COVID-19
SARS-CoV-2
diagnosis
sequencing
variants
Journal
Clinical chemistry and laboratory medicine
ISSN: 1437-4331
Titre abrégé: Clin Chem Lab Med
Pays: Germany
ID NLM: 9806306
Informations de publication
Date de publication:
27 06 2022
27 06 2022
Historique:
received:
09
04
2022
accepted:
10
04
2022
pubmed:
23
4
2022
medline:
26
5
2022
entrez:
22
4
2022
Statut:
epublish
Résumé
This document, endorsed by the IFCC Working Group on SARS-CoV-2 Variants, aims to update previous indications for diagnosing acute SARS-CoV-2 infection, taking into consideration the evidence that has emerged after the origin and spread of new lineages and sub-lineages of the virus characterized by mutated genetics and altered biochemical, biological and clinical characteristics. These indications encompass the use of different diagnostic strategies in specific clinical settings, such as high risk of SARS-CoV-2 infection (symptomatic patients), low risk of SARS-CoV-2 infection (asymptomatic subjects) at hospital admission/contact tracing, testing in asymptomatic subjects, in epidemiologic surveys and/or population screening, along with tentative indications for identification of new lineages and/or sub-lineages of SARS-CoV-2.
Identifiants
pubmed: 35452576
pii: cclm-2022-0345
doi: 10.1515/cclm-2022-0345
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
975-981Informations de copyright
© 2022 Walter de Gruyter GmbH, Berlin/Boston.
Références
Lippi, G, Mattiuzzi, C, Henry, BM. Updated picture of SARS-CoV-2 variants and mutations. Diagnosis 2022;9:11–7. https://doi.org/10.1515/dx-2021-0149.
Lippi, G, Henry, BM. The landscape of SARS-CoV-2 genomic mutations. J Lab Precis Med 2022. https://doi.org/10.21037/jlpm-22-17 [Epub ahead of print].
Bohn, MK, Mancini, N, Loh, TP, Wang, CB, Grimmler, M, Gramegna, M, et al.. IFCC interim guidelines on molecular testing of SARS-CoV-2 infection. Clin Chem Lab Med 2020;58:1993–2000. https://doi.org/10.1515/cclm-2020-1412.
World health Organization. Diagnostic testing for SARS-CoV-2. Available at: https://www.who.int/publications/i/item/diagnostic-testing-for-sars-cov-2 [Last accessed 1 Apr 2022].
US Centers for Disease Control and Prevention. Overview of testing for SARS-CoV-2, the virus that causes COVID-19 - updated Feb. 11, 2022. Available at: https://www.cdc.gov/coronavirus/2019-ncov/hcp/testing-overview.html#TestingInfection [Last accessed 1 Apr 2022].
US Centers for Disease Control and Prevention. Interim guidelines for collecting and handling of clinical specimens for COVID-19 testing. Available at: https://www.cdc.gov/coronavirus/2019-ncov/lab/guidelines-clinical-specimens.html [Last accessed 1 Apr 2022].
European Centre for Disease Prevention and Control. Diagnostic testing and screening for SARS-CoV-2. Available at: https://www.ecdc.europa.eu/en/covid-19/latest-evidence/diagnostic-testing [Last accessed 1 Apr 2022].
Lippi, G, Henry, BM, Sanchis-Gomar, F, Mattiuzzi, C. Updates on laboratory investigations in coronavirus disease 2019 (COVID-19). Acta Biomed 2020;91: e2020030. https://doi.org/10.23750/abm.v91i3.10187.
Lippi, G, Simundic, AM, Plebani, M. Potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19). Clin Chem Lab Med 2020;58:1070–6. https://doi.org/10.1515/cclm-2020-0285.
Wollschläger, P, Todt, D, Gerlitz, N, Pfaender, S, Bollinger, T, Sing, A, et al.. SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. Clin Microbiol Infect 2021;27:1353.e1–1353.e5. https://doi.org/10.1016/j.cmi.2021.05.025.
Metzger, CMJA, Lienhard, R, Seth-Smith, HMB, Roloff, T, Wegner, F, Sieber, J, et al.. PCR performance in the SARS-CoV-2 Omicron variant of concern? Swiss Med Wkly 2021;151:w30120. https://doi.org/10.4414/smw.2021.w30120.
