Comparison of SARS-CoV-2 spike RNA sequences in feces and nasopharynx indicates intestinal replication

Abstract

Background Little is known of possible selection and replication of SARS-CoV-2 in the intestines and if viral load in feces is associated with severity of disease. Therefore, sequence variations of the spike region in strains collected from feces and nasopharynx (NPH) from the same patients were compared. It was also investigated whether viral load in feces related to severity of COVID-19 in hospitalized patients. Results SARS-CoV-2 RNA was found in 88 (79%) fecal samples from 112 patients. The complete spike region could be sequenced in 15 fecal and 14 NPH samples. Fourteen Alpha-variants and one Beta-variant of SARS-CoV-2 were identified. The majority of the viral genetic variants (viral populations) in two fecal samples, but none in NPH, had a reversion of the H69/V70 amino acid deletion normally seen in the Alpha variants. Nine fecal samples contained up to nine minority variants, each which may constitute a separate viral population. Five NPH samples had one genetic variant each, and one NPH sample contained nine minority populations of SARS-CoV-2 spike genes. Conclusions The higher genomic diversity of SARS-CoV-2 in feces compared to NPH, and the reversion of the H69/V70 deletion in Alpha variants from feces indicate a selection of viral strains and replication of SARS-CoV-2 in the gastrointestinal tract.

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“…Positive SARS-CoV-2 RNA in feces has CT value of 34.58 (31.35-36.4). This finding is similar to a previous study that showed an average CT value of 33.4 ± 3.4 calculated from 88 samples [23]. In this study, positive detection of RNA in feces was associated with lower CT value of nasopharyngeal and oropharyngeal (NP/OP) swab (P=0.015).…”

Preferential apical infection of intestinal cell monolayers by SARS-CoV-2 is associated with damage to cellular barrier integrity: Implications for the physiopathology of COVID-19

“…However, none of these strains were isolated from faeces, they were all cultured in vitro from nasopharynx swabs. It should be emphasised that a higher genomic diversity of SARS-CoV-2 in faeces compared to the nasopharynx, highlighted a selection of viral strains that replicate in the gastrointestinal tract [45].…”

Infectivity of exhaled SARS-CoV-2 aerosols is sufficient to transmit covid-19 within minutes

“…Each well was inoculated with 250 µL of collected aerosol sample and 250 µL DMEM with 2% FCS for 1 h at 37 °C and 5% CO 2 , and then 2 mL of DMEM with 2% FCS was added. After 72 h, 100 µL supernatant was removed for further analysis by RT-qPCR and next generation sequencing as previously described 29 . Sequences were analyzed using CLC Genomic Workbench 22 (Qiagen, Hilden, Germany) and mutations were analyzed with low frequency variant detection.…”