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2.
The European respiratory journal ; 2022.
Article in English | EuropePMC | ID: covidwho-1958253

ABSTRACT

Chronic exposure to ambient air pollution has been related to increased mortality in the general population [1]. After the outbreak of SARS-CoV-2 pandemic in 2019, there has been a fast proliferation of epidemiological studies linking ambient air pollution to COVID-19 incidence or adverse prognosis [2]. It has been hypothesised that ambient air pollution might increase human vulnerability to viruses by reducing immune defences, promoting a low-level chronic inflammatory state, or leading to chronic diseases [3]. Most studies applied ecological designs, and failed to account for key individual-level or area-level determinants of COVID-19 spread or severity, such as demographic characteristics of the studied populations, socioeconomic or clinical susceptibility, and area-level proxies of disease spread such as mobility or population density [4].

3.
Epidemiol Prev ; 46(4): 59-69, 2022.
Article in Italian | MEDLINE | ID: covidwho-1955239

ABSTRACT

OBJECTIVES: to quantify the variability of COVID-19 mortality from the beginning of the pandemic to mid-July 2021, in relation to the immigrant status and by Region and period. DESIGN: observational incidence study. SETTING AND PARTICIPANTS: the study population consists of the residents at the beginning of 2020 in seven Regions (Piedmont, Lombardy, Veneto, Emilia-Romagna, Tuscany, Lazio, Sicily) aged <=74 years. MAIN OUTCOME MEASURES: absolute frequency of deaths occurred in subjects who tested positive for SARS-CoV-2, crude and standardized rates (standard: Italian population at the beginning of 2020), and mortality rates ratios (obtained using Poisson models), by immigrant status and stratified by gender, Region of residence, and period. The study period was divided into 5 subperiods: 22.02.2020-25.05.2020, 26.05.2020-02.10.2020, 03.10.2020-26.02.2021, 27.02.2021-16.07.2021. RESULTS: the study includes more than one half of the Italian population and most of the immigrants residing in the country, who are younger than Italians and experienced fewer COVID-19 deaths. Deaths among those who tested positive varied greatly between Regions and periods; standardized rates showed considerable increases over time among immigrants. In terms of rate ratios, there were excesses among immigrant males in the third period (MRR: 1.46; 95%CI 1.30-1.65) and in the fourth period (MRR: 1.55; 95%CI 1, 34-1.81). Among immigrant females, there is an indication of lower risk in the third period (MRR: 0.79; 95%CI 0.65-0.97) and of greater risk in the fourth period (MRR: 1. 46; 95%CI 1.21-1.77). Finally, the effect is modified by the Region of residence, both in the third and in the fourth period for males and only in the fourth period for females. CONCLUSIONS: the risk of premature mortality due to COVID-19 is linked to immigrant status and with an intensity that varies by gender, Region, and period. More accessible tools for prevention, diagnosis and early healthcare can support immigrant communities in managing the risk factors linked to the spread of infections and, in particular, counteract their evolution into more severe disease outcomes.


Subject(s)
COVID-19 , Emigrants and Immigrants , Citizenship , Female , Humans , Italy/epidemiology , Male , Pandemics , SARS-CoV-2 , Sicily
4.
Epidemiol Prev ; 46(1-2): 59-67, 2022.
Article in Italian | MEDLINE | ID: covidwho-1856463

