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Walory J, Ksiazek I, Wegrzynska K, Baraniak A. Comparison of Post-Vaccination Response (Humoral and Cellular) to BNT162b2 in Clinical Cases, Kidney and Pancreas Transplant Recipient with Immunocompetent Subjects over Almost Two Years of Parallel Monitoring. Vaccines (Basel) 2024; 12:844. [PMID: 39203970 PMCID: PMC11360542 DOI: 10.3390/vaccines12080844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 09/03/2024] Open
Abstract
BACKGROUND Vaccination is one of the most effective medical interventions to prevent infectious diseases. The introduction of vaccines against coronavirus acute respiratory syndrome 2 (SARS-CoV-2) was aimed at preventing severe illness and death due to coronavirus disease 2019 (COVID-19). Solid organ transplant recipients (SOTRs) are at high risk of infection with SARS-CoV-2 and serious effects associated with COVID-19, mainly due to the use of immunosuppressive therapies, which further cause suboptimal response to COVID-19 vaccination. AIM OF THE STUDY We aimed to compare post-vaccination response to BNT162b2 in kidney-pancreas transplant recipient, specifically in immunocompetent individuals, over two years of simultaneous monitoring. METHODS To determine the humoral response, the levels of the IgG and IgA anti-S1 antibodies were measured. To assess the cellular response to SARS-CoV-2, the released IFN-γ-S1 was determinate. RESULTS AND CONCLUSION After primary vaccination, compared to immunocompetent subjects, SOTR showed lower seroconversion for both antibody classes. Only the additional dose produced antibodies at the level reached by the control group after the baseline vaccination. During the monitored period, SOTR did not achieve a positive cellular response in contrast to immunocompetent individuals, so in order to obtain longer protection, including immune memory, the adoption of booster doses of the vaccine should be considered.
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Affiliation(s)
- Jaroslaw Walory
- Department of Pharmaceutical Microbiology and Laboratory Diagnostics, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Iza Ksiazek
- Department of Biochemistry and Biopharmaceuticals, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Karolina Wegrzynska
- Department of Pharmaceutical Microbiology and Laboratory Diagnostics, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Anna Baraniak
- Department of Pharmaceutical Microbiology and Laboratory Diagnostics, National Medicines Institute, 00-725 Warsaw, Poland;
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Ceklarz J. Symptom intensity of post-COVID and long COVID syndromes in patients entering rehabilitation treatment. Reumatologia 2024; 62:18-25. [PMID: 38558899 PMCID: PMC10979377 DOI: 10.5114/reum/183912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/09/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction The problem of post-COVID symptoms is still being analysed. Many of them may be related to other conditions, but the new appearance and greater intensity of some of them, e.g. fatigue, musculoskeletal pain, and neuropathic pain, seem to be related to a previous viral infection. Efforts are being made to determine in more detail the most characteristic symptoms of post-COVID syndrome. The conditions of rehabilitation after COVID-19 provide an opportunity for such observations. In rehabilitation centres and sanatoriums, it is possible to compare patients with post-COVID syndrome and other patients referred for rehabilitation, who constitute a natural control group. Such a comparison is the aim of the present work. Material and methods The study included 59 post-COVID-19 patients and 57 sanatorium patients without COVID (non-COVID group) as a control group. The 31-element questionnaire ("Post-COVID syndrome symptoms assessment card") was part of the routine management of post-COVID patients referred for rehabilitation after symptomatic SARS-CoV-2 infection in Polish conditions. In the control group, the questionnaire was introduced as a part of a physical examination and an interview regarding the symptoms reported by the patient before standard rehabilitation. The questions were scored in the scale from 0 to a maximum of 10 points. Each patient gave informed consent to the use of the questionnaire for research purposes. Results Symptoms of the highest intensity in the COVID-19 group were: feeling unwell after physical effort (avg. 6.25 points), chronic fatigue (avg. 5.97 points), dyspnoea on exertion (avg. 5.83 points), concentration disturbances (avg. 4.93), muscle pain (avg. 4.92), joint pain (avg. 4.86), memory disorders (avg. 4.81 points), sleep disorders (avg. 4.05 points), numbness of the limbs (avg. 3.73 points), tingling in the limbs (avg. 3.68 points).Symptoms of highest intensity in patients in the non-COVID-19 group: joint pain (avg. 4.61 points), tingling in the limbs (avg. 2.84 points), numbness of the limbs (avg. 2.79 points), muscle pain (avg. 2.11 points).There was no statistically significant difference between the group under examination and the control group in the following symptoms: fever, diarrhoea, abdominal pain, resting dyspnoea, olfactory disorders, joint pain, tingling in the limbs and numbness of the limbs. Conclusions The results of this study show symptoms of the highest intensity with post-COVID syndromes. However, also symptoms that are a problem both in post-COVID and non-COVID patients, i.e. joint pain, tingling in and numbness of the limbs were identified. This confirms that the control non-COVID group consisted of patients referred for rehabilitation treatment mainly due to musculoskeletal problems and chronic pain.
