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4.
Semin Respir Crit Care Med ; 42(6): 747-758, 2021 12.
Article in English | MEDLINE | ID: covidwho-1585686

ABSTRACT

Respiratory tract infection is one of the most common diseases in human worldwide. Many viruses are implicated in these infections, including emerging viruses, such as the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Identification of the causative viral pathogens of respiratory tract infections is important to select a correct management of patients, choose an appropriate treatment, and avoid unnecessary antibiotics use. Different diagnostic approaches present variable performance in terms of accuracy, sensitivity, specificity, and time-to-result, that have to be acknowledged to be able to choose the right diagnostic test at the right time, in the right patient. This review describes currently available rapid diagnostic strategies and syndromic approaches for the detection of viruses commonly responsible for respiratory diseases.


Subject(s)
Early Diagnosis , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , COVID-19/diagnosis , COVID-19/virology , Humans , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Time Factors
5.
Preprint in English | EuropePMC | ID: ppcovidwho-296187

ABSTRACT

SARS-CoV2 is a new coronavirus which started spreading in December 2019 from Wuhan, China. The seroprevalence of SARS-CoV2 antibodies allows to define a better picture of the spread of SARS-CoV2 infection in the population. The duration of SARS-CoV2 antibodies in the healthy population as well as in immunocompromised patients is still a topic of debate. HIV-infected people are at increased risk of developing complications from contracting a viral illness. Furthermore,their ability to develop and maintain an optimal immunological response to any kind of pathogen appears to be reduced.We analyzed the overall seroprevalence of SARS-CoV2 antibodies in 85 HIV infected-people on ART aged between 5 and 34 years old from May to January 2021. 88,2%of patients were in a good state of viroimmunological control: 23 showed a VL<40cp/ml and 52 had an undetectable VL. When positive for SARS-CoV2 serology, a confirmatory nasopharyngeal swab for PCR assessment and a second serological assay would be performed.Out of the 85 patients, 5 proved to be positive for SARS-CoV2 antibodies (rate of prevalence 5.8%). In all 5 cases the nasopharyngeal swabs were negative and the second assay for SARS-CoV2 antibodies performed in 4 out of 5 patients a week later was negative as well. The anamnestic recall brought no elements of suspicion for a past infection.The duration of SARS-CoV2 antibodies after COVID19 disease is still poorly understood in healthy population and additional studies will be needed to define the durability of humoral responses in immunocompromised children and in particular in HIV infected children under effective ART. It is still unknown whether ART or their immunological impairment may in part mitigate the pathogenesis of SARS-CoV-2 infection. Also, it will be interesting to analyze the impact of vaccination against SARS-CoV2 in HIV infected patients with a satisfactory virological control.

6.
Preprint in English | SSRN | ID: ppcovidwho-292059

ABSTRACT

Background: Breakthrough infections in fully vaccinated HCWs are considered a marker of waning immunity. Serum antibodies represent the most visible and measurable outcome of vaccine-induced B-cell memory. When antibodies decline, memory B cells are expected to persist and perform their function, thus preventing clinical disease. We investigated whether BNT162b2 mRNA vaccine induces durable and in vivo functional B-cell memory against SARS-CoV-2 3, 6 and 9 months after the second dose. Methods: We assessed the duration of SARS-CoV-2 vaccine-induced immunity by measuring specific antibodies and memory B cells 3, 6 and 9 months after vaccination. In fully vaccinated HCWs with breakthrough SARS-CoV-2 infections, we evaluated the humoral and mucosal response of vaccine-induced memory B cells. Findings: Whereas specific serum antibodies decline, anti-Spike memory B cells continue to increase until 9 months after the last vaccine dose. HCWs with breakthrough infections had no signs of waning immunity on the day of the first positive swab. In 3-4 days, memory B cells responded to SARS-CoV-2 infection by producing high levels of specific antibodies in the serum. In the saliva, anti-Spike IgA also rapidly increased in response to the infection. Antibodies to the viral nucleoprotein were produced with the slow kinetics typical of the response to a novel antigen. Interpretation: SARS-CoV-2 specific antibodies physiologically decline months after vaccination. By contrast, memory B cells persist and increase over time. Parenteral administered vaccines do not generate mucosal immunity and serum antibodies reach mucosal sites in small amounts by transudation. In HCWs with SARS-CoV-2 breakthrough infections, memory B cells react by rapidly differentiating into antibody-producing cells and generating IgA for protection of mucosal sites.