ABSTRACT

OBJECTIVES: to estimate the impact of the COVID-19 epidemic on total and cause-specific mortality in people residing and dead in the Municipality of Rome (Italy) in 2020, and to describe the causes of death of subjects with SARS-CoV-2 infection confirmed by molecular test. DESIGN: descriptive analysis of total and cause-specific mortality in 2020 in Rome and comparison with a reference period (2015-2018 for total mortality and 2018 for cause-specific mortality); descriptive analysis of cause-specific mortality in the cohort of SARS-CoV-2 infected subjects. SETTING AND PARTICIPANTS: 27,471 deaths registered in the Lazio mortality-cause Registry, relating to people residing and died in the municipality of Rome in 2020, 2,374 of which died from COVID-19.MAIN OUCOME MEASURES: all-cause mortality by month, gender, age group and place of death, cause-specific mortality (ICD-10 codes). RESULTS: in the municipality of Rome in 2020, an excess of mortality from all causes equal to +10% was observed, with a greater increase in the months of October-December (+27%, +56%, and +26%, respectively) in people aged 50+, with the greatest contribution from the oldest age groups (80+) who died in the nursing homes or at home. Lower mortality was observed in the age groups 0-29 years (-30%) and 40-49 years (-13%). In 2020, COVID-19 represents the fourth cause of death in Rome after malignant tumours, diseases of the circulatory system, and respiratory diseases. Excess mortality was observed from stroke and pneumonia (both in men and women), from respiratory diseases (in men), from diabetes, mental disorders, dementia and Parkinson's disease (in women). On the contrary, mortality is lower for all cancers, for diseases of the blood and haematopoietic organs and for the causes of the circulatory system. The follow-up analysis of SARS-CoV-2 positive subjects residing in Rome shows that a share of deaths (about 20%) reports other causes of death such as cardiovascular diseases, malignant tumours, and diseases of the respiratory system on the certificate collected by the Italian National Statistics Institute. CONCLUSIONS: the 2020 mortality study highlighted excesses for acute and chronic pathologies, indicative of possible delays in the diagnosis or treatment of conditions indirectly caused by the pandemic, but also a share of misclassification of the cause of death that is recognized as COVID-19 death.


Subject(s)
COVID-19 , Adolescent , Adult , Cause of Death , Child , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Italy/epidemiology , Male , Middle Aged , Rome/epidemiology , SARS-CoV-2 , Young Adult
5.
Expert Rev Vaccines ; 21(8): 1147-1157, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1852791

ABSTRACT

BACKGROUND: The waning of the protective effect of COVID-19 vaccines and timing of booster doses are debated. METHODS: Population-based cohort study in the largest Health-Authority of Lazio region, Italy, on 946,156 residents aged 12+ (study period: 1 January 2021-10 January 2022). Vaccine effectiveness (VE) against any SARS-CoV-2 infection (symptomatic or asymptomatic) was estimated through multivariable negative-binomial models using unvaccinated person-time as a reference. RESULTS: The primary vaccination cycle was completed by 81% of residents; of these, 45% received a booster dose. Vaccine coverages were lower for foreigners, and people living in deprived areas, families with children aged 0-11, and households size 1 or 6+. Overall, VE waned from 71% (95% Confidence Interval (CI) 70-73%) 1 month after the second dose to 43% (CI 41-45%) after 4 months and 24% (CI 21-27%) after 6 months, especially in the elderly aged 70+. We observed a prompt restore of VE 15-19 days after the booster dose (69%, CI 67-70%). CONCLUSIONS: Our results support the recommendation of a booster dose 4 months after completion of the primary cycle, giving priority to elderly and fragile individuals. The lower vaccine coverage among social disadvantaged subgroups suggests the need of targeted communication and interventions.


Subject(s)
COVID-19 , Vaccines , Aged , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Vaccines , Child , Cohort Studies , Humans , SARS-CoV-2
6.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-314865

