Rectally shed SARS-CoV-2 in COVID-19 inpatients is consistently lower than respiratory shedding and lacks infectivity

Abstract

Objectives: Assessment of whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been propagated during intestinal passage and infectivity is conserved when shed rectally by hospitalized individuals.

Methods: An exploratory cohort study including 28 inpatients with coronavirus disease 2019 with estimation of RNA levels by RT-PCR and of viral infectivity by culturing of viral material sampled concomitantly and identically from pharynx and rectum.

Results: SARS-CoV-2 RNA was detected more frequently (91%, 30/33 versus 42%, 14/33, p <0.0001) and at higher concentrations (median levels 2 190 186 IU/mL versus 13 014 IU/mL, p <0.0001) in the pharyngeal swabs than in the rectal swabs. For all sample pairs (n = 33) the rectal swabs contained undetectable or lower SARS-CoV-2 RNA concentrations than their paired pharyngeal swabs. Replicative virus was found in 37% (11/30) of the PCR-positive pharyngeal swabs, whereas none of the PCR-positive rectal swabs could be cultured (0%, 0/14) despite containing SARS-CoV-2 RNA concentrations up to 1 544 691 IU/mL.

Conclusions: Our data draw into question whether SARS-CoV-2 is transmitted readily from faeces.

Keywords: Coronavirus disease 2019; Faeces; Gastrointestinal infection; Severe acute respiratory syndrome Coronavirus 2; Shedding; Transmission; Virus.

Fig. 1

SARS-CoV-2 RNA Cp values and infectious viral load in oropharynx and rectal swab samples from inpatients with coronavirus disease 2019. (a) Dot plot showing Cp values of SARS-CoV-2 RNA for the paired pharyngeal and rectal swabs (n = 33). Sample pairs are connected by lines. Red line indicates detection limit. (b) Representative plaque assay of paired pharyngeal and rectal swab samples in ten-fold serial dilution. No plaque-forming units were detected in the rectal swab (two wells belonging to a sample from another patient have been cropped out of the figure). Abbreviations: Cp, crossing point; ND, not detected; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.