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Affiliation(s)
- Jan Ceklarz
- Department of Systemic Rehabilitation, Rabka Sanatorium, Poland
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3
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Van Poelvoorde LAE, Gobbo A, Nauwelaerts SJD, Verhaegen B, Lesenfants M, Janssens R, Hutse V, Fraiture MA, De Keersmaecker S, Herman P, Van Hoorde K, Roosens N. Development of a reverse transcriptase digital droplet polymerase chain reaction-based approach for SARS-CoV-2 variant surveillance in wastewater. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e10999. [PMID: 38414298 DOI: 10.1002/wer.10999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/29/2024]
Abstract
An urgent need for effective surveillance strategies arose due to the global emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although vaccines and antivirals are available, concerns persist about the evolution of new variants with potentially increased infectivity, transmissibility, and immune evasion. Therefore, variant monitoring is crucial for public health decision-making. Wastewater-based surveillance has proven to be an effective tool to monitor SARS-CoV-2 variants within populations. Specific SARS-CoV-2 variants are detected and quantified in wastewater in this study using a reverse transcriptase digital droplet polymerase chain reaction (RT-ddPCR) approach. The 11 designed assays were first validated in silico using a substantial dataset of high-quality SARS-CoV-2 genomes to ensure comprehensive variant coverage. The assessment of the sensitivity and specificity with reference material showed the capability of the developed assays to reliably identify target mutations while minimizing false positives and false negatives. The applicability of the assays was evaluated using wastewater samples from a wastewater treatment plant in Ghent, Belgium. The quantification of the specific mutations linked to the variants of concern present in these samples was calculated using these assays based on the detection of single mutations, which confirms their use for real-world variant surveillance. In conclusion, this study provides an adaptable protocol to monitor SARS-CoV-2 variants in wastewater with high sensitivity and specificity. Its potential for broader application in other viral surveillance contexts highlights its added value for rapid response to emerging infectious diseases. PRACTITIONER POINTS: Robust RT-ddPCR methodology for specific SARS-CoV-2 variants of concern detection in wastewater. Rigorous validation that demonstrates high sensitivity and specificity. Demonstration of real-world applicability using wastewater samples. Valuable tool for rapid response to emerging infectious diseases.
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Affiliation(s)
| | - Andrea Gobbo
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Marie Lesenfants
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Raphael Janssens
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Veronik Hutse
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | | | | | | | | | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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4
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Walory J, Ksiazek I, Karynski M, Baraniak A. Twenty-Month Monitoring of Humoral Immune Response to BNT162b2 Vaccine: Antibody Kinetics, Breakthrough Infections, and Adverse Effects. Vaccines (Basel) 2023; 11:1578. [PMID: 37896981 PMCID: PMC10611136 DOI: 10.3390/vaccines11101578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/29/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Vaccination is one of the most effective life-saving medical interventions, and the introduction of SARS-CoV-2 vaccines was intended to prevent the serious implications of COVID-19. The objectives of the study were (i) to observe the humoral immune response to the BNT162b2 vaccine and SARS-CoV-2 infection (mainly breakthrough infections), (ii) to demonstrate the persistence of anti-SARS-CoV-2 antibodies over time in relation to the number of received vaccine doses and the course of infection, and (iii) to determine the adverse effects after primary vaccine doses. METHODS To assess the humoral response, IgG and IgA anti-S1 antibodies were quantified by ELISA assays. In total, the tests were carried out seven times in almost two years. RESULTS We demonstrated strong immunogenicity (compared to levels before primary vaccination, 150- and 20-fold increases in IgG and IgA, respectively) of the BNT162b2 vaccine. Over time, we observed a systematic decline in antibody levels, which may have contributed to breakthrough infections. Although they caused seroconversion similar to the booster, antibody levels in such patients fell more rapidly than after re-vaccination. On the other hand, in individuals who did not receive booster(s) and who did not present breakthrough infection, anti-SARS-CoV-2 antibodies returned to pre-vaccination levels after 20 months. The most commonly recognized adverse effects were injection site redness and swelling. CONCLUSION Vaccination is highly effective in preventing the most severe outcomes of COVID-19 and should be performed regardless of prior infection. Booster doses significantly enhance anti-SARS-CoV-2 antibody levels and, in contrast to those obtained by breakthrough infection, they remain longer.