ABSTRACT

Background: More detailed temporal analyses of complete (Full) blood count (CBC) parameters, their evolution and relationship to patient age, gender, co-morbidities and management outcomes in survivors and non-survivors with COVID-19 disease could help identify prognostic clinical biomarkers. Methods: From 29 January 2020 until 28 March 2020, we performed a longitudinal cohort study of COVID-19 inpatients at the Italian National Institute for Infectious Diseases, Rome, Italy. Nine CBC parameters as a continuous variable were studied [neutrophils, lymphocytes, monocytes, platelets, mean platelet volume, red blood cell count, haemoglobin concentration, mean red blood cell volume and red blood cell distribution width (RDW %)]. Model-based punctual estimates and difference between survivors and non-survivors, overall, and by co-morbidities, at specific times after symptoms, with relative 95% CI and P-values were obtained by marginal prediction and ANOVA-style joint tests. All analyses were carried out by STATA 15 statistical package. Main Findings: 379 COVID-19 patients [273 (72% were male;mean age was 61.67 (SD 15.60)] were enrolled and 1,805 measures per parameter were analysed. Neutrophil counts were on average significantly higher in non-survivors than in survivors (P<0.001) and lymphocytes were on average higher in survivors (P<0.001). These differences were time dependent. Reverse temporal trends were observed for lymphocyte and neutrophil counts in survivors and non-survivors. Average platelets counts (P<0.001) and median platelets volume (P<0.001) were significantly different in survivors and in non-survivors. The differences were time dependent and consistent with acute inflammation followed either by recovery or by death. Anaemia with anisocytosis were observed in the later phase of COVID-19 disease in non-survivors only. Mortality was significantly higher in patients with diabetes (p=0.005), obesity (p=0.010), chronic renal failure (p=0.001), COPD (p=0.033) cardiovascular diseases (p=0.001) and those >60 years(p=0.001). Age (p=0.042), obesity (p=0.002), chronic renal failure (p=0.002) and cardiovascular diseases (p=0.009) were independently associated with poor patient clinical outcome at 30 day after symptom onset. Interpretation: Increased neutrophil counts, reduced lymphocyte counts, higher median platelet volume, anemia with anisocytosis, in association with obesity, chronic renal failure, COPD, cardiovascular diseases and age >60 years predict poor prognosis in COVID19 patients.Funding Statement: Ricerca Corrente e Finalizzata Italy Ministry of Health, AIRC (IG2018-21880);Regione Lazio (Gruppi di ricerca, E56C18000460002).Declaration of Interests: The authors declare no competing interest.Ethics Approval Statement: This study was approved by the IRB of Italian National Institute for Infectious Diseases “Lazzaro Spallanzani” (INMI), in Rome (Italy).

7.
Front Med (Lausanne) ; 8: 815870, 2021.
Article in English | MEDLINE | ID: covidwho-1674353

ABSTRACT

BACKGROUND: Vaccines for coronavirus disease 2019 (COVID-19) are proving to be very effective in preventing severe illness; however, although rare, post-vaccine infections have been reported. The present study focuses on virological and serological features of 94 infections that occurred in Lazio Region (Central Italy) between 27 December 2020, and 30 March 2021, after one or two doses of mRNA BNT162b2 vaccine. METHODS: We evaluated clinical features, virological (viral load; viral infectiousness; genomic characterisation), and serological (anti-nucleoprotein Ig; anti-Spike RBD IgG; neutralising antibodies, nAb) characteristics of 94 post-vaccine infections at the time of diagnosis. Nasopharyngeal swabs (NPSs) and serum samples were collected in the framework of the surveillance activities on SARS-CoV-2 variants established in Lazio Region (Central Italy) and analysed at the National Institute for Infectious Diseases "L. Spallanzani" in Rome. RESULTS: The majority (92.6%) of the post-vaccine infections showed pauci/asymptomatic or mild clinical course, with symptoms and hospitalisation rate significantly less frequent in patients infected after full vaccination course as compared to patients who received a single dose vaccine. Although differences were not statistically significant, viral loads and isolation rates were lower in NPSs from patients infected after receiving two vaccine doses as compared to patients with one dose. Most cases (84%) had nAb in serum at the time of infection diagnosis, which is a sub-group of vaccinees, were found similarly able to neutralise Alpha and Gamma variants. Asymptomatic individuals showed higher nAb titres as compared to symptomatic cases (median titre: 1:120 vs. 1:40, respectively). Finally, the proportion of post-vaccine infections attributed either to Alpha and Gamma variants was similar to the proportion observed in the contemporary unvaccinated population in the Lazio region, and mutational analysis did not reveal enrichment of a defined set of Spike protein substitutions depending on the vaccination status. CONCLUSION: Our study conducted using real-life data, emphasised the importance of monitoring vaccine breakthrough infections, through the characterisation of virological, immunological, and clinical features associated with these events, in order to tune prevention measures in the next phase of the COVID-19 pandemic.

