Fig. 1

Gut RNA virome in COVID-19 patients and its temporal changes during disease course. a Effect size of SARS-CoV-2 infection (COVID-19) and host factors on fecal RNA virome composition variation. The effect size and statistical significance was determined via PERMANOVA analysis with permutation test (n=999), **p<0.01, *p<0.05. b Heatmap abundance of fecal RNA virus species in COVID-19 patients and non-COVID-19 controls. CPM, count per million reads. c The abundance of SARS-CoV-2 and PMMoV in non-COVID-19 controls and in COVID-19 patients during hospitalization and after disease resolution. Between group comparison was conducted by Mann-Whitney test, ****p<0.0001, **p<0.01, *p<0.05. d Temporal dissimilarity of patient’s fecal RNA virome to non-COVID-19 fecal RNA viromes over the disease course. Virome dissimilarity of the patient to non-COVID-19 subjects was plotted as the average Bray-Curtis dissimilarity between the indicated fecal virome to all non-COVID-19 viromes. The gray area depicts the dissimilarity range (mean ± s.e.) between non-COVID-19 fecal RNA viromes (the dashed line denotes the mean dissimilarity). “CoV n” denotes COVID-19 patient number. “Day0” denotes baseline date when the first stool was collected after hospitalization; the following time points starting with “Day” represents days since baseline stool collection. Patients labeled with asterisk were those who had markedly more dissimilar DNA virome to non-COVID-19 controls after disease resolution versus their baseline differences to non-COVID-19 controls. e The average (median) Bray-Curtis dissimilarity of patient fecal RNA virome to non-COVID-19 fecal RNA virome during the disease course. For box plots, the boxes extend from the 1st to 3rd quartile (25th to 75th percentile), with the median depicted by a horizontal line. Statistical significance was determined by Mann-Whitney test, ****p<0.0001, **p<0.01