SARS-CoV-2 loads in urine, sera and stool specimens in association with clinical features of COVID-19 patients

Abstract

Background: COVID-19 pandemic continues to be a priority in public health worldwide, and factors inherent to SARS-CoV-2 pathogenesis and genomic characteristics are under study. Investigations that evaluate possible risk factors for infection, clinical manifestations, and viral shedding in different specimens also need to clarify possible associations with COVID-19 prognosis and disease outcomes.

Study design: In this study, we evaluated SARS-CoV-2 positivity and estimated viral loads by real-time RT-PCR in stool, sera, and urine samples from 35 patients, with a positive SARS-CoV-2 RNA molecular test in respiratory sample, attended at a University COVID-19 referral hospital in Goiania, Goias, Brazil. Whole-genome sequencing was also performed in samples with higher viral load.

Results: The positivity index was 51.43%, 14.28%, and 5.71% in stool, sera, and urine specimens, respectively. The median viral load was 8.01 × 10⁶ GC/g, 2.03 × 10⁶ GC/mL, and 1.36 × 10⁵ GC/mL in stool, sera, and urine, respectivelly. Of all patients, 88.57% had previous comorbidities, and 48.39% of them had detectable SARS-CoV-2 RNA in at least one type of clinical specimen evaluated by this study (stool, sera or urine). A higher viral load was observed in patients with more than two previous comorbidities and that were classified as severe or critical conditions. Samples with the highest viral loads were sequenced and characterized as B.1.1.33 variant.

Conclusion: We conclude that SARS-CoV-2 RNA is present in more than one type of clinical specimen during the infection, and that the most critical patients had detectable viral RNA in more than one clinical specimen at the same time point.

Keywords: B.1.1.33 variant; SARS-CoV-2 RNA; comorbidity; viral shedding; whole-genome sequencing.

Fig. 1

SARS-CoV-2 RNA positivity indexes in different specimens, according to the patients’ clinical profile. SARS-CoV-2 RNA was detected in urine or sera samples only in patients who presented severe or critical COVID-19.

Fig. 2

SARS-CoV-2 lineages circulating in Goiás between August to October 2020. In blue are the sequences obtained in this study, classified as B.1.1.33 linage. In red are represented the outgroup (Gamma variant). The analysis involved 26 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 27,873 positions in the final dataset.