Evidence of SARS-CoV-2 RNA in an Oropharyngeal Swab Specimen, Milan, Italy, Early December 2019

This study reports the coding-complete genome sequence, with variant identifications and phylogenetic analysis, of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) P.1 variant (20J/501Y.V3), obtained from an oropharyngeal swab specimen from a female Bangladeshi patient diagnosed with coronavirus disease 2019 (COVID-19) with no travel history.

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Oropharyngeal Swab Specimen

10.32388/038oc7 ◽

2020 ◽

Author(s):

Keyword(s):

Oropharyngeal Swab ◽

Swab Specimen

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Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal

Microbiology Resource Announcements ◽

10.1128/mra.00169-20 ◽

2020 ◽

Vol 9 (11) ◽

Cited By ~ 39

Author(s):

Ranjit Sah ◽

Alfonso J. Rodriguez-Morales ◽

Runa Jha ◽

Daniel K. W. Chu ◽

Haogao Gu ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Oropharyngeal Swab ◽

Novel Coronavirus ◽

Swab Specimen

A complete genome sequence was obtained for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab specimen of a Nepalese patient with coronavirus disease 2019 (COVID-19), who had returned to Nepal after traveling to Wuhan, China.

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Development of an Oropharyngeal Swab Assembly

2021 Design of Medical Devices Conference ◽

10.1115/dmd2021-1032 ◽

2020 ◽

Author(s):

Chengyang Peng ◽

Tao Shen

Keyword(s):

Clinical Specimen ◽

Disease Diagnosis ◽

Direct Visualization ◽

Sampling Area ◽

Specimen Collection ◽

Training Requirement ◽

Oropharyngeal Swab ◽

Effective Sampling Area ◽

Swab Specimen

Abstract Oropharyngeal (OP) swabbing is a clinical specimen collection method to diagnose the presence of viral infection in the respiratory tract. During the Covid-19 pandemic, OP swab sampling plays an important role in the disease diagnosis. With its advantages in direct visualization of the swab site and less training requirement on medical professionals, OP swab is massively used for COVID-19 specimen collection in many countries. However, patients may demonstrate less tolerance for the OP swabbing by gagging or closing their mouths, which puts the swab tip in contact with the oral palate or tongue and results in defective sampling. Gagging and other involuntary reactions increase the risk to medical workers who are in direct contact with the patients. To solve these issues, this research presents a novel OP swab assembly which can assist adult patients to collect OP swab specimen by themselves or facilitate adults to collect specimens for their children or disable family members. The OP swab assembly has features to mitigate discomforts in the swab procedures as so to reduce involuntary reactions, minimizing specimen contamination. It also has features to keep the mouth open and constrain the motion of the swab tip in the effective sampling area, furtherly ensuring the high quality of the specimen. Experiments were conducted on a standard adult human skull mannequin by using the presented OP swab assembly. The results demonstrated the feasibility and effectiveness of self-collection for OP swabs using the presented assembly and method.

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Prevalence of COVID-19 Among Children and Adolescents While Easing Lockdown Restrictions in Cologne, North Rhine-Westphalia, Germany

Klinische Pädiatrie ◽

10.1055/a-1341-9530 ◽

2021 ◽

Author(s):

Robert Walter Körner ◽

Lutz Thorsten Weber

Keyword(s):

Children And Adolescents ◽

Medical History ◽

Day Care ◽

Pediatric Patients ◽

Upper Respiratory Tract ◽

Care Facilities ◽

Physical Examinations ◽

Oropharyngeal Swab ◽

Tract Infections ◽

Time Of Presentation

Abstract Background In Germany, widespread full closures of schools and day care facilities were part of lockdown measures to control the spread of coronavirus disease 2019 (COVID-19). In the state of North Rhine-Westphalia closures took place on March 16, 2020 and were gradually eased from end of April 2020 until beginning of June 2020. Objective This study aims to evaluate the prevalence of COVID-19 among children and adolescents during the reopening period of schools and day care facilities in Cologne, North Rhine-Westphalia, Germany. It further depicts medical history and results of physical examinations of pediatric patients undergoing a test for severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2). Methods Testing for SARS-CoV-2 was carried out by a naso- and / or oropharyngeal swab by local pediatricians at the time of presentation. Samples were analyzed by real-time reverse transcription polymerase chain reaction (RT-PCR). Medical history and physical examination results were retrospectively analyzed. Results 525 children and adolescents presented mainly with mild upper respiratory tract infections. Three patients were diagnosed with COVID-19. Their medical history and examination results did not stand out from the other patients. Conclusion A precautious stepwise opening of schools and day care facilities was not associated with the occurrence of a relevant prevalence of COVID-19 among children and adolescents. However, a low general prevalence of COVID-19 at the end of the observation period has to be taken into account. Systematic testing might enable adjusted regulations in favor of full closures, especially in the light of increasing evidence for pediatric patients constituting a low-risk group for COVID-19.

