Ad interim recommendations for diagnosing SARS-CoV-2 infection by the IFCC SARS-CoV-2 variants working group

Abstract 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.

[1]  M. Plebani,et al.  Salivary SARS-CoV-2 antigen rapid detection: A prospective cohort study , 2020, Clinica Chimica Acta.

[2]  G. Lippi,et al.  Potential drawbacks of frequent asymptomatic coronavirus disease 2019 (COVID-19) testing , 2020, Infection Control & Hospital Epidemiology.

[3]  N. Crepaz,et al.  Higher incidence of clear cell adenocarcinoma of the cervix and vagina among women born between 1947 and 1971 in the United States , 2011, Cancer Causes & Control.

[4]  M. Plebani,et al.  The University of Padua salivary-based SARS-CoV-2 surveillance program minimized viral transmission during the second and third pandemic wave , 2022, BMC Medicine.

[5]  Liyuan Liu,et al.  Antibody evasion properties of SARS-CoV-2 Omicron sublineages , 2022, Nature.

[6]  Mathias M. Müller,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 , 2020, Clinical chemistry and laboratory medicine.

[7]  G. Lippi,et al.  IFCC interim guidelines on rapid point-of-care antigen testing for SARS-CoV-2 detection in asymptomatic and symptomatic individuals , 2021, Clinical chemistry and laboratory medicine.

[8]  J. Dogné,et al.  Head-to-Head Comparison of Rapid and Automated Antigen Detection Tests for the Diagnosis of SARS-CoV-2 Infection , 2021, Journal of clinical medicine.

[9]  Devy M. Emperador,et al.  Rapid, point‐of‐care antigen and molecular‐based tests for diagnosis of SARS‐CoV‐2 infection , 2020, The Cochrane database of systematic reviews.

[10]  T. Pumarola,et al.  Next-Generation Sequencing for Confronting Virus Pandemics , 2022, Viruses.

[11]  G. Lippi,et al.  Updated picture of SARS-CoV-2 variants and mutations , 2021, Diagnosis.

[12]  J. Campbell,et al.  The Sensitivity and Costs of Testing for SARS-CoV-2 Infection With Saliva Versus Nasopharyngeal Swabs , 2021, Annals of Internal Medicine.

[13]  G. Lippi,et al.  Neutralizing potency of COVID‐19 vaccines against the SARS‐CoV‐2 Omicron (B.1.1.529) variant , 2022, Journal of medical virology.

[14]  K. Korn,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 , 2021, Clinical Microbiology and Infection.

[15]  Sumit Sharma,et al.  High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing , 2020, bioRxiv.

[16]  O. Schwartz,et al.  Towards SARS-CoV-2 serotypes? , 2022, Nature Reviews Microbiology.

[17]  G. Lippi,et al.  IFCC Interim Guidelines on Molecular Testing of SARS-CoV-2 Infection , 2020, Clinical chemistry and laboratory medicine.

[18]  G. Lippi,et al.  Diagnostic accuracy of the ultrasensitive S-PLEX SARS-CoV-2 N electrochemiluminescence immunoassay , 2022, Clinical chemistry and laboratory medicine.

[19]  M. M. Gromiha,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 , 2022 .

[20]  A. Meyers,et al.  Generation of False-Positive SARS-CoV-2 Antigen Results with Testing Conditions outside Manufacturer Recommendations: A Scientific Approach to Pandemic Misinformation , 2021, medRxiv.

[21]  G. Lippi,et al.  Fujirebio Lumipulse SARS-CoV-2 antigen immunoassay: pooled analysis of diagnostic accuracy , 2022, Diagnosis.

[22]  Arvind Y. M. Sundaram,et al.  Rapid SARS-CoV-2 variant monitoring using PCR confirmed by whole genome sequencing in a high-volume diagnostic laboratory , 2021, Journal of Clinical Virology.

[23]  G. Lippi,et al.  LumiraDX SARS-CoV-2 Antigen Test for Diagnosing Acute SARS-CoV-2 Infection: Critical Literature Review and Meta-Analysis , 2022, Diagnostics.

[24]  K. Dhama,et al.  Challenges of the Omicron (B.1.1.529) Variant and Its Lineages: A Global Perspective , 2022, Chembiochem : a European journal of chemical biology.

[25]  Rose A. Lee,et al.  Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis , 2020, Journal of Clinical Microbiology.

[26]  G. Lippi,et al.  Diagnostic performance of the fully automated Roche Elecsys SARS-CoV-2 antigen electrochemiluminescence immunoassay: a pooled analysis , 2022, Clinical chemistry and laboratory medicine.

[27]  Mario Plebani,et al.  Potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19) , 2020, Clinical chemistry and laboratory medicine.

[28]  S. Porru,et al.  Health Surveillance and Response to SARS-CoV-2 Mass Testing in Health Workers of a Large Italian Hospital in Verona, Veneto , 2020, International journal of environmental research and public health.

[29]  R. Humphries,et al.  Clinical and Infection Prevention Applications of SARS-CoV-2 Genotyping: An IDSA/ASM Consensus Review Document. , 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[30]  J. Dogné,et al.  Analytical Sensitivity of Six SARS-CoV-2 Rapid Antigen Tests for Omicron versus Delta Variant , 2022, Viruses.

[31]  A. Egli,et al.  PCR performance in the SARS-CoV-2 Omicron variant of concern? , 2021, Swiss medical weekly.

[32]  R. Humphries,et al.  Clinical and Infection Prevention Applications of SARS-CoV-2 Genotyping: an IDSA/ASM Consensus Review Document. , 2021, Journal of clinical microbiology.

[33]  G. Lippi,et al.  Updates on laboratory investigations in coronavirus disease 2019 (COVID-19) , 2020, Acta bio-medica : Atenei Parmensis.

[34]  G. Lippi,et al.  The many clinical advantages of reporting the cycle threshold (Ct) value , 2021, Annals of translational medicine.

[35]  R. Evans.  European Centre for Disease Prevention and Control. , 2014, Nursing standard (Royal College of Nursing (Great Britain) : 1987).