected households.

13.
Blood Transfus ; 19(3): 181-189, 2021 05.
Article in English | MEDLINE | ID: covidwho-1067611

ABSTRACT

BACKGROUND: The Milan metropolitan area in Northern Italy was among the most severely hit by the SARS-CoV-2 outbreak. The aim of this study was to examine the seroprevalence trends of SARS-CoV-2 in healthy asymptomatic adults, and the risk factors and laboratory correlates of positive tests. MATERIALS AND METHODS: We conducted a cross-sectional study in a random sample of blood donors, who were asymptomatic at the time of evaluation, at the beginning of the first phase (February 24th to April 8th 2020; n=789). Presence of IgM/IgG antibodies against the SARS-CoV-2-Nucleocapsid protein was assessed by a lateral flow immunoassay. RESULTS: The test had a 100/98.3 sensitivity/specificity (n=32/120 positive/negative controls, respectively), and the IgG test was validated in a subset by an independent ELISA against the Spike protein (n=34, p<0.001). At the start of the outbreak, the overall adjusted seroprevalence of SARS-CoV-2 was 2.7% (95% CI: 0.3-6%; p<0.0001 vs 120 historical controls). During the study period, characterised by a gradual implementation of social distancing measures, there was a progressive increase in the adjusted seroprevalence to 5.2% (95% CI: 2.4-9.0; 4.5%, 95% CI: 0.9-9.2% according to a Bayesian estimate) due to a rise in IgG reactivity to 5% (95% CI: 2.8-8.2; p=0.004 for trend), but there was no increase in IgM+ (p=not significant). At multivariate logistic regression analysis, IgG reactivity was more frequent in younger individuals (p=0.043), while IgM reactivity was more frequent in individuals aged >45 years (p=0.002). DISCUSSION: SARS-CoV-2 infection was already circulating in Milan at the start of the outbreak. The pattern of IgM/IgG reactivity was influenced by age: IgM was more frequently detected in participants aged >45 years. By the end of April, 2.4-9.0% of healthy adults had evidence of seroconversion.


Subject(s)
Asymptomatic Infections/epidemiology , Blood Donors/statistics & numerical data , COVID-19/epidemiology , Pandemics , SARS-CoV-2/immunology , Adult , Age Factors , Antibodies, Viral/blood , Bayes Theorem , COVID-19/immunology , COVID-19 Serological Testing/methods , Confidence Intervals , Cross-Sectional Studies , Female , Humans , Immunoglobulin G/blood , Immunoglobulin M/blood , Italy/epidemiology , Male , Middle Aged , Regression Analysis , Risk Factors , Seroconversion , Seroepidemiologic Studies , Spike Glycoprotein, Coronavirus/immunology
14.
Occup Environ Med ; 2021 Feb 04.
Article in English | MEDLINE | ID: covidwho-1066929

ABSTRACT

OBJECTIVES: Healthcare workers (HCWs) are at high risk of developing SARS-CoV-2 infection. The aim of this single-centre prospective study was to evaluate the trend of SARS-CoV-2 seroprevalence in HCWs working at the primary referral centre for infectious diseases and bioemergencies (eg, COVID-19) in Northern Italy and investigate the factors associated with seroconversion. METHODS: Six hundred and seventy-nine HCW volunteers were tested for anti-SARS-CoV-2 antibodies three times between 4 March and 27 May 2020 and completed a questionnaire covering COVID-19 exposure, symptoms and personal protective equipment (PPE) training and confidence at each time. RESULTS: SARS-CoV-2 seroprevalence rose from 3/679 to 26/608 (adjusted prevalence: 0.5%, 95% CI 0.1 to 1.7% and 5.4%, 95% CI 3.6 to 7.9, respectively) between the first two time points and then stabilised, in line with the curve of the COVID-19 epidemic in Milan. From the first time point, 61.6% of the HCWs had received training in the use of PPE and 17 (61.5%) of those who proved to be seropositive reported symptoms compatible with SARS-CoV-2 infection. Contacts with ill relatives or friends and self-reported symptoms were independently associated with an increased likelihood of seroconversion (p<0.0001 for both), whereas there was no significant association with professional exposure. CONCLUSION: The seroprevalence of SARS-CoV-2 among the HCWs at our COVID-19 referral hospital was low at the time of the peak of the epidemic. The seroconversions were mainly attributable to extrahospital contacts, probably because the hospital readily adopted effective infection control measures. The relatively high number of asymptomatic seropositive HCWs highlights the need to promptly identify and isolate potentially infectious HCWs.

15.
Viruses ; 12(8)2020 07 24.
Article in English | MEDLINE | ID: covidwho-670832

ABSTRACT

The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly-characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.


Subject(s)
Betacoronavirus/classification , Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Bayes Theorem , Betacoronavirus/isolation & purification , COVID-19 , Epidemiological Monitoring , Genome, Viral , Humans , Italy/epidemiology , Likelihood Functions , Molecular Epidemiology , Molecular Typing , Mutation , Phylogeny , SARS-CoV-2 , Time Factors , Whole Genome Sequencing
16.
J Med Virol ; 92(9): 1637-1640, 2020 Sep.
Article in English | MEDLINE | ID: covidwho-87346

ABSTRACT

This report describes the isolation, molecular characterization, and phylogenetic analysis of the first three complete genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolated from three patients involved in the first outbreak of COVID-19 in Lombardy, Italy. Early molecular epidemiological tracing suggests that SARS-CoV-2 was present in Italy weeks before the first reported cases of infection.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Genome, Viral , Genomics , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/genetics , Computational Biology/methods , Genomics/methods , Humans , Italy/epidemiology , Regression Analysis
17.
J Med Virol ; 92(6): 675-679, 2020 06.
Article in English | MEDLINE | ID: covidwho-1969

ABSTRACT

To reconstruct the evolutionary dynamics of the 2019 novel-coronavirus recently causing an outbreak in Wuhan, China, 52 SARS-CoV-2 genomes available on 4 February 2020 at Global Initiative on Sharing All Influenza Data were analyzed. The two models used to estimate the reproduction number (coalescent-based exponential growth and a birth-death skyline method) indicated an estimated mean evolutionary rate of 7.8 × 10-4 subs/site/year (range, 1.1 × 10-4 -15 × 10-4 ) and a mean tMRCA of the tree root of 73 days. The estimated R value was 2.6 (range, 2.1-5.1), and increased from 0.8 to 2.4 in December 2019. The estimated mean doubling time of the epidemic was between 3.6 and 4.1 days. This study proves the usefulness of phylogeny in supporting the surveillance of emerging new infections even as the epidemic is growing.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Genome, Viral , Models, Statistical , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , Base Sequence , Bayes Theorem , Betacoronavirus/classification , Betacoronavirus/isolation & purification , Betacoronavirus/pathogenicity , COVID-19 , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Epidemiological Monitoring , Evolution, Molecular , Humans , Information Dissemination , Open Reading Frames , Phylogeny , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , RNA, Viral/genetics , SARS-CoV-2 , Sequence Alignment , Sequence Homology, Nucleic Acid
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