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Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis

Diagnostics ◽

10.3390/diagnostics11020363 ◽

2021 ◽

Vol 11 (2) ◽

pp. 363

Author(s):

Vânia M. Moreira ◽

Paulo Mascarenhas ◽

Vanessa Machado ◽

João Botelho ◽

José João Mendes ◽

...

Keyword(s):

Systematic Review ◽

Clinical Performance ◽

Point Of Care ◽

Meta Analysis ◽

High Sensitivity ◽

Nasopharyngeal Swab ◽

Sample Collection ◽

Rt Pcr ◽

Oropharyngeal Swab ◽

Nucleic Acid Assays

The rapid and accurate testing of SARS-CoV-2 infection is still crucial to mitigate, and eventually halt, the spread of this disease. Currently, nasopharyngeal swab (NPS) and oropharyngeal swab (OPS) are the recommended standard sampling techniques, yet, these have some limitations such as the complexity of collection. Hence, several other types of specimens that are easier to obtain are being tested as alternatives to nasal/throat swabs in nucleic acid assays for SARS-CoV-2 detection. This study aims to critically appraise and compare the clinical performance of RT-PCR tests using oral saliva, deep-throat saliva/posterior oropharyngeal saliva (DTS/POS), sputum, urine, feces, and tears/conjunctival swab (CS) against standard specimens (NPS, OPS, or a combination of both). In this systematic review and meta-analysis, five databases (PubMed, Scopus, Web of Science, ClinicalTrial.gov and NIPH Clinical Trial) were searched up to the 30th of December, 2020. Case-control and cohort studies on the detection of SARS-CoV-2 were included. The methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2). We identified 1560 entries, 33 of which (1.1%) met all required criteria and were included for the quantitative data analysis. Saliva presented the higher accuracy, 92.1% (95% CI: 70.0–98.3), with an estimated sensitivity of 83.9% (95% CI: 77.4–88.8) and specificity of 96.4% (95% CI: 89.5–98.8). DTS/POS samples had an overall accuracy of 79.7% (95% CI: 43.3–95.3), with an estimated sensitivity of 90.1% (95% CI: 83.3–96.9) and specificity of 63.1% (95% CI: 36.8–89.3). The remaining index specimens could not be adequately assessed given the lack of studies available. Our meta-analysis shows that saliva samples from the oral region provide a high sensitivity and specificity; therefore, these appear to be the best candidates for alternative specimens to NPS/OPS in SARS-CoV-2 detection, with suitable protocols for swab-free sample collection to be determined and validated in the future. The distinction between oral and extra-oral salivary samples will be crucial, since DTS/POS samples may induce a higher rate of false positives. Urine, feces, tears/CS and sputum seem unreliable for diagnosis. Saliva testing may increase testing capacity, ultimately promoting the implementation of truly deployable COVID-19 tests, which could either work at the point-of-care (e.g. hospitals, clinics) or at outbreak control spots (e.g., schools, airports, and nursing homes).

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Streptococcus pneumoniae carriage in school children

Medical alphabet ◽

10.33667/2078-5631-2021-30-57-60 ◽

2021 ◽

Vol 1 (30) ◽

pp. 57-60

Author(s):