7.
Front Immunol ; 12: 727850, 2021.
Article in English | MEDLINE | ID: covidwho-1477821

ABSTRACT

Mass SARS-Cov-2 vaccination campaign represents the only strategy to defeat the global pandemic we are facing. Immunocompromised patients represent a vulnerable population at high risk of developing severe COVID-19 and thus should be prioritized in the vaccination programs and in the study of the vaccine efficacy. Nevertheless, most data on efficacy and safety of the available vaccines derive from trials conducted on healthy individuals; hence, studies on immunogenicity of SARS-CoV2 vaccines in such populations are deeply needed. Here, we perform an observational longitudinal study analyzing the humoral and cellular response following the BNT162b2 mRNA COVID-19 vaccine in a cohort of patients affected by inborn errors of immunity (IEI) compared to healthy controls (HC). We show that both IEI and HC groups experienced a significant increase in anti-SARS-CoV-2 Abs 1 week after the second scheduled dose as well as an overall statistically significant expansion of the Ag-specific CD4+CD40L+ T cells in both HC and IEI. Five IEI patients did not develop any specific CD4+CD40L+ T cellular response, with one of these patients unable to also mount any humoral response. These data raise immunologic concerns about using Ab response as a sole metric of protective immunity following vaccination for SARS-CoV-2. Taken together, these findings suggest that evaluation of vaccine-induced immunity in this subpopulation should also include quantification of Ag-specific T cells.


Subject(s)
Antibodies, Viral/blood , CD4-Positive T-Lymphocytes/immunology , COVID-19 Vaccines/immunology , Immunogenicity, Vaccine/immunology , Primary Immunodeficiency Diseases/immunology , SARS-CoV-2/immunology , Adolescent , Adult , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , CD4 Lymphocyte Count , COVID-19/prevention & control , Female , Humans , Immunity, Cellular/immunology , Immunity, Humoral/immunology , Immunocompromised Host/immunology , Longitudinal Studies , Male , Middle Aged , Vaccination , Young Adult
8.
Cells ; 10(10)2021 09 26.
Article in English | MEDLINE | ID: covidwho-1438527

ABSTRACT

Specific memory B cells and antibodies are a reliable read-out of vaccine efficacy. We analysed these biomarkers after one and two doses of BNT162b2 vaccine. The second dose significantly increases the level of highly specific memory B cells and antibodies. Two months after the second dose, specific antibody levels decline, but highly specific memory B cells continue to increase, thus predicting a sustained protection from COVID-19. We show that although mucosal IgA is not induced by the vaccination, memory B cells migrate in response to inflammation and secrete IgA at mucosal sites. We show that the first vaccine dose may lead to an insufficient number of highly specific memory B cells and low concentration of serum antibodies, thus leaving vaccinees without the immune robustness needed to ensure viral elimination and herd immunity. We also clarify that the reduction of serum antibodies does not diminish the force and duration of the immune protection induced by vaccination. The vaccine does not induce sterilizing immunity. Infection after vaccination may be caused by the lack of local preventive immunity because of the absence of mucosal IgA.


Subject(s)
Antibodies, Viral/immunology , B-Lymphocytes/cytology , COVID-19 Vaccines/therapeutic use , COVID-19/immunology , COVID-19/prevention & control , Immunoglobulin A/immunology , Immunologic Memory , Adult , Antibodies, Neutralizing/blood , Antigens, Viral/immunology , B-Lymphocytes/immunology , Cryopreservation , Female , Health Personnel , Healthy Volunteers , Hospitals, Pediatric , Humans , Immunoglobulin G , Immunoglobulin M/immunology , Lactation , Male , Middle Aged , Mucous Membrane/immunology , Patient Safety , SARS-CoV-2 , Vaccination
10.
Pediatr Res ; 2021 Jun 11.
Article in English | MEDLINE | ID: covidwho-1265938

ABSTRACT

BACKGROUND: The objective of this study is to test how certain signs and symptoms related to COVID-19 in children predict the positivity or negativity of the SARS-CoV-2 nasopharyngeal swab in children. METHODS: We review the data of children who were tested for SARS-CoV-2 for a suspected infection. We compared the clinical characteristics of the subjects who tested positive and negative, including the sensibility, positive and negative predictive value of different combination of signs and symptoms. RESULTS: Of all the suspected infected, 2596 tested negative (96.2%) and 103 tested positive (3.8%). The median age was 7.0 and 5.3 years for the positive and negative ones, respectively. The female to male ratio was ~1:1.3. Fever and respiratory symptoms were mostly reported. Most positive children had a prior exposure to SARS-CoV-2-infected subjects (59.2%). A total of 99.3% of patients without fever nor exposure to the virus proved negative to the SARS-CoV-2 test. CONCLUSIONS: Our study suggests that a child without fever or contact with infected subjects is SARS-CoV-2 negative. If this were to be confirmed, many resources would be spared, with improved care of both COVID-19 and not COVID-19-affected children. IMPACT: Key message: lack of fever and exposure to SARS-CoV-2-infected people highly predicts a negative results of the SARS-CoV-2 nasopharyngeal swab in the paediatric population. Added value to the current literature: this is the first article to prove this point. IMPACT: reduction of emergency department accesses of children with suspected SARS-CoV-2 infection; increased outpatient management of children with cough or other common respiratory symptoms of infancy; sparing of many human and material health resources.

