Quantitative SARS-CoV-2 viral-load curves in paired saliva and nasal swabs inform appropriate respiratory sampling site and analytical test sensitivity required for earliest viral detection

Abstract

Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and pre-symptomatic spread of COVID-19, curb the spread of viral variants by travelers, and maximize efficacy of therapeutic treatments. We designed a study to evaluate the preferred test sensitivity and sample type (saliva and nasal swab) for detecting early infections of COVID-19. We performed a case-ascertained study to monitor household contacts of individuals recently diagnosed with a SARS-CoV-2 infection. From those individuals, we obtained twice-daily self-collected anterior-nares nasal swabs and saliva samples and quantified SARS-CoV-2 RNA viral loads in those samples using high-sensitivity RT-qPCR and RT-ddPCR assays. We found that SARS-CoV-2 RNA first appears in saliva and then in nasal-swab samples. A high-sensitivity (limit of detection of ~103 copies/mL) RNA test detected SARS-CoV-2 virus in saliva 1.5 to 4.5 days before the viral load in the paired nasal-swab samples exceeded the limit of detection of low-sensitivity tests. It was possible to observe a high (>107-108 copies/mL) viral load in saliva samples while the paired nasal swab was either negative or had low (~103 copies/mL) viral load. Our results indicate that both sampling site and test sensitivity must be considered to ensure early detection of SARS-CoV-2 infection: high-sensitivity tests that use saliva can detect SARS-CoV-2 infection days earlier than low-sensitivity tests that use nasal swabs. Furthermore, early in the infection, low-sensitivity tests that use nasal swabs may miss SARS-CoV-2-positive individuals with very high and potentially infectious viral loads in saliva.

Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections in K-12 schools and universities

“…Saliva in comparison, can be reliably self-collected, reducing the burden on healthcare workers and arrives in a format that can readily be pooled [ 6 , 7 , 12 ]. Furthermore, a recent study demonstrated that SAR-CoV-2 was detected in saliva using RT-PCR 1.5–4.5 days before the viral load could be detected in a paired nasal swab [13] , which may explain how an independent group observed a higher efficiency of detecting asymptomatic infected individuals using saliva pooling (pool size of up to 12) when compared to nasal swabbing methods [14] . Although there are many publications discussing pooling, most of these studies consist of predictive modeling, proof-of-concept testing protocols and strategic analyses [ 12 , 15 , 16 ].…”

Laboratory Diagnosis of SARS-CoV-2 Pneumonia

“…Of note, a recent study from Huang et al demonstrated higher RNA expression of the ACE2 receptor and the TMPRSS2 internalization protease in epithelial cells of the glands and oral mucosae, which translated into a higher salivary viral burden [ 17 ]. Moreover, recent evidence provided by Savela et al suggests that high-sensitivity saliva-based tests can detect the presence of SARS-CoV-2 earlier in the infection when compared to self-collected anterior-nares nasal swabs [ 18 ].…”

Testing Saliva to Reveal the Submerged Cases of the COVID-19 Iceberg

“…Compared to the gold standard nasopharyngeal swab, testing saliva for SARS-CoV-2 has been shown to have at least equal, and sometimes higher, sensitivity for detecting asymptomatic carriers (Savela et al, 2021 ; Yokota et al, 2021 ). Recent meta-analyses comparing the efficiency of PCR detection when applied to nasopharyngeal and saliva samples (Butler-Laporte et al, 2021 ; Cañete et al, 2021 ; Khiabani and Amirzade-Iranaq, 2021 ; Lee et al, 2021 ; Moreira et al, 2021 ), confirm the high specificity of saliva, with sensitivity positively correlating with stage of infection (i.e., early) and sampling technique (Tan et al, 2021 ).…”

“…Studies have demonstrated that SARS-CoV-2 RNA can appear in saliva 24–48 h prior to detection by nasopharyngeal swabs (Wyllie et al, 2020 ; Borghi et al, 2021 ), and 1.5–4.5 days prior to detection by anterior nasal swabs (Savela et al, 2021 ). In line with this, evidence also suggests that viral replication in the oral cavity may precede that within the nasopharynx, with multiple oral cells susceptible to SARS-CoV-2 infection (Huang et al, 2021 ).…”