Antigen concentration, viral load, and test performance for SARS-CoV-2 in multiple specimen types

The relationship between N-antigen concentration and viral load within a specimen and across different specimens is essential for interpretation of rapid diagnostic tests (RDT) clinical performance in different use cases. A prospective study was conducted in Porto Velho, Brazil, to investigate RDT performance in different specimen types as a function of the correlation between antigen concentration and viral load. The study included 214 close contacts with recent exposures to confirmed cases, aged 12 years and older and with various levels of vaccination. Antigen concentration was measured in nasopharyngeal swab (NPS), anterior nares swab (ANS), and saliva specimens. Reverse transcriptase (RT)–PCR was conducted on the NPS and saliva specimens, and two RDTs were conducted on ANS and one on saliva. Antigen concentration correlated with viral load when measured in the same specimen type but not across specimen types. Antigen levels were higher in symptomatic cases compared to asymptomatic/oligosymptomatic cases and lower in saliva compared to NPS and ANS samples. Discordant results between the RDTs conducted on ANS and the RT-PCR on NPS were resolved by antigen concentration values. The analytical limit-of-detection of RDTs can be used to predict the performance of the tests in populations for which the antigen concentration is known. The antigen dynamics across different sample types observed in SARS-CoV-2 disease progression support use of RDTs in nasal samples. Given lower antigen concentrations in saliva, tests using saliva is expected to require improved analytical sensitivity to achieve clinical sensitivity similar to testing of nasal samples. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by grants from The Rockefeller Foundation [2020 HTH 039] and Amazon.com [2D-04020007] to Gonzalo J Domingo. Felipe Gomes Naveca and Valdinete Alves do Nascimento were supported by the National Council for Scientific and Technological Development [grant 403276/2020-9] and Inova Fiocruz / Fundacao Oswaldo Cruz [grant VPPCB-007-FIO-18-2-30 - Knowledge generation]. Felipe Gomes Naveca is a National Council for Scientific and Technological Development (CNPq) fellow. Benchmarking work cited and that was used in analysis was funded by the Bill & Melinda Gates Foundation (https://www.gatesfoundation.org/) via grant INV-016821. The Bill & Melinda Gates Foundation did not have any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: WCG Institutional Review Board (1301165), the CEPEM ethics committee, and Brazil's National Research Ethics Commission approved this study (44351421.0.0000.0011). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced are available online at the Harvard Dataverse