12.
Viruses ; 13(5)2021 05 01.
Article in English | MEDLINE | ID: covidwho-1224249

ABSTRACT

To complement RT-qPCR testing for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, many countries have introduced the use of rapid antigen tests. As they generally display lower real-life performances than expected, their correct positioning as frontline screening is still controversial. Despite the lack of data from daily clinical use, third generation microfluidic assays (such as the LumiraDx SARS-CoV-2 Ag test) have recently been suggested to have similar performances to RT-qPCR and have been proposed as alternative diagnostic tools. By analyzing 960 nasopharyngeal swabs from 960 subjects at the emergency department admissions of a tertiary COVID-19 hospital, LumiraDx assay demonstrated a specificity of 97% (95% CI: 96-98), and a sensitivity of 85% (95% CI: 82-89) in comparison with RT-qPCR, which increases to 91% (95% CI: 86-95) for samples with a cycle threshold ≤ 29. Fifty false-negative LumiraDx-results were confirmed by direct quantification of genomic SARS-CoV-2 RNA through droplet-digital PCR (median (IQR) load = 5880 (1657-41,440) copies/mL). Subgenomic N and E RNAs were detected in 52% (n = 26) and 56% (n = 28) of them, respectively, supporting the presence of active viral replication. Overall, the LumiraDx test complies with the minimum performance requirements of the WHO. Yet, the risk of a misrecognition of patients with active COVID-19 persists, and the need for confirmatory RT-qPCR should not be amended.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , SARS-CoV-2/genetics , Aged , Antigens, Viral/analysis , COVID-19/genetics , COVID-19/immunology , Emergency Service, Hospital , Female , Humans , Italy/epidemiology , Male , Microfluidic Analytical Techniques/methods , Middle Aged , Nasopharynx/virology , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/immunology , SARS-CoV-2/pathogenicity , Sensitivity and Specificity
13.
BMC Infect Dis ; 21(1): 184, 2021 Feb 17.
Article in English | MEDLINE | ID: covidwho-1088583

ABSTRACT

BACKGROUND: Recent studies showed that plasma SARS-CoV-2 RNA seems to be associated with worse COVID-19 outcome. However, whether specific population can be at higher risk of viremia are to date unexplored. METHODS: This cross-sectional proof-of-concept study included 41 SARS-CoV-2-positive adult individuals (six affected by haematological malignancies) hospitalized at two major hospital in Milan, for those demographic, clinical and laboratory data were available. SARS-CoV-2 load was quantified by ddPCR in paired plasma and respiratory samples. To assess significant differences between patients with and patients without viremia, Fisher exact test and Wilcoxon test were used for categorical and continuous variables, respectively. RESULTS: Plasma SARS-CoV-2 RNA was found in 8 patients (19.5%), with a median (IQR) value of 694 (209-1023) copies/mL. Viremic patients were characterized by an higher mortality rate (50.0% vs 9.1%; p = 0.018) respect to patients without viremia. Viremic patients were more frequently affected by haematological malignancies (62.5% vs. 3.0%; p < 0.001), and had higher viral load in respiratory samples (9,404,000 [586,060-10,000,000] vs 1560 [312-25,160] copies/mL; p = 0.002). CONCLUSIONS: Even if based on a small sample population, this proof-of-concept study poses the basis for an early identification of patients at higher risk of SARS-CoV-2 viremia, and therefore likely to develop severe COVID-19, and supports the need of a quantitative viral load determination in blood and respiratory samples of haematologic patients with COVID-19 in order to predict prognosis and consequently to help their further management.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/blood , COVID-19/diagnosis , RNA, Viral/blood , Adult , Aged , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Prognosis , Proof of Concept Study , SARS-CoV-2/genetics , Serologic Tests , Viral Load , Viremia/virology
15.
Nat Commun ; 12(1): 434, 2021 01 19.
Article in English | MEDLINE | ID: covidwho-1038209

ABSTRACT

From February to April 2020, Lombardy (Italy) reported the highest numbers of SARS-CoV-2 cases worldwide. By analyzing 346 whole SARS-CoV-2 genomes, we demonstrate the presence of seven viral lineages in Lombardy, frequently sustained by local transmission chains and at least two likely to have originated in Italy. Six single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. The seven lineages, and the presence of local transmission clusters within three of them, revealed that sustained community transmission was underway before the first COVID-19 case had been detected in Lombardy.