8.
Viruses ; 13(6)2021 06 17.
Article in English | MEDLINE | ID: covidwho-1286941

ABSTRACT

In European countries, autochthonous acute hepatitis E cases are caused by Hepatitis E Virus (HEV) genotype 3 and are usually observed as sporadic cases. In mid/late September 2019, a hepatitis E outbreak caused by HEV genotype 3 was recognized by detection of identical/highly similar HEV sequences in some hepatitis E cases from two Italian regions, Abruzzo and Lazio, with most cases from this latter region showing a link with Abruzzo. Overall, 47 cases of HEV infection were finally observed with onsets from 8 June 2019 to 6 December 2019; they represent a marked increase as compared with just a few cases in the same period of time in the past years and in the same areas. HEV sequencing was successful in 35 cases. The phylogenetic analysis of the viral sequences showed 30 of them grouped in three distinct molecular clusters, termed A, B, and C: strains in cluster A and B were of subtype 3e and strains in cluster C were of subtype 3f. No strains detected in Abruzzo in the past years clustered with the strains involved in the present outbreak. The outbreak curve showed partially overlapped temporal distribution of the three clusters. Analysis of collected epidemiological data identified pork products as the most likely source of the outbreak. Overall, the findings suggest that the outbreak might have been caused by newly and almost simultaneously introduced strains not previously circulating in this area, which are possibly harbored by pork products or live animals imported from outside Abruzzo. This possibility deserves further studies in this area in order to monitor the circulation of HEV in human cases as well as in pigs and wild boars.


Subject(s)
Disease Outbreaks , Genotype , Hepatitis E virus/classification , Hepatitis E virus/genetics , Hepatitis E/epidemiology , Hepatitis E/transmission , Adult , Aged , Aged, 80 and over , Animals , Female , Hepatitis E/virology , Hepatitis E virus/pathogenicity , Humans , Italy/epidemiology , Male , Middle Aged , Phylogeny , Pork Meat/virology , RNA, Viral , Risk Factors , Sus scrofa/virology , Swine , Swine Diseases/transmission , Swine Diseases/virology
9.
Biomolecules ; 11(3)2021 03 13.
Article in English | MEDLINE | ID: covidwho-1136455

ABSTRACT

COVID-19 pandemic is a dramatic health, social and economic global challenge. There is urgent need to maximize testing capacity. Rapid Antigen Tests (RAT) represent good candidates for point-of-care and mass surveillance testing to rapidly identify SARS-CoV-2-infected people, counterbalancing lower sensitivity vs. gold standard molecular tests with fast results and possible recurrent testing. We describe the results obtained with the testing algorithm implemented at points of entry (airports and ports) in the Lazio Region (Italy), using the STANDARD F COVID-19 Antigen Fluorescence ImmunoAssay (FIA), followed by molecular confirmation of FIA-positive samples. From mid-August to mid-October 2020, 73,643 RAT were reported to the Regional Surveillance Information System for travelers at points of entry in Lazio Region. Of these, 1176 (1.6%) were FIA-positive, and the proportion of RT-PCR-confirmed samples was 40.5%. Our data show that the probability of confirmation was directly dependent from the semi-quantitative FIA results. In addition, the molecularly confirmed samples were those with high levels of virus and that were actually harboring infectious virus. These results support public health strategies based on early mass screening campaigns by RAT in settings where molecular testing is not feasible or easily accessible, such as points of entry. This approach would contribute to promptly controlling viral spread through travel, which is now of particular concern due to the spread of SARS-CoV-2 variants.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Immunoassay/methods , Mass Screening/methods , SARS-CoV-2/isolation & purification , Animals , Antigens, Viral/immunology , COVID-19/immunology , Chlorocebus aethiops , Humans , Italy , Pandemics/prevention & control , Point-of-Care Testing , ROC Curve , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Sensitivity and Specificity , Vero Cells
10.
Front Genet ; 12: 625607, 2021.
Article in English | MEDLINE | ID: covidwho-1106023

ABSTRACT

We report phylogenetic and mutational analysis by NGS of six SARS-CoV-2 strains from patients flying from Bangladesh to Italy (July 2020). Data suggest that no further circulation of such imported strains occurred in Italy, stating the efficacy of early screening at the point of entry and supporting the importance of molecular epidemiology in monitoring the efficacy of control measures.

