Viral RNA Load and Infectivity of SARS-CoV-2 in Paired Respiratory and Oral Specimens from Symptomatic, Asymptomatic, or Postsymptomatic Individuals

Abstract

In the present study, we assessed the diagnostic sensitivity and determined the viral RNA load and infectivity of SARS-CoV-2 in paired respiratory (nasopharyngeal and anterior nares) and oral samples (saliva and sublingual swab). Samples were collected from 77 individuals of which 75 were diagnosed with COVID-19 and classified as symptomatic (n = 29), asymptomatic (n = 31), or postsymptomatic (n = 15). Specimens were collected at one time point from each individual, between day 1 and 23 after the initial COVID-19 diagnosis, and included self-collected saliva (S), or sublingual (SL) swab, and bilateral anterior nares (AN) swab, followed by health care provider collected nasopharyngeal (NP) swab. Sixty-three specimen sets were tested using five assay/platforms. The diagnostic sensitivity of each assay/platform and specimen type was determined. Of the 63 specimen sets, SARS-CoV-2 was detected in 62 NP specimens, 52 AN specimens, 59 saliva specimens, and 31 SL specimens by at least one platform. Infectious SARS-CoV-2 was isolated from 21 NP, 13 AN, 12 saliva, and one SL specimen out of 50 specimen sets. SARS-CoV-2 isolation was most successful up to 5 days after initial COVID-19 diagnosis using NP specimens from symptomatic patients (16 of 24 positives, 66.67%), followed by specimens from asymptomatic patients (5 of 17 positives, 29.41%), while it was not very successful with specimens from postsymptomatic patients. Benefits of self-collected saliva and AN specimens balance the loss of sensitivity relative to NP specimens. Therefore, saliva and AN specimens are acceptable alternatives for symptomatic SARS-CoV-2 diagnostic testing or surveillance with increased sampling frequency of asymptomatic individuals. IMPORTANCE The dynamics of infection with SARS-CoV-2 have a significant impact on virus infectivity and in the diagnostic sensitivity of molecular and classic virus detection tests. In the present study we determined the diagnostic sensitivity of paired respiratory (nasopharyngeal and anterior nares swabs) and oral secretions (saliva and sublingual swab) and assessed infectious virus shedding patterns by symptomatic, asymptomatic, or postsymptomatic individuals. Understanding the diagnostic performance of these specimens and the patterns of infectious virus shedding in these bodily secretions provides critical information to control COVID-19, and may help to refine guidelines on isolation and quarantine of positive individuals and their close contacts identified through epidemiological investigations.

Keywords: RT-PCR; SARS-CoV-2; anterior nares; diagnostic; saliva; virus isolation.

FIG 1

Paired specimen sets collected for this study. Specimens were excluded if testing was not performed on all platforms and if SARS-CoV-2 RNA was not detected from any specimen by any platform. After filtering, 63 sets of paired specimens were used for analyses. Of those, 50 sample sets were used for virus isolation.

FIG 2

SARS-CoV-2 cycle threshold (Ct) value across paired specimen types collected from 63 positive individuals. SARS-CoV-2 cycle threshold (Ct) values obtained using the EZ-SARS-CoV-2 assay on the ABI 7500 platform are shown on the y axis. Specimen types included nasopharyngeal swabs (NP, n = 59 with positive Ct values), anterior nares swabs (AN, n = 51 with positive Ct values), saliva (S, n = 54 with positive Ct values), and sublingual swabs (SL, n = 26 with positive Ct values), and are shown on the x axis. The horizontal line in each specimen type indicates the median value (NP = 26.13, AN = 26.19, S = 26.26, SL = 0; 0 Ct value indicates not detected).

FIG 3

SARS-CoV-2 cycle threshold (Ct) values within sets of respiratory and oral specimens collected from 24 positive individuals. SARS-CoV-2 cycle threshold (Ct) values obtained using the EZ-SARS-CoV-2 assay on the ABI 7500 platform are shown on the y axis. Specimen types are shown on the x axis (NP = nasopharyngeal swab, AN = anterior nares swab, S = saliva, SL = sublingual swab). Each paired set collected from an individual patient is distinguished by a different color and symbol combination.

FIG 4

Success of SARS-CoV-2 isolation by specimen type. Specimen types are shown along the x axis (NP = nasopharyngeal swab, AN = anterior nares swab, S = saliva, SL = sublingual swab), and the percent of specimens yielding positive SARS-CoV-2 virus isolation is shown on the y axis.

FIG 5

SARS-CoV-2 isolation from paired respiratory and oral specimens collected from 50 positive individuals. SARS-CoV-2 cycle threshold (Ct) values are shown on the y axis. Days between initial diagnostic test and specimen collection for this study are on the x axis. Successful virus isolation (filled/black symbols) or lack of virus isolation (open symbols) is shown for each specimen.