Abstract
Saliva as a sample matrix has been an attractive alternative for the detection of SARS-CoV-2. However, due to potential variability in collection and processing steps, evaluating a proposed workflow amongst the local population is recommended. Here, we aim to validate the collection and treatment of human saliva as a direct specimen for RT-qPCR-based detection of SARS-CoV-2 in Indonesia. We demonstrated that SARS-CoV-2 target genes were detected in saliva specimens and remained stable for five days either refrigerated or stored at room temperature. The method of processing saliva specimens described in this report bypasses the need for an RNA-extraction process, thereby reducing the cost, time, and manpower required for processing samples. The developed method was tested across nine commercial kits, including the benchmark, to demonstrate its wide applicability on multiple existing workflows. Our developed method achieved an 86% overall agreement rate compared to paired nasopharyngeal and oropharyngeal swab specimens (NPOP). With the assistance of a saliva sampling device, the collection was found to be more convenient for individuals and improved the overall agreement rate to 97%.
Highlights
The first COVID-19 case was reported to the World Health Organization (WHO) on December 31, 2019, and the disease was declared a pandemic on March 11, 2020 (Timeline of WHO’s response to COVID-19)
We found an 89.3% overall agreement between specimens extracted from saliva and nasopharyngeal and oropharyngeal (NPOP), consisting of 84.5% positive percent agreement (PPA) and 100% negative percent agreement (NPA) (Table 1, Supplementary 3)
Numerous references have reported the use of human saliva as an attractive specimen for detection of SARS-CoV-2 infection for its practicality in sampling and processing (Azzi et al, 2020; Ott et al, 2020; Iwasaki et al, 2020; Vogels et al, 2020; Watkins et al, 2020; Wyllie et al, 2020; Xu et al, 2020)
Summary
The first COVID-19 case was reported to the World Health Organization (WHO) on December 31, 2019, and the disease was declared a pandemic on March 11, 2020 (Timeline of WHO’s response to COVID-19). One of the modalities used to diagnose COVID-19 is a nucleic acid amplification test (NAAT), including Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR), which commonly targets the envelope (E), Saliva PCR for SARS-CoV-2 nucleocapsid (N), RNA-dependent RNA polymerase (RdRP), and spike (S) genes (World Health Organization, 2020). Specimens that could be used for NAAT include those obtained from the upper and lower respiratory tracts and gastrointestinal tracts (Wang et al, 2020). Specimens commonly collected from the upper respiratory tracts are nasopharyngeal and oropharyngeal (NPOP) swabs, and those obtained from the lower respiratory tract include bronchoalveolar lavage. The rate of detecting positive infection from bronchoalveolar lavage is superior to that of NPOP swabs; it is commonly obtained from inpatients with severe illness or those undergoing mechanical ventilation (Wang et al, 2020). The stool has been used as a specimen for NAAT methods for SARS-CoV-2 detection, including among children (Zhang et al, 2020)
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