11.
Epidemiol Prev ; 44(5-6 Suppl 2): 144-151, 2020.
Article in Italian | MEDLINE | ID: covidwho-1068134

ABSTRACT

BACKGROUND: one of the most affected European countries by the COVID-19 epidemic is Italy; data show the strong geographical heterogeneity of the epidemic. OBJECTIVES: to propose an analysis strategy to ascertain the non-random nature of the spatial spread of COVID-19 cases infection and identify any territorial aggregations, in order to enhance contact tracing activities in specific areas of the Lazio Region (Central Italy) and a large urban area as Rome. METHODS: all cases of COVID-19 of the Lazio Region notified to the Regional Service for Epidemiology, Surveillance, and Control of Infectious Diseases (Seresmi) with daily updates from the beginning of the epidemic to April 27, 2020 were considered. The analyses were carried out considering two periods (the first from the beginning of the epidemic to April 6 and the second from the beginning of the epidemic to April 27) and two different levels of spatial aggregation: the entire Lazio region excluding the Municipality of Rome, where the 377 municipalities represent the area units, and the Municipality of Rome, where the area units under study are the 155 urban areas (ZUR). The Scan statistic of Kulldorff was used to ascertain the non-random nature of the spatial spread of infected cases and to identify any territorial aggregations of cases of COVID-19 infection, using a retrospective spatial analysis in two overlapping periods. RESULTS: analysis was conducted at regional level in the two survey periods and revealed the presence of 7 localized clusters. In the Municipality of Rome, a single cluster (Historic Centre) was identified in the first period which includes 7 urban areas, while in the second period two distinct clusters (Omo and Farnesina) were observed. CONCLUSIONS: Scan statistics are an important surveillance tool for monitoring disease outbreaks during the active phase of the epidemic and a useful contribution to epidemiological surveillance during the COVID-19 epidemic in a specific territory.


Subject(s)
COVID-19/epidemiology , Pandemics , SARS-CoV-2 , Spatial Analysis , COVID-19/transmission , Cluster Analysis , Geography, Medical , Humans , Italy/epidemiology , Population Surveillance , Retrospective Studies , Rome/epidemiology , Urban Health
12.
PLoS One ; 15(12): e0244129, 2020.
Article in English | MEDLINE | ID: covidwho-999830

ABSTRACT

BACKGROUND: Detailed temporal analyses of complete (full) blood count (CBC) parameters, their evolution and relationship to patient age, gender, co-morbidities and management outcomes in survivors and non-survivors with COVID-19 disease, could identify prognostic clinical biomarkers. METHODS: From 29 January 2020 until 28 March 2020, we performed a longitudinal cohort study of COVID-19 inpatients at the Italian National Institute for Infectious Diseases, Rome, Italy. 9 CBC parameters were studied as continuous variables [neutrophils, lymphocytes, monocytes, platelets, mean platelet volume, red blood cell count, haemoglobin concentration, mean red blood cell volume and red blood cell distribution width (RDW %)]. Model-based punctual estimates, as average of all patients' values, and differences between survivors and non-survivors, overall, and by co-morbidities, at specific times after symptoms, with relative 95% CI and P-values, were obtained by marginal prediction and ANOVA- style joint tests. All analyses were carried out by STATA 15 statistical package. MAIN FINDINGS: 379 COVID-19 patients [273 (72% were male; mean age was 61.67 (SD 15.60)] were enrolled and 1,805 measures per parameter were analysed. Neutrophils' counts were on average significantly higher in non-survivors than in survivors (P<0.001) and lymphocytes were on average higher in survivors (P<0.001). These differences were time dependent. Average platelets' counts (P<0.001) and median platelets' volume (P<0.001) were significantly different in survivors and non-survivors. The differences were time dependent and consistent with acute inflammation followed either by recovery or by death. Anaemia with anisocytosis was observed in the later phase of COVID-19 disease in non-survivors only. Mortality was significantly higher in patients with diabetes (OR = 3.28; 95%CI 1.51-7.13; p = 0.005), obesity (OR = 3.89; 95%CI 1.51-10.04; p = 0.010), chronic renal failure (OR = 9.23; 95%CI 3.49-24.36; p = 0.001), COPD (OR = 2.47; 95% IC 1.13-5.43; p = 0.033), cardiovascular diseases (OR = 4.46; 95%CI 2.25-8.86; p = 0.001), and those >60 years (OR = 4.21; 95%CI 1.82-9.77; p = 0.001). Age (OR = 2.59; 95%CI 1.04-6.45; p = 0.042), obesity (OR = 5.13; 95%CI 1.81-14.50; p = 0.002), renal chronic failure (OR = 5.20; 95%CI 1.80-14.97; p = 0.002) and cardiovascular diseases (OR 2.79; 95%CI 1.29-6.03; p = 0.009) were independently associated with poor clinical outcome at 30 days after symptoms' onset. INTERPRETATION: Increased neutrophil counts, reduced lymphocyte counts, increased median platelet volume and anaemia with anisocytosis, are poor prognostic indicators for COVID19, after adjusting for the confounding effect of obesity, chronic renal failure, COPD, cardiovascular diseases and age >60 years.


