SARS-CoV-2 loads in urine, sera and stool specimens in association with clinical features of COVID-19 patients

Abstract

Background COVID-19 pandemic continues to be a priority in public health worldwide, and factors inherent to SARS-CoV-2 pathogenesis and genomic characteristics are under study. Investigations that evaluate possible risk factors for infection, clinical manifestations, and viral shedding in different specimens also need to clarify possible associations with COVID-19 prognosis and disease outcomes. Study design In this study, we evaluated SARS-CoV-2 positivity and estimated viral loads by real-time RT-PCR in stool, sera, and urine samples from 35 patients, with a positive SARS-CoV-2 RNA molecular test in respiratory sample, attended at a University COVID-19 referral hospital in Goiania, Goias, Brazil. Whole-genome sequencing was also performed in samples with higher viral load. Results The positivity index was 51.43%, 14.28%, and 5.71% in stool, sera, and urine specimens, respectively. The median viral load was 8.01 × 10 6 GC/g, 2.03 × 10 6 GC/mL, and 1.36 × 10 5 GC/mL in stool, sera, and urine, respectivelly. Of all patients, 88.57% had previous comorbidities, and 48.39% of them had detectable SARS-CoV-2 RNA in at least one type of clinical specimen evaluated by this study (stool, sera or urine). A higher viral load was observed in patients with more than two previous comorbidities and that were classified as severe or critical conditions. Samples with the highest viral loads were sequenced and characterized as B.1.1.33 variant. Conclusion We conclude that SARS-CoV-2 RNA is present in more than one type of clinical specimen during the infection, and that the most critical patients had detectable viral RNA in more than one clinical specimen at the same time point.

Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1)

“…L438F mutation was detected several times before, but has not become widespread [104]. One of the most frequently co-occurring with S:T478K non-spike mutation [62].…”

Evidence of SARS-CoV-2 bacteriophage potential in human gut microbiota

“…1 are in line with additional ones reported more recently, like evidence that gut virome is affected by the SARS-CoV-2 infection and may play an important role in the disease progression of coronavirus disease 2019 (COVID-19), 2 the presence of SARS-CoV-2 nucleoprotein (N) in intestinal epithelial cells of approximately 35% of patients with COVID-19 even several weeks or months after initial diagnosis, 3 the high rate of positive polymerase chain reaction (PCR) findings in more than one type of clinical specimen collected up to 43 days after COVID-19 patients had presented the first symptom. 4 To investigate these observations in more detail, we designed and carried out three different experiments, which make use of electron microscopy (EM), mass spectrometry and next-generation sequencing (NGS). The sample A described in Ref.…”

Divergence of wastewater SARS-CoV-2 and reported laboratory-confirmed COVID-19 incident case data coincident with wide-spread availability of at-home COVID-19 antigen tests

“…The duration and magnitude of SARS-CoV-2 RNA shedding via human excretions that enter wastewater might change as different SARS-CoV-2 variants circulate 32 . To date, there are limited quantitative, externally valid data (i.e., measurements reported as concentrations with units of copies per mass or volume of excretion) on SARS-CoV-2 RNA in excretions among individuals infected with different variants, particularly with the newer variants that have emerged over the last year 33,34 . There is one study that inferred that the changing relationship between wastewater SARS-CoV-2 RNA concentration and case data between the Delta and Omicron surges in Arizona, USA was caused by changes in shedding 35 .…”