1
|
Lalle E, Mazzotta V, Sberna G, Fabeni L, Garbuglia AR, Mastrorosa I, D’Abramo A, Nicastri E, Girardi E, Antinori A, Maggi F, Bordi L. Saliva Is a Sensitive and Accessible Sample Both for SARS-CoV-2 Detection and for the Evaluation of Treatment Effectiveness in Follow-Up Studies. Viruses 2024; 16:1040. [PMID: 39066203 PMCID: PMC11281700 DOI: 10.3390/v16071040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/18/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Despite emerging evidence indicating that molecular SARS-CoV-2 tests performed on saliva have diagnostic sensitivity and specificity comparable to those observed with nasopharyngeal swabs (NPSs), most in vivo follow-up studies on the efficacy of drugs against SARS-CoV-2 have been performed on NPSs, not considering saliva as a possible alternative matrix. For this reason, in this study, we used, in parallel, saliva and NPS samples for the detection of SARS-CoV-2 by real-time RT-PCR in patients receiving Tixagevimab/Cilgavimab, Nirmatrelvir/Ritonavir, or Sotrovimab as a treatment against SARS-CoV-2. Our results showed a good correlation between the NPS and saliva samples for each drug; moreover, comparable changes in the cycle threshold (Ct) levels in saliva and NPSs were observed both 7 days and 30 days after treatment, thus confirming that the saliva represents a good matrix for in vivo follow-up studies verifying the effectiveness of treatments against SARS-CoV-2.
Collapse
Affiliation(s)
- Eleonora Lalle
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy
| | - Valentina Mazzotta
- Clinical and Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy (I.M.)
| | - Giuseppe Sberna
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy
| | - Anna Rosa Garbuglia
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy
| | - Ilaria Mastrorosa
- Clinical and Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy (I.M.)
| | - Alessandra D’Abramo
- Clinical and Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy (I.M.)
| | - Emanuele Nicastri
- Clinical and Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy (I.M.)
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy
| | - Andrea Antinori
- Clinical and Research Department, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy (I.M.)
| | - Fabrizio Maggi
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy
| | - Licia Bordi
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy
| |
Collapse
|
2
|
Eptaminitaki GC, Parakatselaki ME, Petroulaki C, Marinopoulou D, Pitsikaki A, Tseliou M, Zafiropoulos A, Sourvinos G. Rapid identification of SARS-CoV-2 variants: Validation of the Simplexa SARS-CoV-2 Variant Direct assay. J Virol Methods 2023:114759. [PMID: 37257757 PMCID: PMC10226276 DOI: 10.1016/j.jviromet.2023.114759] [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: 03/07/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/02/2023]
Abstract
The circulation of certain SARS-CoV-2 variants may have a great impact on the epidemiological status of a geographical area; therefore, it is important that their presence is monitored. Currently, the gold standard method used to identify newly emerged variants is sequencing of either genes or whole genomes. However, since this method is relatively expensive and has a long turnaround time, other rapid strategies should also be employed. The current study aimed to evaluate the performance of the Simplexa® SARS-CoV-2 Variants Direct assay, which is a RT-PCR that determines the variant present in a nasopharyngeal swab sample in approximately two hours. Totally, 527 positive samples for SARS-CoV-2 were analyzed from January until December 2022 and next-generation sequencing (NGS) was used as the reference method. The assay showed high sensitivity, ranging from 94.12% to 100%, depending on the variant. The assay also showed high specificity, reaching 100% for Delta and BA.1 variants, and 99.74% and 98.67% for BA.2 and BA.4/BA.5 variants, respectively. Moreover, the assay was able to identify the correct variant category in the presence of any subvariant in the sample. We conclude that the assay can be used to facilitate faster monitoring of circulating SARS-CoV-2 variants, however sequencing cannot be completely replaced, since new variants always emerge, and constant updates are needed, so that the user is able to interpret the melting curve patterns.
Collapse
Affiliation(s)
- Giasemi C Eptaminitaki
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Maria-Eleni Parakatselaki
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Chara Petroulaki
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Dimitra Marinopoulou
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Anthi Pitsikaki
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Melpomeni Tseliou
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - Alexandros Zafiropoulos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| | - George Sourvinos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003 Crete, Greece.
| |
Collapse
|
3
|
Bordi L, Sberna G, Lalle E, Fabeni L, Mazzotta V, Lanini S, Corpolongo A, Garbuglia AR, Nicastri E, Girardi E, Vaia F, Antinori A, Maggi F. Comparison of SARS-CoV-2 Detection in Nasopharyngeal Swab and Saliva Samples from Patients Infected with Omicron Variant. Int J Mol Sci 2023; 24:ijms24054847. [PMID: 36902277 PMCID: PMC10003189 DOI: 10.3390/ijms24054847] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
To compare the detection of the SARS-CoV-2 Omicron variant in nasopharyngeal-swab (NPS) and oral saliva samples. 255 samples were obtained from 85 Omicron-infected patients. SARS-CoV-2 load was measured in the NPS and saliva samples by using Simplexa™ COVID-19 direct and Alinity m SARS-CoV-2 AMP assays. Results obtained with the two diagnostic platforms showed very good inter-assay concordance (91.4 and 82.4% for saliva and NPS samples, respectively) and a significant correlation among cycle threshold (Ct) values. Both platforms revealed a highly significant correlation among Ct obtained in the two matrices. Although the median Ct value was lower in NPS than in saliva samples, the Ct drop was comparable in size for both types of samples after 7 days of antiviral treatment of the Omicron-infected patients. Our result demonstrates that the detection of the SARS-CoV-2 Omicron variant is not influenced by the type of sample used for PCR analysis, and that saliva can be used as an alternative specimen for detection and follow-up of Omicron-infected patients.