Subject(s)
COVID-19/blood , Biomarkers/blood , Blood Cell Count , COVID-19/immunology , Cohort Studies , Demography/methods , Erythrocyte Indices/immunology , Female , Humans , Inflammation/blood , Inflammation/immunology , Leukocyte Count/methods , Longitudinal Studies , Lymphocytes/immunology , Male , Mean Platelet Volume/methods , Middle Aged , Neutrophils/immunology , Prognosis , Rome , Survivors
14.
SSRN; 2020.
Preprint | SSRN | ID: ppcovidwho-705

ABSTRACT

Background: Italy is undergoing an unprecedented COVID-1 epidemic - one of the largest and most lethal outbreaks outside China. The higher death rate observed c

15.
J Clin Virol ; 129: 104539, 2020 08.
Article in English | MEDLINE | ID: covidwho-633896

ABSTRACT

BACKGROUND: Serological tests for anti-SARS-CoV-2 antibodies are becoming of great interest to determine seroprevalence in a given population, define previous exposure and identify highly reactive human donors for the generation of convalescent serum as therapeutic. OBJECTIVES: We evaluated the diagnostic performance of the Abbott ARCHITECT SARS-CoV-2 IgG test, a fully automated indirect immunoassay that detects antibodies directed to a recombinant SARS-CoV-2 Nucleocapsid antigen. STUDY DESIGN: Abbott ARCHITECT SARS-CoV-2 IgG immunoassay was compared to an indirect immunofluorescence assay (IFA) on sera from patients with COVID-19 collected at different days after symptoms onset or infected by other human coronaviruses. Comparison with neutralization test was also performed. RESULTS: After 7, 14 and >14 days after onset ARCHITECT was positive on 8.3 %; 61.9 % and 100 % of the tested samples compared to 58.3 %; 85.7 % and 100 % by IFA. The sensitivity was 72 % vs. IFA and 66.7 % vs. a real-time PCR, the specificity was 100 %. On 18 samples with neutralizing activity, 17 were positive by Abbott ARCHITECT SARS-CoV-2 IgG. CONCLUSIONS: In our study, Abbott ARCHITECT SARS-CoV-2 IgG assay showed a satisfactory performance, with a very high specificity. IgG reactivity against SARSCoV-2 N antigen was detectable in all patients by two weeks after symptoms onset. In addition, concordance between this serological response and viral neutralization suggests that a strong humoral response may be predictive of a neutralization activity, regardless of the target antigens. This finding supports the use of this automated serological assay in diagnostic algorithm and public health intervention, especially for high loads of testing.


Subject(s)
Antibodies, Viral/blood , Betacoronavirus/immunology , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Fluorescent Antibody Technique, Indirect/methods , Neutralization Tests/methods , Pneumonia, Viral/diagnosis , Serologic Tests/methods , Adolescent , Adult , Aged , Aged, 80 and over , Antibodies, Neutralizing/blood , COVID-19 , COVID-19 Testing , Child , Child, Preschool , Female , Humans , Immunoglobulin G/blood , Infant , Infant, Newborn , Male , Middle Aged , Pandemics , SARS-CoV-2 , Sensitivity and Specificity , Young Adult
16.
J Transl Med ; 18(1): 233, 2020 06 10.
Article in English | MEDLINE | ID: covidwho-592324