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Affiliation(s)
- Jaroslaw Walory
- Department of Biomedical Research, National Medicines Institute, 00-725 Warsaw, Poland
| | - Iza Ksiazek
- Department of Biochemistry and Biopharmaceuticals, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Michal Karynski
- Department of Falsified Medicines and Medical Devices, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Anna Baraniak
- Department of Biomedical Research, National Medicines Institute, 00-725 Warsaw, Poland
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5
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Feldberg L, Zvi A, Yahalom-Ronen Y, Schuster O. Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis. Biomedicines 2023; 11:2373. [PMID: 37760814 PMCID: PMC10525290 DOI: 10.3390/biomedicines11092373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
The spread of SARS-CoV-2 variants of concern (VOCs) is of great importance since genetic changes may increase transmissibility, disease severity and reduce vaccine effectiveness. Moreover, these changes may lead to failure of diagnostic measures. Therefore, variant-specific diagnostic methods are essential. To date, genetic sequencing is the gold-standard method to discriminate between variants. However, it is time-consuming (taking several days) and expensive. Therefore, the development of rapid diagnostic methods for SARS-CoV-2 in accordance with its genetic modification is of great importance. In this study we introduce a Mass Spectrometry (MS)-based methodology for the diagnosis of SARS-CoV-2 in propagated in cell-culture. This methodology enables the universal identification of SARS-CoV-2, as well as variant-specific discrimination. The universal identification of SARS-CoV-2 is based on conserved markers shared by all variants, while the identification of specific variants relies on variant-specific markers. Determining a specific set of peptides for a given variant consists of a multistep procedure, starting with an in-silico search for variant-specific tryptic peptides, followed by a tryptic digest of a cell-cultured SARS-CoV-2 variant, and identification of these markers by HR-LC-MS/MS analysis. As a proof of concept, this approach was demonstrated for four representative VOCs compared to the wild-type Wuhan reference strain. For each variant, at least two unique markers, derived mainly from the spike (S) and nucleocapsid (N) viral proteins, were identified. This methodology is specific, rapid, easy to perform and inexpensive. Therefore, it can be applied as a diagnostic tool for pathogenic variants.
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Affiliation(s)
- Liron Feldberg
- Department of Analytical Chemistry, Israel Institute for Biological Research (IIBR), Ness Ziona 74100, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research (IIBR), Ness Ziona 74100, Israel;
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research (IIBR), Ness Ziona 74100, Israel;
| | - Ofir Schuster
- Department of Infectious Diseases, Israel Institute for Biological Research (IIBR), Ness Ziona 74100, Israel;
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Specchiarello E, Matusali G, Carletti F, Gruber CEM, Fabeni L, Minosse C, Giombini E, Rueca M, Maggi F, Amendola A, Garbuglia AR. Detection of SARS-CoV-2 Variants via Different Diagnostics Assays Based on Single-Nucleotide Polymorphism Analysis. Diagnostics (Basel) 2023; 13:1573. [PMID: 37174964 PMCID: PMC10177602 DOI: 10.3390/diagnostics13091573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by fast evolution with the appearance of several variants. Next-Generation Sequencing (NGS) technology is considered the gold standard for monitoring known and new SARS-CoV-2 variants. However, the complexity of this technology renders this approach impracticable in laboratories located in areas with limited resources. We analyzed the capability of the ThermoFisher TaqPath COVID-19 RT-PCR (TaqPath) and the Seegene Novaplex SARS-CoV-2 Variant assay (Novaplex) to detect Omicron variants; the Allplex VariantII (Allplex) was also evaluated for Delta variants. Sanger sequencing (SaS) was the reference method. The results obtained with n = 355 nasopharyngeal samples were: negative with TaqPath, although positive with other qualitative molecular assays (n = 35); undetermined (n = 40) with both the assays; negative for the ∆69/70 mutation and confirmed as the Delta variant via SaS (n = 100); positive for ∆69/70 and confirmed as Omicron BA.1 via SaS (n = 80); negative for ∆69/70 and typed as Omicron BA.2 via SaS (n = 80). Novaplex typed 27.5% of samples as undetermined with TaqPath, 11.4% of samples as negative with TaqPath, and confirmed 100% of samples were Omicron subtypes. In total, 99/100 samples were confirmed as the Delta variant with Allplex with a positive per cent agreement (PPA) of 98% compared to SaS. As undermined samples with Novaplex showed RdRp median Ct values (Ct = 35.4) statistically higher than those of typed samples (median Ct value = 22.0; p < 0.0001, Mann-Whitney test), the inability to establish SARS-CoV-2 variants was probably linked to the low viral load. No amplification was obtained with SaS among all 35 negative TaqPath samples. Overall, 20% of samples which were typed as negative or undetermined with TaqPath, and among them, twelve were not typed even by SaS, but they were instead correctly identified with Novaplex. Although full-genome sequencing remains the elected method to characterize new strains, our data show the high ability of a SNP-based assay to identify VOCs, also resolving samples typed as undetermined with TaqPath.
