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2.
Clin Infect Dis ; 2022 Jan 21.
Article in English | MEDLINE | ID: covidwho-1722269

ABSTRACT

We identified the first case in Italy of SARS-CoV-2 B.1.1.529 variant by whole genome sequencing in an Italian subject travelling from Mozambique. Specific mutation profiles deserve further investigations to clarify potential effects on vaccination efficacy. This case highlights the crucial role of rapid and continuous surveillance of SARS-CoV-2 variant circulation.

3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-317012

ABSTRACT

An Italian male with no link to China SARS-CoV-2 epidemic presented at Emergency Room with severe respiratory impairment. The RT-PCR on 20th February, 2020, nasopharyngeal swab revealed SARS-CoV-2 infection, confirmed with viral culture and sequencing. This was the first identified autochthonous SARS-CoV-2 transmission in Italy, that unveiled global pathogen diffusion.

4.
Microorganisms ; 10(2)2022 Jan 25.
Article in English | MEDLINE | ID: covidwho-1649302

ABSTRACT

Herein, we report a case of an Italian male infected by Delta sublineage AY.4 harboring an atypical deletion, leading to a N gene target failure (NGTF) by a commercial molecular assay for SARS-CoV-2 diagnosis (AllplexTM SARS-CoV-2 Assay, Seegene). A 59-year-old unvaccinated patient was hospitalized for pulmonary embolism, with first negative results obtained by both molecular and antigen tests. After several days of viral negativity, he presented positive results for E and RdRP/S genes, but negative in N gene. Negativity in N gene was repeatedly confirmed in the following days. Suspecting an infection by the Omicron variant, SARS-CoV-2 genome sequencing was rapidly performed from nasopharyngeal swab by MiSeq and revealed the presence of the Delta sublineage AY.4 variant with an atypical deletion of six nucleotides, leading to G214-G215 deletion in the Nucleocapsid, thus responsible for NGTF. The analysis of GISAID sequences (N = 2,618,373 12 January 2022) showed that G214-G215 deletion is rarely occurring in most circulating Delta lineages and sublineages in the globe and Europe, with an overall prevalence never exceeding 0.2%. Hence, this study highlights the importance to perform SARS-CoV-2 sequencing and to characterize novel mutations/deletions that could jeopardize the proper interpretation of molecular diagnostic tests. Based on these assumptions, the role of deletions in the recently identified Omicron variant deserves further investigation.

5.
J Acquir Immune Defic Syndr ; 88(3): 299-304, 2021 11 01.
Article in English | MEDLINE | ID: covidwho-1574388

ABSTRACT

BACKGROUND: We assessed the impact of the coronavirus disease 2019 (COVID-19) pandemic on HIV suppression rates in people living with HIV (PLWH) attending a large Italian HIV clinic. SETTING: The HIV outpatient clinic of the Infectious Diseases Department of Luigi Sacco Hospital, Milan, Italy, which serves more than 5000 PLWH per year. METHODS: A before and after quasi-experimental study design was used to make a retrospective assessment of the monthly trend of HIV-RNA determinations of ≥50 among the PLWH attending our clinic, with "before" being the period from January 1, 2016 to February 20, 2020, and "after" being the period from February 21, 2020 to December 31, 2020 (the COVID-19 period). Interrupted time series analysis was used to evaluate any changes in the trend. RESULTS: During the study period, 70,349 HIV-RNA viral load determinations were made, and the percentage of HIV-RNA viral load determinations of <50 copies/mL increased from 88.4% in 2016 to 93.2% in 2020 (P < 0.0001). There was a significant monthly trend toward a decrease in the number of HIV-RNA determinations of ≥50 copies/mL before the pandemic (ß -0.084; standard error 0.015; P < 0.001), and this did not significantly change after it started (ß -0.039, standard error 0.161; P = 0.811). CONCLUSIONS: A high prevalence of viral suppression was maintained among the PLWH referring to our clinic, despite the structural barriers raised by the COVID-19 pandemic. The use of simplified methods of delivering care (such as teleconsultations and multiple antiretroviral treatment prescriptions) may have contributed to preserving this continuum.


Subject(s)
Anti-HIV Agents/therapeutic use , COVID-19/complications , COVID-19/epidemiology , HIV Infections/complications , HIV Infections/epidemiology , Ambulatory Care Facilities , Anti-HIV Agents/administration & dosage , Delivery of Health Care/methods , HIV Infections/drug therapy , HIV-1 , Humans , Italy/epidemiology , RNA, Viral/blood , SARS-CoV-2 , Viral Load/drug effects
6.
Clin Case Rep ; : e04154, 2021 May 06.
Article in English | MEDLINE | ID: covidwho-1217347

ABSTRACT

An Italian male with no link to China Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) epidemic presented at Emergency Room (ER) with severe respiratory impairment. The RT-PCR on 20 February 2020, nasopharyngeal swab revealed SARS-CoV-2 infection, confirmed with viral culture and sequencing. This was the first identified autochthonous SARS-CoV-2 transmission in Italy, that unveiled global pathogen diffusion. This clinical case highlights an underestimation of SARS-CoV-2 circulation, making initial containment measures unfit to face the real situation and delaying the management of potentially affected SARS-CoV-2 patients.

