Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms

ABSTRACT The ability to detect SARS-CoV-2 in the upper respiratory tract ceases after 2 to 3 weeks post-symptom-onset in most patients. In contrast, SARS-CoV-2 can be detected in the stool of some patients for greater than 4 weeks, suggesting that stool may hold utility as an additional source for diagnosis. We validated the Cepheid Xpert Xpress SARS-CoV-2 and Hologic Panther Fusion real-time RT-PCR assays for detection of viral RNA in stool specimens and compared performance. We utilized remnant stool specimens (n = 79) from 77 patients with gastrointestinal symptoms. Forty-eight patients had PCR-confirmed COVID-19, and 29 either were nasopharyngeal/oropharyngeal PCR negative or presented for reasons unrelated to COVID-19 and were not tested. Positive percent agreement between the Cepheid and Hologic assays was 93% (95% confidence interval [CI]: 81.1% to 98.2%), and negative percent agreement was 96% (95% CI: 89% to 0.99%). Four discrepant specimens (Cepheid positive only, n = 2; Hologic positive only, n = 2) exhibited average cycle threshold (CT) values of >37 for the targets detected. Of the 48 patients with PCR-confirmed COVID-19, 23 were positive by both assays (47.9%). For the negative patient group, 2/29 were positive by both assays (6.9%). The two stool PCR-positive, nasopharyngeal/oropharyngeal PCR-negative patients were SARS-CoV-2 IgG positive. Our results demonstrate acceptable agreement between two commercially available molecular assays and support the use of stool PCR to confirm diagnosis when SARS-CoV-2 is undetectable in the upper respiratory tract.

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A comparative analysis of outcomes after surgical reconstruction of stenoses in the upper respiratory tract in children

Russian Journal of Pediatric Surgery ◽

10.18821/1560-9510-2021-25-4-235-243 ◽

2021 ◽

Vol 25 (4) ◽

pp. 235-243

Author(s):

A. Yu. Razumovsky ◽

Z. B. Mitupov ◽

V. E. Rachkov ◽

N. S. Stepanenko ◽

A. V. Adler ◽

...

Keyword(s):

Respiratory Tract ◽

Plastic Surgery ◽

Costal Cartilage ◽

Treatment Technique ◽

Upper Respiratory Tract ◽

Surgical Time ◽

Significant Difference ◽

Upper Respiratory ◽

Group 2 ◽

Group 1

Introduction. Definition " upper respiratory tract stenosis " (URTS) includes a large number of nosologies. The most common are cicatricial stenoses, in particular, post-intubation ones as well as bilateral paralysis of the larynx. An important issue for nowadays is choosing the curative modality for such patients.Purpose. To compare outcomes after treating children with URTS.Material and methods. The authors have assessed results of treatment of 110 patients who had reconstructive surgery in 2010-2019. Patients were divided into two groups depending on the nosology: stenosis of the upper respiratory tract (n = 71) and bilateral paralysis of the larynx (n-39). In each group, four types of surgeries were performed: costal cartilage plasty, plasty with T-tube (TT), a modified version of plasty with TT, plasty with a stent. The choice of treatment technique was determined mostly by the tendency to make this or that type of surgery in authors' departments, as well as by the nosology, severity of the disease and patient's age. Decannulation terms, surgical time, early and late postoperative complications as well as relapse-free period were assessed.Results. 66% patients were decannulated in Group 1; in Group 2 - 69%. Group 1 a statistically reliable comparison was possible between the following techniques: costal cartilage plasty and laryngeal stent plasty (p > 0.005) as well as plasty with TT implantation and the proposed modified technique (p > 0.005). While using Mann-Whitney test and Log Rank, the authors found out that in Group 1 there were no significant difference in surgical time, relapse-free period and stenosis degree (p > 0.005). However, decannulation terms after plastic surgery of the larynx with costal cartilage implantation are longer than after plastic surgery with stent implantation (p < 0.005). In Group 2, the authors compared three abovementioned curative modalities, excluding laryngeal plasty with TT implantation. Thus, surgical time for costal cartilage plasty is longer, if to compare to other two techniques (p < 0.005). There is also no significant difference in decannulation terms and relapse-free periods between all three techniques (p > 0.005).Conclusion. The results obtained have demonstrated the effectiveness of long-term stenting with TT placement in children, mainly with cicatricial stenoses, and in older children. The trial also revealed that laryngoplasty with costal cartilage in children with bilateral laryngeal paralysis is an effectiveness choice too.

