Analysis of viral load in different specimen types and serum antibody levels of COVID-19 patients

Li, Ling; Tan, Chianru; Zeng, Jia; Luo, Chen; Hu, Shi; Peng, Yanke; Li, Wenjuan; Zhi-xiong, Xie; Ling, Yueming; Zhang, Xuejun; Deng, E.; Xu, Haixia; Wang, Jue; Xie, Yudi; Zhou, Yubin; Zhang, Wei; Guo, Yong; Liu, Zhong

doi:10.1186/s12967-020-02693-2

Cited by 45 publications

(50 citation statements)

References 21 publications

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“… 16 Another study reports anal swab positivity rate of 24.32%, and found two subjects with positive anal swab but negative nasopharyngeal swab. 17 This is similar to our finding, where one patient had positive anal swab result with negative nasopharyngeal swab RT-PCR. This particular patient had two negative nasopharyngeal swab 2 days apart, both negative, but CT scan showed multifocal ground glass opacities and the patient is considered a COVID-19 probable case.…”

Section: Discussionsupporting

confidence: 91%

The value of anal swab RT-PCR for COVID-19 diagnosis in adult Indonesian patients

Abdullah

Sudrajat

Muzellina

et al. 2021

BMJ Open Gastroenterol

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ObjectiveThis study will test the performance of the anal swab PCR test when compared with the nasopharyngeal swab PCR test as a diagnostic tool for COVID-19.DesignAn observational descriptive study which included hospitalised suspected, or probable cases of hopitalised COVID-19 patients, conducted in Dr. Cipto Mangunkusumo National Hospital, Ciputra Hospital, Mitra Keluarga Depok Hospital and Mitra Keluarga Kelapa Gading Hospital, Indonesia. Epidemiological, clinical, laboratory and radiology data were obtained. Nasopharyngeal and anal swabs specimens were collected for SARS-CoV-2 RNA detection.ResultsWe analysed 136 subjects as part of this study. The clinical spectrum of COVID-19 manifesation in this study was typical of hospitalised patients, with 25% classified as mild cases, 14.7% in severe condition and 12.5% of subjects classified as having acute respiratory distress syndrome. When compared with nasopharyngeal swab as the standard specimen for reverse transcription polymerase chain reaction (RT-PCR) detection of SARS-CoV-2 antigen, the sensitivity and specificity of the anal swab was 36.7% and 93.8%, respectively. The positive and negative predictive value were 97.8% and 16.5 %, respectively. The performance of the anal swab remained similar when only the subgroup of patients with gastrointestinal symptoms (n=92, 67.6%) was analysed (sensitivity 40% and specificity 91.7%). Out of all the subjects included in analysis, 67.6% had gastrointestinal symptoms. Similarly, 73.3% of patients in the anal swab-positive group had gastrointestinal symptoms. The two most common gastrointestinal symptoms in the subjects’ population were nausea and anorexia.ConclusionAnal swab specimen has low sensitivity (36.7%) but high specificity (93.8%) for detecting SARS-CoV-2 antigen by RT-PCR. Only one additional positive result was found by anal swab among the nasopharyngeal swab-negative group. Anal swab may not be needed as an additional test at the beginning of a patient’s diagnostic investigation and nasopharyngeal swab RT-PCR remains as the standard diagnostic test for COVID-19.

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Section: Discussionsupporting

confidence: 91%

The value of anal swab RT-PCR for COVID-19 diagnosis in adult Indonesian patients

Abdullah

Sudrajat

Muzellina

et al. 2021

BMJ Open Gastroenterol

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“…One such method is wastewater-based epidemiology (WBE), which has provided community-scale information on drug use, personal care products, antibiotic resistance, and pathogen circulation ( Choi et al, 2018 ). SARS-CoV-2 is a promising candidate for WBE because its RNA can be detected in stool of infected individuals ( Li et al, 2021 ; Parasa et al, 2020 ), and wastewater surveillance has been shown to provide early detection of population-level increases in occurrence compared to clinical data in some locations ( Ahmed et al, 2021 ; Chavarria-Miró et al, 2021 ; D'Aoust et al, 2021a ; Gerrity et al, 2021 ; Hata and Honda, 2020 ; Kumar et al, 2021 ; Medema et al, 2020 ; Nemudryi et al, 2020 ; Peccia et al, 2020 ; Randazzo et al, 2020b , 2020a , Wong et al, 2021 ; Zhu et al, 2021 ). However, one meta-analysis study reported that SARS-CoV-2 was detected in stool samples from only 41% of infected patients ( Parasa et al, 2020 ), and the viral load has been shown to vary with disease progression ( Benefield et al, 2020 ; Walsh et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area

