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3.
J Clin Virol Plus ; 2(3): 100084, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1851466
4.
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
5.
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.

6.
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
7.
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.

9.
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.

10.
JMIR Res Protoc ; 11(1): e29892, 2022 Jan 25.
Article in English | MEDLINE | ID: covidwho-1649492

ABSTRACT

BACKGROUND: The novel coronavirus has a high mortality rate (over 1% for patients older than 50 years). This can only be partially ascribed to other comorbidities. A possible explanation is a factor that assures a prompt response to SARS-CoV-2 in younger people, independent from the novelty of the virus itself. A factor is believed to stimulate the immune system and provide immunity against more antigens. The only external stimulation received by healthy people is vaccination (eg, the diphtheria, tetanus, and pertussis [DTP] vaccine). One hypothesis is that vaccination helps develop specific immunity but generates sprouting immunity against antigens in transit. The underlying immunological phenomena are the "bystander effect" and "trained immunity." The developed immunity gives protection for years until it naturally fades out. After the fifth decade of life, the immune system is almost incompetent when a viral infection occurs, and thus, at this stage, the novel coronavirus can enter the body and cause acute respiratory distress syndrome. OBJECTIVE: The initial aim is to demonstrate that blood monocytes and natural killer cells show overpowering hyperactivity, while CD4+ and CD8+ T cells experience impediments to their defensive functions in patients with severe SARS-CoV-2 infection. The secondary objectives are to correlate clinical data and vaccination history with laboratory immune patterns in order to identify protective factors. Subsequently, we are also interested in characterizing the phenotypes and state of the degree of activation of peripheral blood mononuclear cells, including monocytes, natural killer cells, and CD4+ and CD8+ T cells, in healthy subjects vaccinated with the Pfizer vaccine. METHODS: Data will be collected using the following 3 approaches: (1) an experimental analysis to study the innate immune response and to identify genetic profiles; (2) an epidemiological analysis to identify the patients' vaccination history; and (3) a clinical analysis to detect the immunological profile. RESULTS: The protocol was approved by the Ethics Committee on April 16, 2020, and the study started on April 27, 2020. As of February 2021, enrollment has been completed. Immunological analysis is ongoing, and we expect to complete this analysis by December 2022. CONCLUSIONS: We will recognize different populations of patients, each one with a specific immunological pattern in terms of cytokines, soluble factor serum levels, and immune cell activity. Anamnestic data, such as preceding vaccinations and comorbidities, biochemical findings like lymphocyte immunophenotyping, and pre-existing persistent cytomegalovirus infection, allow depicting the risk profile of severe COVID-19. Proof of the roles of these immunological phenomena in the development of COVID-19 can be the basis for the implementation of therapeutic immunomodulatory treatments. TRIAL REGISTRATION: ClinicalTrials.gov NCT04375176; https://clinicaltrials.gov/ct2/show/NCT04375176. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/29892.

11.
Int J Infect Dis ; 116: 271-272, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1596505

ABSTRACT

The Delta variant of concern (VOC) of SARS-CoV-2 has become dominant worldwide. In this article, we report a cluster caused by B.1.617.2 harboring the additional mutation of concern (MOC) F490S. We observed that 5 fully vaccinated subjects aged between 47 and 84 years were infected with this variant. The immune escape mutation F490S, first identified in the Lambda VOI, appears to impair vaccine efficacy and is rapidly increasing in prevalence worldwide.


Subject(s)
COVID-19 , SARS-CoV-2 , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19 Vaccines , Humans , Middle Aged , Mutation , SARS-CoV-2/genetics
12.
EBioMedicine ; 75: 103788, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1587926

ABSTRACT

BACKGROUND: Although the BNT162b2 COVID-19 vaccine is known to induce IgG neutralizing antibodies in serum protecting against COVID-19, it has not been studied in detail whether it could generate specific immunity at mucosal sites, which represent the primary route of entry of SARS-CoV-2. METHODS: Samples of serum and saliva of 60 BNT162b2-vaccinated healthcare workers were collected at baseline, two weeks after the first dose and two weeks after the second dose. Anti-S1-protein IgG and IgA total antibodies titres and the presence of neutralizing antibodies against the Receptor Binding Domain in both serum and saliva were measured by quantitative and by competitive ELISA, respectively. FINDINGS: Complete vaccination cycle generates a high serum IgG antibody titre as a single dose in previously infected seropositive individuals. Serum IgA concentration reaches a plateau after a single dose in seropositive individuals and two vaccine doses in seronegative subjects. After the second dose IgA level was higher in seronegative than in seropositive subjects. In saliva, IgG level is almost two orders of magnitude lower than in serum, reaching the highest values after the second dose. IgA concentration remains low and increases significantly only in seropositive individuals after the second dose. Neutralizing antibody titres were much higher in serum than in saliva. INTERPRETATION: The mRNA BNT162b2 vaccination elicits a strong systemic immune response by drastically boosting neutralizing antibodies development in serum, but not in saliva, indicating that at least oral mucosal immunity is poorly activated by this vaccination protocol, thus failing in limiting virus acquisition upon its entry through this route. FUNDING: This work was funded by the Department of Medicine and Surgery, University of Insubria, and partially supported by Fondazione Umberto Veronesi (COVID-19 Insieme per la ricerca di tutti, 2020).