Collapse
Affiliation(s)
- Licia Bordi
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
- Correspondence: ; Tel.: +39-0655170693
| | - Giuseppe Sberna
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Eleonora Lalle
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Valentina Mazzotta
- Clinical and Research Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Simone Lanini
- Clinical and Research Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Angela Corpolongo
- Clinical and Research Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Anna Rosa Garbuglia
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Emanuele Nicastri
- Clinical and Research Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Francesco Vaia
- General and Health Management Direction, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Andrea Antinori
- Clinical and Research Department, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy
| |
Collapse
|
4
|
Valentina M, Alessandro CL, Francesca C, Silvia R, Eleonora L, Claudia C, Jessica P, Ilaria M, Serena V, Lavinia F, Alessandra V, Gaetano M, Fabrizio C, Simone L, Emanuela C, Eugenia M, Raffaella L, Pierluca P, Enrico G, AnnaRosa G, Francesco V, Fabrizio M, Emanuele N, Andrea A. Viral load decrease in SARS-CoV-2 BA.1 and BA.2 Omicron sublineages infection after treatment with monoclonal antibodies and direct antiviral agents. J Med Virol 2022; 95:e28186. [PMID: 36184918 PMCID: PMC9539310 DOI: 10.1002/jmv.28186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 01/11/2023]
Abstract
The efficacy on the Omicron variant of the approved early coronavirus disease-2019 (COVID-19) therapies, especially monoclonal antibodies, has been challenged by in vitro neutralization data, while data on in vivo antiviral activity are lacking. We assessed potential decrease from Day 1 to Day 7 viral load (VL) in nasopharyngeal swabs of outpatients receiving Sotrovimab, Molnupiravir, Remdesivir, or Nirmatrelvir/ritonavir for mild-to-moderate COVID-19 due to sublineages BA.1 or BA.2, and average treatment effect by weighted marginal linear regression models. A total of 521 patients (378 BA.1 [73%], 143 [27%] BA.2) received treatments (Sotrovimab 202, Molnupiravir 117, Nirmatrelvir/ritonavir 84, and Remdesivir 118): median age 66 years, 90% vaccinated, median time from symptoms onset 3 days. Day 1 mean VL was 4.12 log2 (4.16 for BA.1 and 4.01 for BA.2). The adjusted analysis showed that Nirmatrelvir/ritonavir significantly reduced VL compared to all the other drugs, except versus Molnupiravir in BA.2. Molnupiravir was superior to Remdesivir in both BA.1 and BA.2, and to Sotrovimab in BA.2. Sotrovimab had better activity than Remdesivir only against BA.1. Nirmatrelvir/ritonavir showed the greatest antiviral activity against Omicron variant, comparable to Molnupiravir only in the BA.2 subgroup. VL decrease could be a valuable surrogate of drug activity in the context of the high prevalence of vaccinated people and low probability of hospital admission.
Collapse
Affiliation(s)
- Mazzotta Valentina
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly,PhD course in Microbiology, Immunology, Infectious Diseases, and Transplants (MIMIT)University of Rome Tor VergataRomeItaly
| | - Cozzi Lepri Alessandro
- Centre for Clinical Research, Epidemiology, Modelling and Evaluation (CREME)Institute for Global HealthUCLLondonUK
| | - Colavita Francesca
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Rosati Silvia
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Lalle Eleonora
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Cimaglia Claudia
- Clinical Epidemiology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Paulicelli Jessica
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Mastrorosa Ilaria
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Vita Serena
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Fabeni Lavinia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Vergori Alessandra
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Maffongelli Gaetano
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Carletti Fabrizio
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Lanini Simone
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Caraffa Emanuela
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Milozzi Eugenia
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Libertone Raffaella
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Piselli Pierluca
- Clinical Epidemiology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Girardi Enrico
- Scientific Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Garbuglia AnnaRosa
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Vaia Francesco
- General Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Maggi Fabrizio
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Nicastri Emanuele
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | - Antinori Andrea
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCSRomeItaly
| | | |
Collapse
|
5
|
SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods. Pathogens 2022; 11:pathogens11091058. [PMID: 36145490 PMCID: PMC9504725 DOI: 10.3390/pathogens11091058] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Since the beginning of COVID-19 pandemic the Real Time sharing of genome sequences of circulating virus supported the diagnostics and surveillance of SARS-CoV-2 and its transmission dynamics. SARS-CoV-2 straightaway showed its tendency to mutate and adapt to the host, culminating in the emergence of variants; so it immediately became of crucial importance to be able to detect them quickly but also to be able to monitor in depth the changes on the whole genome to early identify the new possibly emerging variants. In this scenario, this manuscript aims to provide an overview of the existing methods for the identification of SARS-CoV-2 variants (from rapid method based on identification of one or more specific mutations to Whole Genome sequencing approach-WGS), taking into account limitations, advantages and applications of them in the field of diagnosis and surveillance of SARS-CoV-2.
Collapse
|