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Paired nasopharyngeal and deep lung testing for SARS-CoV2 reveals a viral gradient in critically ill patients: a multi-centre study

10.1101/2020.07.19.20156869 ◽

2020 ◽

Author(s):

Islam Hamed ◽

Nesreen Shaban ◽

Marwan Nassar ◽

Sam Love ◽

Martin D Curran ◽

...

Keyword(s):

Viral Load ◽

Respiratory Tract ◽

Critically Ill ◽

Critically Ill Patients ◽

Lower Respiratory Tract ◽

Limit Of Detection ◽

Upper Respiratory Tract ◽

Rt Pcr ◽

Multi Centre Study ◽

Upper Respiratory

Introduction Samples for diagnostic tests for SARS-CoV-2 can be obtained from the upper (nasopharyngeal/oropharyngeal swabs) or lower respiratory tract (sputum or tracheal aspirate or broncho-alveolar lavage - BAL). Data from different testing sites indicates different rates of positivity. Reverse-transcriptase polymerase chain reaction (RT-PCR) allows for semi-quantitative estimates of viral load as time to crossing threshold (Ct) is inversely related to viral load. Objectives The objective of our study was to evaluate SARS-CoV2 RNA loads between paired nasopharyngeal (NP) and deep lung (endotracheal aspirate or BAL) samples from critically ill patients. Methods SARS-CoV-2 RT-PCR results were retrospectively reviewed for 51 critically ill patients from 5 intensive care units in 3 hospitals ; Addenbrookes Hospital Cambridge (3 units), Royal Papworth Cambridge (1 unit), and Royal Sunderland Hospital (1 unit). At the times when paired NP and deep lung samples were obtained, one patient had been on oxygen only, 6 patients on non-invasive ventilation, 18 patients on ECMO, and 26 patients mechanically ventilated. Results Results collected showed significant gradient between NP and deep lung viral loads. Median Ct value was 29 for NP samples and 24 for deep lung samples. Of 51 paired samples, 16 were negative (below limit of detection) on NP swabs but positive (above limit of detection) on deep lung sample, whilst 2 were negative on deep sample but positive on NP (both patients were on ECMO). Conclusions It has been suggested that whilst SARS-CoV1 tends to replicate in the lower respiratory tract, SARS-CoV2 replicates more vigorously in the upper respiratory tract. These data challenge that assumption. These data suggest that viral migration to, and proliferation in, the lower respiratory tract may be a key factor in the progression to critical illness and the development of severe acute respiratory syndrome (SARS). Factors which promote this migration should be examined for association with severe COVID-19. From a practical point of view, patients with suspected severe COVID-19 should have virological samples obtained from the lower respiratory tract where-ever possible, as upper respiratory samples have a significant negative rate.

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The clinical sensitivity of a single SARS-CoV-2 upper respiratory tract RT-PCR test for diagnosing COVID-19 using convalescent antibody as a comparator

Clinical Medicine ◽

10.7861/clinmed.2020-0555 ◽

2020 ◽

Vol 20 (6) ◽

pp. e209-e211 ◽

Cited By ~ 3

Author(s):

Abigail Holborow ◽

Hibo Asad ◽

Lavinia Porter ◽

Poppy Tidswell ◽

Claire Johnston ◽

...