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Affiliation(s)
- Eliana Specchiarello
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Giulia Matusali
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Fabrizio Carletti
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Cesare Ernesto Maria Gruber
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Claudia Minosse
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Alessandra Amendola
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
| | - Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani (IRCCS), 00149 Rome, Italy
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7
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Van Poelvoorde LAE, Picalausa C, Gobbo A, Verhaegen B, Lesenfants M, Herman P, Van Hoorde K, Roosens NHC. Development of a Droplet Digital PCR to Monitor SARS-CoV-2 Omicron Variant BA.2 in Wastewater Samples. Microorganisms 2023; 11:microorganisms11030729. [PMID: 36985302 PMCID: PMC10059707 DOI: 10.3390/microorganisms11030729] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Wastewater-based surveillance can be used as a complementary method to other SARS-CoV-2 surveillance systems. It allows the emergence and spread of infections and SARS-CoV-2 variants to be monitored in time and place. This study presents an RT-ddPCR method that targets the T19I amino acid mutation in the spike protein of the SARS-CoV-2 genomes, which is specific to the BA.2 variant (omicron). The T19I assay was evaluated both in silico and in vitro for its inclusivity, sensitivity, and specificity. Moreover, wastewater samples were used as a proof of concept to monitor and quantify the emergence of the BA.2 variant from January until May 2022 in the Brussels-Capital Region which covers a population of more than 1.2 million inhabitants. The in silico analysis showed that more than 99% of the BA.2 genomes could be characterized using the T19I assay. Subsequently, the sensitivity and specificity of the T19I assay were successfully experimentally evaluated. Thanks to our specific method design, the positive signal from the mutant probe and wild-type probe of the T19I assay was measured and the proportion of genomes with the T19I mutation, characteristic of the BA.2 mutant, compared to the entire SARS-CoV-2 population was calculated. The applicability of the proposed RT-ddPCR method was evaluated to monitor and quantify the emergence of the BA.2 variant over time. To validate this assay as a proof of concept, the measurement of the proportion of a specific circulating variant with genomes containing the T19I mutation in comparison to the total viral population was carried out in wastewater samples from wastewater treatment plants in the Brussels-Capital Region in the winter and spring of 2022. This emergence and proportional increase in BA.2 genomes correspond to what was observed in the surveillance using respiratory samples; however, the emergence was observed slightly earlier, which suggests that wastewater sampling could be an early warning system and could be an interesting alternative to extensive human testing.
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Affiliation(s)
| | - Corinne Picalausa
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Andrea Gobbo
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | | | - Marie Lesenfants
- Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | | | | | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
- Correspondence:
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8
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Clinical Validation of GenBody COVID-19 Ag, Nasal and Nasopharyngeal Rapid Antigen Tests for Detection of SARS-CoV-2 in European Adult Population. Biomedicines 2023; 11:biomedicines11020493. [PMID: 36831028 PMCID: PMC9953360 DOI: 10.3390/biomedicines11020493] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Accurate and rapid identification of COVID-19 is critical for effective patient treatment and disease outcomes, as well as the prevention of SARS-CoV-2 transmission. Rapid antigen tests (RATs) for identifying SARS-CoV-2 are simpler, faster and less expensive than molecular assays. Any new product to be considered a medical device is subject to evaluation and data analysis to verify the in vitro diagnostic ability to achieve its intended purpose. Clinical validation of such a test is a prerequisite before clinical application. This study was a clinical validation on adult Europeans of GenBody COVID-19 Ag, nasal and nasopharyngeal RATs. A set of 103 positive and 301 negative from nose and nasopharynx samples confirmed by RT-qPCR were examined. The tests were safe to use and showed 100% specificity in both specimens, and high sensitivity of 94.17% (95%CI 87.75% to 97.83%) and 97.09% (95%CI 91.72% to 99.4%), respectively. The parameters were significantly better for samples with higher virus loads (the highest for CT ≤ 25). The GenBody COVID-19 Ag RATs are inexpensive (compared to RT-qPCR), reliable and rapid with high sensitivity and specificity, making them suitable for diagnosis and timely isolation and treatment of COVID-19 patients, contributing to the better control of virus spread.
