Implications in the quantitation of SARS-CoV2 copies in concurrent nasopharyngeal swabs, whole mouth fluid and respiratory droplets
Authors: Kannian Priya , Jayaraman Bagavad Gita , Alamelu Swarna , Lavanya Chandra , Kumarasamy Nagalingeswaran , Rajan Gunaseelan , Ranganathan Kannan , Mahanathi Pasuvaraj , Ashwini Veeraraghavan , Challacombe Stephen J. , Webster-Cyriaque Jennifer , Johnson Newell W. 
Published: January 2021

Importance

The nasopharyngeal swab (NPS) is considered the ideal diagnostic specimen for Covid-19, while WMF is recently promoted due to collection simplicity and importance in disease transmission. There is limited knowledge on the relative viral load in these samples – NPS, whole mouth fluid (WMF) and respiratory droplets (RD; another important source in transmission), on how the loads vary with disease severity and on how much virus is shed.

Objective

To quantify and compare SARS-CoV2 copies in the NPS, WMF and RD samples, and correlate with disease severity.

Design

Cross sectional study.

Setting

Tertiary care multi-speciality hospital with limited resources in a low-to-middle income country.

Participants

Eighty suspected COVID-19 patients were recruited from the COVID-19 out-patient clinic and hospital isolation wards.

Intervention

Concurrent NPS, WMF and RD samples were collected from all the recruited patients and tested for SARS-CoV2 copies by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR).

Main outcomes and measures

The main outcome was COVID-19 measured by SARS-CoV2 quantitative RT-PCR in NPS samples. COVID-19 disease severity was determined according to NIH criteria. Virus shedding was defined as the presence of SARS-CoV2 copies in the WMF and RD samples.

Results

SARS-CoV2 was detected in 55/80 (69%) of the NPS samples. Of these 55, WMF and RD samples were positive in 44 (80%) and 17 (31%), respectively. The concordance of WMF with NPS was 84% (p=0.02). SARS-CoV2 copy numbers were comparable in the NPS (median: 8.74×10^5) and WMF (median: 3.07×10^4), but lower in RD samples (median: 3.60×10^2). Patients with mild disease had higher copies in the NPS (median: 3.46×10^6), while patients with severe disease had higher copies in the WMF (median: 1.34×10^6) and RD samples (median: 4.29×10^4). The 25-75% interquartile range of NPS SARS-CoV2 copies was significantly higher in the WMF (p=0.0001) and RD (p=0.01) positive patients.

Conclusion and relevance

SARS-CoV2 copies are highest in NPS samples. WMF is a reliable surrogate sample for diagnosis. High copy numbers in the NPS imply initial virological phase and higher risk of virus shedding via WMF and RD.

Key points

Question

How the numbers of SARS-CoV2 copies in nasopharyngeal swab (NPS) samples might reflectvirus shedding from the whole upper aerodigestive tract and indicatedisease severity?

Findings

In this cross-sectional study involving 80 suspected COVID-19 patients, the data indicate higher SARS-CoV2 copies in NPS samples of patients with mild disease,and in the whole mouth fluid (WMF) and respiratory droplet (RD) samples of patients with severe disease. Patients with higher SARS-CoV2 copies in the NPS shed the virus in the WMF and RD samples at statistically higher levels.

Meaning

High SARS-CoV2 copies in NPS samples imply initial virological phase withhigh levels of shedding through both WMF and RD.