Bastos, ML, Perlman-Arrow, S, Menzies, D, Campbell, JR. The sensitivity and costs of testing for SARS-CoV-2 infection with saliva versus nasopharyngeal swabs : a systematic review and meta-analysis. Ann Intern Med 2021;174:501–10. https://doi.org/10.7326/m20-6569.
Lee, RA, Herigon, JC, Benedetti, A, Pollock, NR, Denkinger, CM. Performance of saliva, oropharyngeal swabs, and nasal swabs for SARS-CoV-2 molecular detection: a systematic review and meta-analysis. J Clin Microbiol 2021;59:e02881–20. https://doi.org/10.1128/JCM.02881-20.
Basso, D, Aita, A, Navaglia, F, Mason, P, Moz, S, Pinato, A, et al.. The University of Padua salivary-based SARS-CoV-2 surveillance program minimized viral transmission during the second and third pandemic wave. BMC Med 2022;20:96. https://doi.org/10.1186/s12916-022-02297-1.
Mohapatra, RK, Kandi, V, Verma, S, Dhama, K. Challenges of the omicron (B.1.1.529) variant and its lineages: a global perspective. Chembiochem 2022: e202200059. https://doi.org/10.1002/cbic.202200059.
Sharma, D, Ye, C, Lippi, G, Torrelles, JB, Martinez-Sobrido, L, Gromiha, MM, et al.. In silico evaluation of the impact of the Omicron variant on the sensitivity of RT-qPCR assays for SARS-CoV-2 detection using whole genome sequencing. Res Sq 2022. https://doi.org/10.21203/rs.3.rs-1220446/v1 [Epub ahead of print].
Lippi, G, Plebani, M. The many clinical advantages of reporting the cycle threshold (Ct) value. Ann Transl Med 2022. https://doi.org/10.21037/atm-22-1104 [Epub ahead of print].
Buchta, C, Görzer, I, Chiba, P, Camp, JV, Holzmann, H, Puchhammer-Stöckl, E, et al.. Variability of cycle threshold values in an external quality assessment scheme for detection of the SARS-CoV-2 virus genome by RT-PCR. Clin Chem Lab Med 2020;59:987–94. https://doi.org/10.1515/cclm-2020-1602.
Porru, S, Carta, A, Monaco, MGL, Verlato, G, Battaggia, A, Parpaiola, M, et al.. Health surveillance and response to SARS-CoV-2 mass testing in health workers of a large Italian hospital in Verona, Veneto. Int J Environ Res Publ Health 2020;17:5104. https://doi.org/10.3390/ijerph17145104.
Dinnes, J, Deeks, JJ, Berhane, S, Taylor, M, Adriano, A, Davenport, C, et al.. Rapid, point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection. Cochrane Database Syst Rev 2021;3:CD013705. https://doi.org/10.1002/14651858.CD013705.
Lippi, G, Henry, BM, Plebani, M. LumiraDX SARS-CoV-2 antigen test for diagnosing acute SARS-CoV-2 infection: critical literature review and meta-analysis. Diagnostics 2022;12:947. https://doi.org/10.3390/diagnostics12040947.
Lippi, G, Henry, BM, Adeli, K, Plebani, M. Fujirebio Lumipulse SARS-CoV-2 antigen immunoassay: pooled analysis of diagnostic accuracy. Diagnosis 2022;9:149–56. https://doi.org/10.1515/dx-2022-0021.
Lippi, G, Henry, BM, Montagnana, M, Plebani, M. Diagnostic accuracy of the ultrasensitive S-PLEX SARS-CoV-2 N electrochemiluminescence immunoassay. Clin Chem Lab Med 2022;60:e121–4. https://doi.org/10.1515/cclm-2022-0155.
Lippi, G, Henry, BM, Adeli, K. Diagnostic performance of the fully automated Roche Elecsys SARS-CoV-2 antigen electrochemiluminescence immunoassay: a pooled analysis. Clin Chem Lab Med 2022;60:655–61. https://doi.org/10.1515/cclm-2022-0053.
Lippi, G, Nocini, R, Henry, BM. Critical literature review and pooled analysis of diagnostic accuracy of Ortho Vitros SARS-CoV-2 Antigen Test for diagnosing acute SARS-CoV-2 infections. J Med Biochem 2022;41:1–9.