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/immunology , Immunity, Mucosal/drug effects , Immunization, Secondary , Adult , COVID-19/prevention & control , Female , Health Personnel , Humans , Immunoglobulin A/immunology , Immunoglobulin G/immunology , Male , Middle Aged , Saliva/immunology
13.
JMIR Res Protoc ; 11(1): e29892, 2022 Jan 25.
Article in English | MEDLINE | ID: covidwho-1547130

ABSTRACT

BACKGROUND: The novel coronavirus has a high mortality rate (over 1% for patients older than 50 years). This can only be partially ascribed to other comorbidities. A possible explanation is a factor that assures a prompt response to SARS-CoV-2 in younger people, independent from the novelty of the virus itself. A factor is believed to stimulate the immune system and provide immunity against more antigens. The only external stimulation received by healthy people is vaccination (eg, the diphtheria, tetanus, and pertussis [DTP] vaccine). One hypothesis is that vaccination helps develop specific immunity but generates sprouting immunity against antigens in transit. The underlying immunological phenomena are the "bystander effect" and "trained immunity." The developed immunity gives protection for years until it naturally fades out. After the fifth decade of life, the immune system is almost incompetent when a viral infection occurs, and thus, at this stage, the novel coronavirus can enter the body and cause acute respiratory distress syndrome. OBJECTIVE: The initial aim is to demonstrate that blood monocytes and natural killer cells show overpowering hyperactivity, while CD4+ and CD8+ T cells experience impediments to their defensive functions in patients with severe SARS-CoV-2 infection. The secondary objectives are to correlate clinical data and vaccination history with laboratory immune patterns in order to identify protective factors. Subsequently, we are also interested in characterizing the phenotypes and state of the degree of activation of peripheral blood mononuclear cells, including monocytes, natural killer cells, and CD4+ and CD8+ T cells, in healthy subjects vaccinated with the Pfizer vaccine. METHODS: Data will be collected using the following 3 approaches: (1) an experimental analysis to study the innate immune response and to identify genetic profiles; (2) an epidemiological analysis to identify the patients' vaccination history; and (3) a clinical analysis to detect the immunological profile. RESULTS: The protocol was approved by the Ethics Committee on April 16, 2020, and the study started on April 27, 2020. As of February 2021, enrollment has been completed. Immunological analysis is ongoing, and we expect to complete this analysis by December 2022. CONCLUSIONS: We will recognize different populations of patients, each one with a specific immunological pattern in terms of cytokines, soluble factor serum levels, and immune cell activity. Anamnestic data, such as preceding vaccinations and comorbidities, biochemical findings like lymphocyte immunophenotyping, and pre-existing persistent cytomegalovirus infection, allow depicting the risk profile of severe COVID-19. Proof of the roles of these immunological phenomena in the development of COVID-19 can be the basis for the implementation of therapeutic immunomodulatory treatments. TRIAL REGISTRATION: ClinicalTrials.gov NCT04375176; https://clinicaltrials.gov/ct2/show/NCT04375176. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/29892.

14.
Emerg Microbes Infect ; 10(1): 2010-2015, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1526149

ABSTRACT

The SARS-CoV-2 variant of concern (VOC) "Delta" is currently defined by PANGOLIN as a cluster of 33 different AY sublineages. Delta (in particular B.1.617.2) is largely and rapidly replacing the Alpha VOC as the dominant clade in most countries. To date, variations in the Spike protein of the Delta VOC have largely been limited. We report here the results of a genomic surveillance programme from Northern Italy. We identified several Delta sublineages harbouring mutations previously reported in GISAID at extremely low frequencies and in different combinations. Two patients (one of them vaccinated) tested positive for a Delta sublineage harbouring S71F, T250I, T572I and K854N. More patients tested positive for G769 V plus C1248F, A352S, and R158G and C1248F, respectively. Genomic surveillance of Delta variants should be encouraged to anticipate immune escape and deploy countermeasures.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Adult , Aged , Evolution, Molecular , Female , Humans , Italy/epidemiology , Male , Middle Aged , Young Adult
15.
Emerg Infect Dis ; 27(10): 2728-2731, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1486746

ABSTRACT

We report in vivo selection of a severe acute respiratory syndrome coronavirus 2 spike mutation (Q493R) conferring simultaneous resistance to bamlanivimab and etesivimab. This mutation was isolated from a patient who had coronavirus disease and was treated with these drugs.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Humans , Mutation , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/genetics
18.
Oral Dis ; 27 Suppl 3: 707-709, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1434792

ABSTRACT

We report two cases of COVID-19 showing negative respiratory swabs but positive salivary samples at the same time. These findings rise the concern about how to manage these patients before hospital discharging, thus avoiding contagion among their family members or a second coronavirus wave once the lockdown is over.


Subject(s)
COVID-19 , Communicable Disease Control , Hospitals , Humans , Patient Discharge , SARS-CoV-2
19.
Emerg Infect Dis ; 27(12): 3180-3182, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1403446

ABSTRACT

The Delta variant of concern of severe acute respiratory syndrome coronavirus 2 is dominant worldwide. We report a case cluster caused by Delta sublineage B.1.617.2 harboring the mutation E484K in Italy during July 11-July 29, 2021. This mutation appears to affect immune response and vaccine efficacy; monitoring its appearance is urgent.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Italy/epidemiology , Mutation
20.
Front Public Health ; 8: 569209, 2020.
Article in English | MEDLINE | ID: covidwho-1389248

ABSTRACT

Only 4 months after the beginning of SARS-CoV-2 epidemic, the world is facing a global pandemic due to a complex and insidious virus that today constantly poses new challenges. In this study, we highlight a persistent shedding of SARS-CoV-2 RNA into the urine, even in patients with a negative nasopharyngeal swab and in patients considered recovered. What does it mean? Besides the fact that the kidney is a probable site of viral replication, the prolonged viral excretion is a matter of great concern for our drainage system contamination.


Subject(s)
COVID-19/transmission , COVID-19/urine , SARS-CoV-2 , Urine/virology , Virus Shedding , Waste Water/virology , Adult , Aged , Aged, 80 and over , Female , Humans , Italy , Male , Middle Aged , Pandemics , Pilot Projects , Risk Factors
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