Keyword(s):

Respiratory Tract ◽

Upper Respiratory Tract ◽

Rt Pcr ◽

Clinical Sensitivity ◽

Upper Respiratory ◽

Pcr Test

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Viremia and Nasal and Rectal Shedding of Rotavirus in Gnotobiotic Pigs Inoculated with Wa Human Rotavirus

Journal of Virology ◽

10.1128/jvi.79.9.5428-5436.2005 ◽

2005 ◽

Vol 79 (9) ◽

pp. 5428-5436 ◽

Cited By ~ 69

Author(s):

M. S. Azevedo ◽

L. Yuan ◽

K.-I. Jeong ◽

A. Gonzalez ◽

T. V. Nguyen ◽

...

Keyword(s):

Respiratory Tract ◽

Gastrointestinal Symptoms ◽

Upper Respiratory Tract ◽

Virus Shedding ◽

Diarrhea Virus ◽

Human Rotavirus ◽

Basolateral Side ◽

Gnotobiotic Pigs ◽

Upper Respiratory ◽

Tract Infections

ABSTRACT Respiratory symptoms with rotavirus shedding in nasopharyngeal secretions have been reported in children with and without gastrointestinal symptoms (Zheng et al., 1991, J. Med. Virol. 34:29-37). To investigate if attenuated and virulent human rotavirus (HRV) strains cause upper respiratory tract infections or viremia in gnotobiotic pigs, we inoculated them with attenuated or virulent HRV intranasally, intravenously, or orally or via feeding tube (gavage) and assayed virus shedding. After oral or intranasal inoculation with attenuated HRV, the pigs remained asymptomatic, but 79 to 95% shed virus nasally and 5 to 17% shed virus rectally. After inoculation by gavage, no pigs shed virus nasally or rectally, but all pigs seroconverted with antibodies to HRV. No viremia was detected through postinoculation day 10. Controls inoculated intranasally with nonreplicating rotavirus-like particles or mock inoculated did not shed virus. In contrast, 100% of pigs inoculated with virulent HRV (oral, intranasal, or gavage) developed diarrhea, shed virus nasally and rectally, and had viremia. The infectivity of sera from the viremic virulent HRV-inoculated pigs was confirmed by inoculating gnotobiotic pigs orally with pooled HRV-positive serum. Serum-inoculated pigs developed diarrhea and fecal and nasal virus shedding and seroconverted with serum and intestinal HRV antibodies. Pigs inoculated intravenously with serum or intestinal contents from the viremic virulent HRV-inoculated pigs developed diarrhea, virus shedding, and viremia, similar to the orally inoculated pigs. This study provides new evidence that virulent HRV causes transient viremia and upper respiratory tract infection in addition to gastrointestinal infection in gnotobiotic pigs, confirming previous reports of rotavirus antigenemia (Blutt et al., Lancet 362:1445-1449, 2003). Our data also suggest that intestinal infection might be initiated from the basolateral side of the epithelial cells via viremia. Additionally, virus shedding patterns indicate a different pathogenesis for attenuated versus virulent HRV.

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RELATIONSHIP BETWEEN CLASS I-II MALOCCLUSIONS AND UPPER RESPIRATORY TRACT DISEASES

Актуальні проблеми сучасної медицини Вісник Української медичної стоматологічної академії ◽

10.31718/2077-1096.21.3.173 ◽

2021 ◽

Vol 21 (3) ◽

pp. 173-177

Author(s):

А. Stasiuk ◽

Е.Е. Vyzhenko ◽

Yu. K. Sokolohorska-Nykina ◽

V. D. Kuroyedova

Keyword(s):