ABSTRACT

BACKGROUND: Epidemiological, virological and pathogenetic characteristics of SARS-CoV-2 infection are under evaluation. A better understanding of the pathophysiology associated with COVID-19 is crucial to improve treatment modalities and to develop effective prevention strategies. Transcriptomic and proteomic data on the host response against SARS-CoV-2 still have anecdotic character; currently available data from other coronavirus infections are therefore a key source of information. METHODS: We investigated selected molecular aspects of three human coronavirus (HCoV) infections, namely SARS-CoV, MERS-CoV and HCoV-229E, through a network based-approach. A functional analysis of HCoV-host interactome was carried out in order to provide a theoretic host-pathogen interaction model for HCoV infections and in order to translate the results in prediction for SARS-CoV-2 pathogenesis. The 3D model of S-glycoprotein of SARS-CoV-2 was compared to the structure of the corresponding SARS-CoV, HCoV-229E and MERS-CoV S-glycoprotein. SARS-CoV, MERS-CoV, HCoV-229E and the host interactome were inferred through published protein-protein interactions (PPI) as well as gene co-expression, triggered by HCoV S-glycoprotein in host cells. RESULTS: Although the amino acid sequences of the S-glycoprotein were found to be different between the various HCoV, the structures showed high similarity, but the best 3D structural overlap shared by SARS-CoV and SARS-CoV-2, consistent with the shared ACE2 predicted receptor. The host interactome, linked to the S-glycoprotein of SARS-CoV and MERS-CoV, mainly highlighted innate immunity pathway components, such as Toll Like receptors, cytokines and chemokines. CONCLUSIONS: In this paper, we developed a network-based model with the aim to define molecular aspects of pathogenic phenotypes in HCoV infections. The resulting pattern may facilitate the process of structure-guided pharmaceutical and diagnostic research with the prospect to identify potential new biological targets.


Subject(s)
Betacoronavirus/physiology , Coronavirus Infections/genetics , Coronavirus Infections/virology , Gene Regulatory Networks , Host-Pathogen Interactions , Models, Biological , Pneumonia, Viral/genetics , Pneumonia, Viral/virology , Protein Interaction Mapping , COVID-19 , Humans , Membrane Glycoproteins/metabolism , Pandemics , SARS-CoV-2 , Signal Transduction/genetics , Viral Envelope Proteins
17.
Emerg Infect Dis ; 26(8): 1842-1845, 2020 08.
Article in English | MEDLINE | ID: covidwho-403054

ABSTRACT

We report phylogenetic and mutational analysis of severe acute respiratory syndrome coronavirus 2 virus strains from the Lazio region of Italy and provide information about the dynamics of virus spread. Data suggest effective containment of clade V strains, but subsequently, multiple waves of clade G strains were circulating widely in Europe.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Pandemics , Phylogeny , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , RNA, Viral/genetics , Adult , Aged , Betacoronavirus/classification , Betacoronavirus/pathogenicity , Bronchoalveolar Lavage Fluid/virology , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Female , High-Throughput Nucleotide Sequencing , Hospitalization , Humans , Italy/epidemiology , Male , Middle Aged , Mutation , Nasopharynx/virology , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Prospective Studies , Real-Time Polymerase Chain Reaction , SARS-CoV-2 , Severity of Illness Index , Time Factors
18.
Euro Surveill ; 25(11)2020 03.
Article in English | MEDLINE | ID: covidwho-10076

ABSTRACT

Data concerning the transmission of the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) in paucisymptomatic patients are lacking. We report an Italian paucisymptomatic case of coronavirus disease 2019 with multiple biological samples positive for SARS-CoV-2. This case was detected using the World Health Organization protocol on cases and contact investigation. Current discharge criteria and the impact of extra-pulmonary SARS-CoV-2 samples are discussed.


Subject(s)
Asymptomatic Infections , Coronavirus Infections/diagnosis , Coronavirus/isolation & purification , Feces/virology , Lung/diagnostic imaging , Nasopharynx/virology , Pneumonia, Viral/diagnosis , Travel , Virus Shedding , Antibodies, Viral/immunology , Betacoronavirus , COVID-19 , COVID-19 Testing , China , Clinical Laboratory Techniques , Contact Tracing , Coronavirus/genetics , Coronavirus Infections/transmission , Coronavirus Infections/virology , Humans , Italy , Lung/pathology , Male , Pandemics , Pneumonia, Viral/therapy , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Quarantine , Radiography, Thoracic , Real-Time Polymerase Chain Reaction , SARS-CoV-2 , Tomography, X-Ray Computed , World Health Organization , Young Adult
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