Subject(s)
COVID-19/prevention & control , Genome, Viral/genetics , Genomics/methods , Polymorphism, Single Nucleotide , SARS-CoV-2/genetics , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19/virology , Epidemics , Female , Geography , Humans , Italy/epidemiology , Male , Middle Aged , Phylogeny , Prevalence , Retrospective Studies , SARS-CoV-2/classification , SARS-CoV-2/physiology
16.
PLoS One ; 15(11): e0242765, 2020.
Article in English | MEDLINE | ID: covidwho-937237

ABSTRACT

OBJECTIVE: Through a hospital-based SARS-CoV-2 molecular and serological screening, we evaluated the effectiveness of two months of lockdown and two of surveillance, in Milan, Lombardy, the first to be overwhelmed by COVID-19 pandemics during March-April 2020. METHODS: All subjects presenting at the major hospital of Milan from May-11 to July-5, 2020, underwent a serological screening by chemiluminescent assays. Those admitted were further tested by RT-PCR. RESULTS: The cumulative anti-N IgG seroprevalence in the 2753 subjects analyzed was of 5.1% (95%CI = 4.3%-6.0%), with a peak of 8.4% (6.1%-11.4%) 60-63 days since the peak of diagnoses (March-20). 31/106 (29.2%) anti-N reactive subjects had anti-S1/S2 titers >80 AU/mL. Being tested from May-18 to June-5, or residing in the provinces with higher SARS-CoV-2 circulation, were positively and independently associated with anti-N IgG reactivity (OR [95%CI]: 2.179[1.455-3.264] and 3.127[1.18-8.29], respectively). In the 18 RT-PCR positive, symptomatic subjects, anti-N seroprevalence was 33.3% (95% CI: 14.8%-56.3%). CONCLUSION: SARS-CoV-2 seroprevalence in Milan is low, and in a downward trend after only 60-63 days since the peak of diagnoses. Italian confinement measures were effective, but the risk of contagion remains concrete. In hospital-settings, the performance of molecular and serological screenings upon admission remains highly advisable.


Subject(s)
Communicable Disease Control/methods , Coronavirus Infections/prevention & control , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Adolescent , Adult , Aged , Aged, 80 and over , Antibodies, Viral/blood , Betacoronavirus , COVID-19 , Child , Coronavirus Infections/epidemiology , Female , Humans , Immunoglobulin G/blood , Italy/epidemiology , Male , Middle Aged , Pneumonia, Viral/epidemiology , SARS-CoV-2 , Seroepidemiologic Studies , Young Adult
17.
PLoS One ; 15(9): e0236311, 2020.
Article in English | MEDLINE | ID: covidwho-748965

ABSTRACT

Since SARS-CoV-2-based disease (COVID-19) spreads as a pandemic, the necessity of a highly sensitive molecular diagnosis that can drastically reduce false negatives reverse transcription PCR (rtPCR) results, raises as a major clinical need. Here we evaluated the performance of a ddPCR-based assay to quantify SARS-CoV-2 titer in 55 suspected COVID-19 cases with negative rtPCR results thanks to in-house ddPCR assay (targeting RdRp and host RNaseP). Samples were collected at ASST-GOM Niguarda between February and May 2020 at hospital admission. Clinical and imaging data were obtained for clinical staging and definition of disease severity. Patients were mainly female (45.5%) with a median age of 73 (57-84) years. ddPCR-based assay detected SARS-CoV-2 genome in nasopharyngeal samples of 19 (34.5%) patients (median viral-load: 128 copies/mL, IQR: 72-345). In 15 of them (78.9%), chest CT showed a classical COVID-19 bilateral interstitial pneumonia; 14 patients (73.7%) showed severe COVID-19 manifestations. ddPCR did not identify any trace of SARS-CoV-2 genome in the respiratory samples of the remaining 36 patients. The serological assay performed in a subgroup of 34 patients at the later stage of illness (from 3 days to 90 days after) confirmed the presence of SARS-CoV-2 antibodies in all patients tested positive for SARS-CoV-2 in ddPCR (100%). Contrariwise, negative tests were observed in 95.0% ddPCR negative patients (P<0.001). Thanks to a ddPCR-based assay, we achieved a rapid and accurate SARS-CoV-2 diagnosis in rtPCR-negative respiratory samples of individuals with COVID-19 suspect, allowing the rapid taking care and correct management of these patients.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Nasopharynx/virology , Pneumonia, Viral/diagnosis , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction/methods , Aged , Aged, 80 and over , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/pathology , Coronavirus Infections/virology , Female , Humans , Limit of Detection , Male , Middle Aged , Pandemics , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , RNA, Viral/metabolism , SARS-CoV-2 , Severity of Illness Index , Viral Load
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