Basso, D, Aita, A, Padoan, A, Cosma, C, Navaglia, F, Moz, S, et al.. Salivary SARS-CoV-2 antigen rapid detection: a prospective cohort study. Clin Chim Acta 2021;517:54–9. https://doi.org/10.1016/j.cca.2021.02.014.
Favresse, J, Gillot, C, Oliveira, M, Cadrobbi, J, Elsen, M, Eucher, C, et al.. Head-to-Head comparison of rapid and automated antigen detection tests for the diagnosis of SARS-CoV-2 infection. J Clin Med 2021;10:265. https://doi.org/10.3390/jcm10020265.
Patriquin, G, Davidson, RJ, Hatchette, TF, Head, BM, Mejia, E, Becker, MG, et al.. Generation of false-positive SARS-CoV-2 antigen results with testing conditions outside manufacturer Recommendations: a scientific approach to pandemic misinformation. Microbiol Spectr 2021;9: e0068321. https://doi.org/10.1128/Spectrum.00683-21.
Bayart, J-L, Degosserie, J, Favresse, J, Gillot, C, Didembourg, M, Djokoto, HP, et al.. Analytical sensitivity of six SARS-CoV-2 rapid antigen tests for omicron versus Delta variant. Viruses 2022;14:654.
Lippi, G, Henry, BM, Sanchis-Gomar, F. Potential drawbacks of frequent asymptomatic coronavirus disease 2019 (COVID-19) testing. Infect Control Hosp Epidemiol 2021;42:1405–6. https://doi.org/10.1017/ice.2020.1305.
Bohn, MK, Lippi, G, Horvath, AR, Erasmus, R, Grimmler, M, Gramegna, M, et al.. IFCC interim guidelines on rapid point-of-care antigen testing for SARS-CoV-2 detection in asymptomatic and symptomatic individuals. Clin Chem Lab Med 2021;59:1507–15. https://doi.org/10.1515/cclm-2021-0455.
Patriquin, G, Davidson, RJ, Hatchette, TF, Head, BM, Mejia, E, Becker, MG, et al.. Generation of false-positive SARS-CoV-2 antigen results with testing conditions outside manufacturer Recommendations: a scientific approach to pandemic misinformation. Microbiol Spectr 2021;9: e0068321. https://doi.org/10.1128/Spectrum.00683-21.
Greninger, AL, Dien Bard, J, Colgrove, RC, Graf, EH, Hanson, KE, Hayden, MK, et al.. Clinical and infection prevention applications of SARS-CoV-2 genotyping: an IDSA/ASM consensus review document. Clin Infect Dis 2021;1:e0165921. https://doi.org/10.1093/cid/ciab761.
Quer, J, Colomer-Castell, S, Campos, C, Andrés, C, Piñana, M, Cortese, MF, et al.. Next-generation sequencing for confronting virus pandemics. Viruses 2022;14:600. https://doi.org/10.3390/v14030600.
Bhoyar, RC, Jain, A, Sehgal, P, Divakar, MK, Sharma, D, Imran, M, et al.. High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing. PLoS One 2021;16: e0247115. https://doi.org/10.1371/journal.pone.0247115.
Lind, A, Barlinn, R, Landaas, ET, Andresen, LL, Jakobsen, K, Fladeby, C, et al.. Rapid SARS-CoV-2 variant monitoring using PCR confirmed by whole genome sequencing in a high-volume diagnostic laboratory. J Clin Virol 2021;141:104906. https://doi.org/10.1016/j.jcv.2021.104906.
Iketani, S, Liu, L, Guo, Y, Liu, L, Chan, JF, Huang, Y, et al.. Antibody evasion properties of SARS-CoV-2 Omicron sublineages. Nature 2022. https://doi.org/10.1038/s41586-022-04594-4 [Epub ahead of print].
Simon-Loriere, E, Schwartz, O. Towards SARS-CoV-2 serotypes? Nat Rev Microbiol 2022;20:187–8. https://doi.org/10.1038/s41579-022-00708-x.
Lippi, G, Mattiuzzi, C, Henry, BM. Neutralizing potency of COVID-19 vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant. J Med Virol 2022;94:1799–802. https://doi.org/10.1002/jmv.27575.