Respiratory Tract ◽

Morphological Changes ◽

Class I ◽

Upper Respiratory Tract ◽

Average Value ◽

Group I ◽

Significant Difference ◽

Upper Respiratory ◽

Group 2 ◽

Distal Occlusion

In recent years, there has been an increase in the prevalence of dental anomalies among children, and sagittal occlusion anomalies range from 33 to 67% of them. Quite high prevalence of distal occlusion causes morphological changes in the structure of the dentition that lead not only to functional impairment in the dentofacial system, but also in the entire oropharyngeal area. This forces scientists to search for new methods for the diagnosis and differential diagnosis of the conditions. The purpose of this study is to determine and compare anatomical dimensions (anteroposterior size and volume) of the upper respiratory tract in patients with occlusion pathology class I and II on the basis of cone-beam computed tomography. We measured the width of the upper, lower part of the pharynx according to the McNamara method, and the volume on 46 tomograms of patients with dentoalveolar anomalies aged from 8 to 29 years, who were divided into two groups according to the ANB angle into classes I and II. The patients of the group I had the average volume of 10.1 ± 1.27 cm3. According to the McNamara method, the width of the upper pharynx was 17.41 ± 0.44 mm, and width of the lower pharynx was 10.1 ± 0.73 mm. The patients of group 2 showed that the average value of the airpassageways volume was 9.3 ± 0.71 cm3. There was a statistically significant difference in the reduction of the width of the upper pharynx (р˂0, 05). Decrease in the width of the lower respiratory tract in the 1st and 2nd groups in the patients aged 15-29 years may be associated with changes in the cervical spine, resulting from postural disorders of the locomotive apparatus, which increases with age and affects the severity of the dental anomaly and the narrowing of the airways in the lower part.

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SARS-CoV-2 Detection in Fecal Sample from a Patient with Typical Findings of COVID-19 Pneumonia on CT but Negative to Multiple SARS-CoV-2 RT-PCR Tests on Oropharyngeal and Nasopharyngeal Swab Samples

Medicina ◽

10.3390/medicina57030290 ◽

2021 ◽

Vol 57 (3) ◽

pp. 290

Author(s):

Barbara Brogna ◽

Carlo Brogna ◽

Mauro Petrillo ◽

Adriana Modestina Conte ◽

Giulio Benincasa ◽

...

Keyword(s):

Respiratory Tract ◽

Clinical Symptoms ◽

Nasopharyngeal Swab ◽

Upper Respiratory Tract ◽

Rt Pcr ◽

Chain Reaction ◽

Negative Results ◽

Upper Respiratory ◽

Polymerase Chain ◽

Pcr Test

Reverse transcriptase polymerase chain reaction (RT-PCR) negative results in the upper respiratory tract represent a major concern for the clinical management of coronavirus disease 2019 (COVID-19) patients. Herein, we report the case of a 43-years-old man with a strong clinical suspicion of COVID-19, who resulted in being negative to multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RT-PCR tests performed on different oropharyngeal and nasopharyngeal swabs, despite serology having confirmed the presence of SARS-CoV-2 IgM. The patient underwent a chest computed tomography (CT) that showed typical imaging findings of COVID-19 pneumonia. The presence of viral SARS-CoV-2 was confirmed only by performing a SARS-CoV-2 RT-PCR test on stool. Performing of SARS-CoV-2 RT-PCR test on fecal samples can be a rapid and useful approach to confirm COVID-19 diagnosis in cases where there is an apparent discrepancy between COVID-19 clinical symptoms coupled with chest CT and SARS-CoV-2 RT-PCR tests’ results on samples from the upper respiratory tract.

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Viral load in upper respiratory tract of COVID-19 patients detected by digital PCR

10.21203/rs.3.rs-29834/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Jiankang Zhao ◽

Haibo Li ◽

Hui Li ◽

Qiaoling Wu ◽

Ke Wu ◽

...

Keyword(s):

Viral Load ◽

Respiratory Tract ◽

Digital Pcr ◽

Upper Respiratory Tract ◽

Rt Pcr ◽

Lung Lesions ◽

Viral Loads ◽

Ct Value ◽

Upper Respiratory ◽

Close Contacts

Abstract Background: Upper respiratory tract specimens are widely applicable for the diagnosis of COVID-19. To date, no study has analyzed the actual viral loads in upper respiratory tract and its relationship with the severity of lung lesions, Ct value of RT-PCR and transmission capacity in COVID-19 patients.Methods: We retrospectively enrolled nine COVID-19 patients. Clinical data and close contacts of these patients were investigated. Respiratory samples were tested for SARS-CoV-2 with both normal RT-PCR and droplet digital PCR.Results: All the COVID-19 patients complicated with pneumonia. Viral loads in nasopharyngeal swabs were accurately quantified, and they had no direct correspondence with the severity of lung lesions. The Cycle Threshold (Ct) value of RT-PCR was approximately consistent with the absolute quantification of digital PCR. The spearman correlation coefficient between them was -0.952 with P value < 0.001. Close contacts of patients with very low viral load or no detected virus were not infected.Conclusions: Viral loads in nasopharyngeal swabs, could not predict the severity of lung lesions revealed by CT in COVID-19 patients. The infectious capacity of patients with low or absent viral load in upper respiratory tract was relatively weak, and wearing mask might be helpful for lower its spread.

