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. 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. 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.

中文翻译：

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粪便和鼻咽中 SARS-CoV-2 刺突 RNA 序列的比较表明肠道复制

关于 SARS-CoV-2 在肠道中可能的选择和复制以及粪便中的病毒载量是否与疾病的严重程度有关，我们知之甚少。因此，比较了从同一患者的粪便和鼻咽 (NPH) 收集的菌株中尖峰区域的序列变异。还调查了粪便中的病毒载量是否与住院患者的 COVID-19 严重程度有关。在 112 名患者的 88 份 (79%) 粪便样本中发现了 SARS-CoV-2 RNA。可以在 15 个粪便和 14 个 NPH 样本中对完整的尖峰区域进行测序。鉴定了 SARS-CoV-2 的 14 个 Alpha 变体和 1 个 Beta 变体。两个粪便样本中的大多数病毒遗传变异体（病毒群体），但在 NPH 中没有，具有通常在 Alpha 变异体中看到的 H69/V70 氨基酸缺失的逆转。九个粪便样本包含多达九个少数变体，每一个都可能构成一个单独的病毒种群。五个 NPH 样本各有一个遗传变异，一个 NPH 样本包含九个少数群体的 SARS-CoV-2 刺突基因。与 NPH 相比，粪便中 SARS-CoV-2 的基因组多样性更高，并且粪便中 Alpha 变体中 H69/V70 缺失的恢复表明病毒株的选择和 SARS-CoV-2 在胃肠道中的复制。