7.
J Med Virol ; 93(3): 1752-1757, 2021 03.
Article in English | MEDLINE | ID: covidwho-1196461

ABSTRACT

The first identification of autochthonous transmission of SARS-CoV-2 in Italy was documented by the Laboratory of Clinical Microbiology, Virology and Bioemergencies of L. Sacco Hospital (Milano, Italy) on 20th February 2020 in a 38 years old male patient, who was found positive for pneumonia at the Codogno Hospital. Thereafter Lombardy has reported the highest prevalence of COVID-19 cases in the country, especially in Milano, Brescia and Bergamo provinces. The aim of this study was to assess the potential presence of different viral clusters belonging to the six main provinces involved in Lombardy COVID-19 cases in order to highlight peculiar province-dependent viral characteristics. A phylogenetic analysis was conducted on 20 full length genomes obtained from patients addressing to several Lombard hospitals from February 20th to April 4th, 2020, aligned with 41 Italian viral genome assemblies available on GISAID database as of 30th March, 2020: two main monophyletic clades, containing 8 and 53 isolates, respectively, were identified. Noteworthy, Bergamo isolates mapped inside the small clade harbouring M gene D3G mutation. The molecular clock analysis estimated a cluster divergence approximately one month before the first patient identification, supporting the hypothesis that different SARS-CoV-2 strains had spread worldwide at different times, but their presence became evident only in late February along with Italian epidemic emergence. Therefore, this epidemiological reconstruction suggests that virus initial circulation in Lombardy was ascribable to multiple introduction. The phylogenetic reconstruction robustness, however, will be improved when more genomic sequences are available, in order to guarantee a complete epidemiological surveillance.


Subject(s)
COVID-19/epidemiology , SARS-CoV-2/genetics , Adult , COVID-19/virology , Disease Outbreaks , Genome, Viral/genetics , Genomics/methods , Geography , Humans , Italy/epidemiology , Male , Phylogeny
8.
Int J Infect Dis ; 104: 631-633, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1093057

ABSTRACT

This study addressed the case of a patient with prolonged COVID-19 viral shedding, reported by Real-Time PCR, until 71 days from symptom onset. However, viral culture received negative results after 30 days from symptom onset. Therefore, viral culture may be a worthwhile test for patients requiring discharge, in particular for those presenting prolonged viral shedding.


Subject(s)
COVID-19/virology , SARS-CoV-2/isolation & purification , Virus Shedding , Aged, 80 and over , Cell Culture Techniques , Humans , Male , Patient Discharge , Real-Time Polymerase Chain Reaction , Time Factors
9.
Eur J Intern Med ; 76: 36-42, 2020 06.
Article in English | MEDLINE | ID: covidwho-377283

ABSTRACT

BACKGROUND: Tocilizumab, a humanized monoclonal antibody, targets IL-6 receptors blocking downstream pro-inflammatory effects of IL-6. In preliminary reports it was suggested to be beneficial in patients with severe COVID-19. METHODS: In this open-label prospective study we describe clinical characteristics and outcome of 51 patients hospitalized with confirmed and severe COVID-19 pneumonia treated with tocilizumab intravenously. All patients had elevated IL-6 plasma level (>40 pg/mL) and oxygen saturation <93% in ambient air. Clinical outcomes, oxygen support, laboratory data and adverse events were collected over a follow-up of 30 days. RESULTS: Forty-five patients (88%) were on high-flow oxygen supplementation, six of whom with invasive ventilation. From baseline to day 7 after tocilizumab we observed a dramatic drop of body temperature and CRP value with a significant increase in lymphocyte count (p<0.001). Over a median follow-up time of 34 days from tocilizumab, 34 patients (67%) showed an improvement in their clinical severity class; 31 were discharged; 17 (33%) showed a worsening of their clinical status, of these 14 died (27%). The mortality rate was significantly associated with mechanical ventilation at baseline (83.3% vs 20% of patients on non-invasive oxygen support; p=0.0001). The most frequent side effects were an increase of hepatic enzymes (29%), thrombocytopenia (14%), and serious bacterial and fungal infections (27%). CONCLUSION: Tocilizumab exerts a rapidly beneficial effect on fever and inflammatory markers, although no significant impact on the clinical outcome can be inferred by our results. Critically ill patients seem to have a high risk of serious infections with this drug.


Subject(s)
Antibodies, Monoclonal, Humanized , Coronavirus Infections , Pandemics , Pneumonia, Viral , Receptors, Interleukin-6/antagonists & inhibitors , Respiration, Artificial/methods , Respiratory Insufficiency , Antibodies, Monoclonal, Humanized/administration & dosage , Antibodies, Monoclonal, Humanized/adverse effects , Antiviral Agents/adverse effects , Betacoronavirus/drug effects , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/blood , Coronavirus Infections/epidemiology , Coronavirus Infections/physiopathology , Coronavirus Infections/therapy , Female , Fever/diagnosis , Fever/drug therapy , Humans , Italy/epidemiology , Lymphocyte Count/methods , Male , Middle Aged , Outcome and Process Assessment, Health Care , Pneumonia, Viral/blood , Pneumonia, Viral/diagnosis , Pneumonia, Viral/drug therapy , Pneumonia, Viral/epidemiology , Pneumonia, Viral/etiology , Pneumonia, Viral/physiopathology , Pneumonia, Viral/therapy , Respiratory Insufficiency/etiology , Respiratory Insufficiency/therapy , Retrospective Studies , SARS-CoV-2
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