Implications in the quantitation of SARS-CoV2 copies in concurrent nasopharyngeal swabs, whole mouth fluid and respiratory droplets

Kannian, P.; Jayaraman, B. G.; Alamelu, S.; Lavanya, C.; Kumarasamy, N.; Rajan, G.; Ranganathan, K.; Mahanathi, P.; Ashwini, V.; Challacombe, S. J.; Webster-Cyriaque, J.; Johnson, N. W.

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 multispeciality 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: 8.74x10^5) and WMF (median: 3.07x10^4), but lower in RD samples (median: 3.60x10^2). Patients with mild disease had higher copies in the NPS (median: 3.46x10^6), while patients with severe disease had higher copies in the WMF (median: 1.34x10^6) and RD samples (median: 4.29x10^4). 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.