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9
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Lai A, Bergna A, Della Ventura C, Menzo S, Bruzzone B, Sagradi F, Ceccherini-Silberstein F, Weisz A, Clementi N, Brindicci G, Vicenti I, Sasset L, Caucci S, Corvaro B, Ippoliti S, Acciarri C, De Pace V, Lanfranchi L, Bellocchi MC, Giurato G, Ferrarese R, Lagioia A, Francisci D, Colombo ML, Lazzarin S, Ogliastro M, Cappelletti MR, Iannetta M, Rizzo F, Torti C, Fumi M, d’Avenia M, Brusa S, Greco F, Menchise A, Letizia V, Vaccaro E, Santoro CR, Fraccalvieri C, Testa S, Carioti L, Rocco T, Saracino A, Cattelan A, Clementi M, Sarmati L, Riva A, Galli M, Antinori S, Zehender G. Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April-December 2021 in Italy. Viruses 2022; 14:v14112508. [PMID: 36423117 PMCID: PMC9699621 DOI: 10.3390/v14112508] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 is constantly evolving, leading to new variants. We analysed data from 4400 SARS-CoV-2-positive samples in order to pursue epidemiological variant surveillance and to evaluate their impact on public health in Italy in the period of April-December 2021. The main circulating strain (76.2%) was the Delta variant, followed by the Alpha (13.3%), the Omicron (5.3%), and the Gamma variants (2.9%). The B.1.1 lineages, Eta, Beta, Iota, Mu, and Kappa variants, represented around 1% of cases. There were 48.2% of subjects who had not been vaccinated, and they had a lower median age compared to the vaccinated subjects (47 vs. 61 years). An increasing number of infections in the vaccinated subjects were observed over time, with the highest proportion in November (85.2%). The variants correlated with clinical status; the largest proportion of symptomatic patients (59.6%) was observed with the Delta variant, while subjects harbouring the Gamma variant showed the highest proportion of asymptomatic infection (21.6%), albeit also deaths (5.4%). The Omicron variant was only found in the vaccinated subjects, of which 47% had been hospitalised. The diffusivity and pathogenicity associated with the different SARS-CoV-2 variants are likely to have relevant public health implications, both at the national and international levels. Our study provides data on the rapid changes in the epidemiological landscape of the SARS-CoV-2 variants in Italy.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
- Correspondence: ; Tel.: +39-0250319775
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Carla Della Ventura
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Stefano Menzo
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | | | - Fabio Sagradi
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | | | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Nicola Clementi
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | | | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Lolita Sasset
- Infectious Diseases Unit, Azienda Ospedale Università di Padova, 35128 Padova, Italy
| | - Sara Caucci
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Benedetta Corvaro
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Silvia Ippoliti
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Carla Acciarri
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | | | - Leonardo Lanfranchi
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Maria C. Bellocchi
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Roberto Ferrarese
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | | | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, Santa Maria della Misericordia Hospital, University of Perugia, 06123 Perugia, Italy
| | - Martina L. Colombo
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Samuel Lazzarin
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Matilde Ogliastro
- Department of Health Sciences (DISSAL), University of Genoa, 16126 Genoa, Italy
| | - Maria R. Cappelletti
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Marco Iannetta
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Carlo Torti
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Maurizio Fumi
- UOC Patologia Clinica, AO San Pio Benevento, 82100 Benevento, Italy
| | - Morena d’Avenia
- UOSVD di Citopatologia e Screening, Department of Laboratory Medicines, 70131 Bari, Italy
| | - Stefano Brusa
- Department of Translational Medical Sciences, Università Federico II, 80138 Naples, Italy
| | - Francesca Greco
- UOC Microbiologia e Virologia, PO Cosenza, 87100 Cosenza, Italy
| | - Angela Menchise
- Microbiology and Virology Laboratory, A.O.R. San Carlo Potenza, 85100 Potenza, Italy
| | - Vittoria Letizia
- UOSD Genetics and Molecular Biology, AORN Sant’Anna e San Sebastiano di Caserta, 81100 Caserta, Italy
| | - Emilia Vaccaro
- Molecular Biology Units, AOU ‘S. Giovanni di Dio e Ruggi d’Aragona’ Università di Salerno, 84131 Salerno, Italy
| | | | | | - Sophie Testa
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Teresa Rocco
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | | | - Annamaria Cattelan
- Infectious Diseases Unit, Azienda Ospedale Università di Padova, 35128 Padova, Italy
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | - Loredana Sarmati
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Agostino Riva
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Spinello Antinori
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
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