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Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020

Eurosurveillance ◽

10.2807/1560-7917.es.2020.25.32.2001483 ◽

2020 ◽

Vol 25 (32) ◽

Cited By ~ 43

Author(s):

Anika Singanayagam ◽

Monika Patel ◽

Andre Charlett ◽

Jamie Lopez Bernal ◽

Vanessa Saliba ◽

...

Keyword(s):

Viral Load ◽

Severe Acute Respiratory Syndrome ◽

Respiratory Tract ◽

Symptom Onset ◽

Infectious Virus ◽

Upper Respiratory Tract ◽

Threshold Values ◽

Rt Pcr ◽

Cycle Threshold ◽

Upper Respiratory

Severe acute respiratory syndrome coronavirus 2 viral load in the upper respiratory tract peaks around symptom onset and infectious virus persists for 10 days in mild-to-moderate coronavirus disease (n = 324 samples analysed). RT-PCR cycle threshold (Ct) values correlate strongly with cultivable virus. Probability of culturing virus declines to 8% in samples with Ct > 35 and to 6% 10 days after onset; it is similar in asymptomatic and symptomatic persons. Asymptomatic persons represent a source of transmissible virus.

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Sensitivity of RT-PCR testing of upper respiratory tract samples for SARS-CoV-2 in hospitalised patients: a retrospective cohort study

10.1101/2020.06.19.20135756 ◽

2020 ◽

Cited By ~ 4

Author(s):

Thomas C Williams ◽

Elizabeth Wastnedge ◽

Gina McAllister ◽

Ramya Bhatia ◽

Kate Cuschieri ◽

...

Keyword(s):

Respiratory Tract ◽

Clinical Diagnosis ◽

Gold Standard ◽

Upper Respiratory Tract ◽

Repeated Testing ◽

Rt Pcr ◽

Hospitalised Patients ◽

Human Rnase ◽

Increased Sensitivity ◽

Upper Respiratory

ABSTRACTObjectivesTo determine the sensitivity and specificity of RT-PCR testing of upper respiratory tract (URT) samples from hospitalised patients with COVID-19, compared to the gold standard of a clinical diagnosis.MethodsAll URT RT-PCR testing for SARS-CoV-2 in NHS Lothian, Scotland, United Kingdom between the 7th of February and 19th April 2020 (inclusive) was reviewed, and hospitalised patients were identified. All URT RT-PCR tests were analysed for each patient to determine the sequence of negative and positive results. For those who were tested twice or more but never received a positive result, case records were reviewed, and a clinical diagnosis of COVID-19 allocated based on clinical features, discharge diagnosis, and radiology and haematology results. For those who had negative URT RT-PCR tests but a clinical diagnosis of COVID-19, respiratory samples were retested using a multiplex respiratory panel, a second SARS-CoV-2 RT-PCR assay, and a human RNase P control.ResultsCompared to the gold standard of a clinical diagnosis of COVID-19, the sensitivity of an initial URT RT-PCR for COVID-19 was 82.2% (95% confidence interval 79.0-85.1%). Two consecutive URT RT-PCR tests increased sensitivity to 90.6% (CI 88.0-92.7%). A further 2.2% and 0.9% of patients who received a clinical diagnosis of COVID-19 were positive on a third and fourth test.ConclusionsThe sensitivity of a single RT-PCR test of an URT sample in hospitalised patients is 82.2%. Sensitivity increases to 90.6% when patients are tested twice. A proportion of cases with clinically defined COVID-19 never test positive on URT RT-PCR despite repeated testing.

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