Excretion of SARS-CoV-2 through faecal specimens

Abstract

Coronavirus disease 2019 (COVID-19) has become a pandemic with increasing numbers of cases worldwide. SARS-CoV-2, the causative virus of COVID-19, is mainly transmitted through respiratory droplets or through direct and indirect contact with an infected person. The possibility of potential faecal-oral transmission was investigated in this study. We collected 258 faecal specimens from nine provinces in China and detected the nucleic acid of SARS-CoV-2 using real-time RT-PCR. Vero cells were used to isolate the virus from SARS-CoV-2 nucleic acid positive samples, after which sequencing of Spike gene in eight samples was performed. In all, 93 of 258 (36%) stool samples were positive for SARS-CoV-2 RNA. The positive rates of critical, severe, moderate, and mild patients were 54.4%, 56.1%, 30.8%, and 33.3%, respectively. The content of nucleic acid increased within 2 weeks after the onset of the disease. From the perspective of clinical typing, the nucleic acid can be detected in the faeces of critical patients within two weeks and until four to five weeks in the faeces of severe and mild patients. SARS-CoV-2 was isolated from stool specimens of two severe patients. Four non-synonymous mutations in Spike gene were newly detected in three stool samples. A small number of patients had strong faecal detoxification ability. The live virus in faeces could be an important source of contamination, which may lead to infection and further spread in areas with poor sanitary conditions. The findings of this study have public health significance and they should be considered when formulating disease control strategies.

Keywords: COVID-19; clinical typing; faecal specimens; faecal-oral transmission; public health.

Figure 1.

Distribution of nucleic acid content in faecal specimens of COVID-19 patients. Y-axis represents Ct values and X-axis represents the intervals from the onset to sampling (weeks). Various clinical classifications, case numbers and P values are shown above each of the charts. Case numbers of each interval group are indicated on the top. Ct values are marked with black solid circles. The median value of each set of data is indicated by a horizontal line.

Figure 2.

Correlation between Ct values in throat swab/stool specimens from the same COVID-19 patients and disease severity. (A) Mild cases, (B) Moderate cases, (C) Severe cases, (D) Overall. Y axis represents Ct values of throat swab and X axis represents Ct values of stool.. Various clinical classifications and case numbers are shown above each of the charts.. In this study, the CT value of the negative samples was counted as 40.

Figure 3.

Phylogenetic analyses of Spike gene sequences of (A) representative SARS-CoV-2 and other beta-coronaviruses; (B) representative SARS-CoV-2 Spike gene sequences. The strains identified in this study are indicated by black dots, the first isolated Wuhan-Hu-1 strain (GenBank No. NC_045512) is indicated by red dot. The D614G mutation Spike gene sequences were further obtained from GISAID database to compare with the sequences identified in this study.

Figure 4.

Cytopathic effect (CPE) as analysed through electron microscopy after inoculating stool suspension into Vero cells. (A) Complete CPE was observed using optical microscopy after inoculating stool suspension of strain HLJ002 into Vero cells and a virus particle with typical morphology of coronavirus was observed using transmission electron microscopy at (B) high magnification and (C) low magnification, respectively.