et al. 2021

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Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be integrated with COVID-19 case data to inform timely pandemic response. However, more research is needed to apply and develop systematic methods to interpret the true SARS-CoV-2 signal from noise introduced in wastewater samples (e.g., from sewer conditions, sampling and extraction methods, etc.). In this study, raw wastewater was collected weekly from five sewersheds and one residential facility. The concentrations of SARS-CoV-2 in wastewater samples were compared to geocoded COVID-19 clinical testing data. SARS-CoV-2 was reliably detected (95% positivity) in frozen wastewater samples when reported daily new COVID-19 cases were 2.4 or more per 100,000 people. To adjust for variation in sample fecal content, four normalization biomarkers were evaluated: crAssphage, pepper mild mottle virus, Bacteroides ribosomal RNA (rRNA), and human 18S rRNA. Of these, crAssphage displayed the least spatial and temporal variability. Both unnormalized SARS-CoV-2 RNA signal and signal normalized to crAssphage had positive and significant correlation with clinical testing data (Kendall's Tau-b (τ)=0.43 and 0.38, respectively), but no normalization biomarker strengthened the correlation with clinical testing data. Locational dependencies and the date associated with testing data impacted the lead time of wastewater for clinical trends, and no lead time was observed when the sample collection date (versus the result date) was used for both wastewater and clinical testing data. This study supports that trends in wastewater surveillance data reflect trends in COVID-19 disease occurrence and presents tools that could be applied to make wastewater signal more interpretable and comparable across studies.

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“…Blood samples from non-COVID-19 controls were collected following routine guidelines 18 . The COVID-19 patients were classified as mild (clinical symptoms with no sign of pneumonia), moderate (fever and respiratory symptoms), severe (any of the above criteria and following respiratory distress: ≥ 30 breaths/min; oxygen saturation: ≤ 93% at rest; arterial partial pressure of oxygen/fraction of inspired oxygen: ≤ 300 mmHg; cases with chest imaging that shows lesion progression within 24-48 h > 50%), or critical (any of the above criteria and following respiratory failure, mechanical ventilation, shock, organ failure, and requires ICU care) 19 .…”

mentioning

confidence: 99%

Plasma microbiome in COVID-19 subjects: an indicator of gut barrier defects and dysbiosis

Prasad

Floyd

et al. 2021

Preprint

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The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) symptoms. We asked whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n=30) and healthy control (n=16) were collected during hospitalization. Plasma microbiome was analyzed using 16S rRNA sequencing, metatranscriptomic analysis, and gut permeability markers including FABP-2, PGN and LPS in both patient cohorts. Almost 65% (9 out 14) COVID-19 patients showed abnormal presence of gut microbes in their bloodstream. Plasma samples contained predominately Proteobacteria, Firmicutes, and Actinobacteria. The abundance of gram-negative bacteria (Acinetobacter, Nitrospirillum, Cupriavidus, Pseudomonas, Aquabacterium, Burkholderia, Caballeronia, Parabhurkholderia, Bravibacterium, and Sphingomonas) was higher than the gram-positive bacteria (Staphylococcus and Lactobacillus) in COVID-19 subjects. The levels of plasma gut permeability markers FABP2 (1282 [plusmn]199.6 vs 838.1[plusmn]91.33; p=0.0757), PGN (34.64[plusmn]3.178 vs 17.53[plusmn]2.12; p<0.0001), and LPS (405.5[plusmn]48.37 vs 249.6[plusmn]17.06; p=0.0049) were higher in COVID-19 patients compared to healthy subjects. These findings support that the intestine may represent a source for bacteremia and may contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.

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Analysis of viral load in different specimen types and serum antibody levels of COVID-19 patients

Cited by 45 publications

References 21 publications

The value of anal swab RT-PCR for COVID-19 diagnosis in adult Indonesian patients

The value of anal swab RT-PCR for COVID-19 diagnosis in adult Indonesian patients

Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area

Plasma microbiome in COVID-19 subjects: an indicator of gut barrier defects and dysbiosis

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