I. N. Protasova ◽

N. V. Bakhareva ◽

N. A. Ilyenkova ◽

E. S. Sokolovskaya ◽

T. A. Elistratova ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Antimicrobial Resistance ◽

School Children ◽

Clonal Diversity ◽

Multidrug Resistant ◽

Clonal Structure ◽

Serotype Distribution ◽

Antibiotic Resistant ◽

Oropharyngeal Swab ◽

Resistant Strains

Purpose. To investigate the serotype distribution, clonal structure and antimicrobial resistance of pneumococci isolated from schoolchildren.Materials and methods. During the period from 2012 to 2018 we examined 498 healthy school children aged 6 to 17 years. Oropharyngeal swab was taken from each child for culture, after that all S. pneumoniae strains were genotyped for serotype and ST-type deduction (PCR and sequencing, respectively). Antimicrobial resistance was also determined.Results. Pneumococcal culture was positive in 10.6 % of children. S. pneumoniae isolates belonged to seven serogroups and seven serotypes. Serogroup 6 and serotype 19F strains (15.1% each), and serogroup 9 strains (13.2%) were the most prevalent. S. pneumoniae33FA/37 and 3 (9.4 and 5.7%), serogroups 15 and 18 (7.6 and 5.7%), and 10A serotype (3.8%) were determined at a lower frequency. 20 detected ST-types belonged to 14 clonal complexes (CCs); CC156, CC447, and CC320 were predominant. 1.9% of isolates were penicillin-resistant; 13.2% – macrolide-, clindamycin-, and tetracycline-resistant. S. pneumoniae antibiotic resistant strains belonged to multidrug-resistant CCs 320, 315, and 156.Conclusion. S. pneumoniae prevalence in school children is not high. Pneumococcal population is characterized by serotype and clonal diversity including ‘invasive’ serotypes and genotypes. Most of strains are susceptible to antimicrobials.

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Comparison among nasopharyngeal swab, nasal wash, and oropharyngeal swab for respiratory virus detection in adults with acute pharyngitis

BMC Infectious Diseases ◽

10.1186/1471-2334-13-281 ◽

2013 ◽

Vol 13 (1) ◽

Cited By ~ 22

Author(s):

Li Li ◽

Qiao-Yan Chen ◽

Yun-Ying Li ◽

Yan-Fang Wang ◽

Zi-Feng Yang ◽

...

Keyword(s):

Respiratory Virus ◽

Virus Detection ◽

Nasopharyngeal Swab ◽

Nasal Wash ◽

Acute Pharyngitis ◽

Oropharyngeal Swab

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At-home self-collection of saliva, oropharyngeal swabs and dried blood spots for SARS-CoV-2 diagnosis and serology: post-collection acceptability of specimen collection process and patient confidence in specimens

10.1101/2020.06.10.20127845 ◽

2020 ◽

Cited By ~ 1

Author(s):

Mariah Valentine-Graves ◽

Eric Hall ◽

Jodie Guest ◽

Elizabeth Adam ◽

Rachel Valencia ◽

...

Keyword(s):

Immune Response ◽

Educational Level ◽

Laboratory Testing ◽

Dried Blood Spots ◽

Specimen Collection ◽

Oropharyngeal Swab ◽

Race Ethnicity ◽

Patient Confidence ◽

Blood Spot ◽

At Home

AbstractBackgroundOptions to increase the ease of testing for SARS-CoV-2 infection and immune response are needed. Self-collection of diagnostic specimens at home offers an avenue to allow people to test for SARS-CoV-2 infection or immune response without traveling to a clinic or laboratory. Before this study, survey respondents indicated willingness to self-collect specimens for COVID-related tests, but hypothetical willingness can differ from post-collection acceptability after participants collect specimens.Methods153 US adults were enrolled in a study of the willingness and feasibility of patients to self-collect three diagnostic specimens (saliva, oropharyngeal swab (OPS) and dried blood spot (DBS) card) while observed by a clinician through a telehealth session. After the specimens were collected, 148 participants participated in a survey about the acceptability of the collection, packing and shipping process, and their confidence in the samples collected for COVID-related laboratory testing.ResultsA large majority of participants (>84%) reported that collecting, packing and shipping of saliva, OPS, and DBS specimens were acceptable. Nearly nine in 10 (87%) reported being confident or very confident that the specimens they collected were sufficient for laboratory analysis. There were no differences in acceptability for any specimen type, packing and shipping, or confidence in samples by gender, age, race/ethnicity, or educational level.ConclusionsSelf-collection of specimens for SARS-CoV-2 testing and preparing and shipping specimens for analysis were acceptable in a diverse group of US adults. Further refinement of materials and instructions to support self-collection of saliva, OPS and DBS specimens for COVID-related testing is needed.Trial registrationNo intervention was tested in this study

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Wide application of minimally processed saliva on multiple RT-PCR kits for SARS-CoV-2 detection in Indonesia

10.1101/2021.04.01.21254743 ◽

2021 ◽

Author(s):

Caroline Mahendra ◽

Maria M. M. Kaisar ◽

Suraj R. Vasandani ◽

Sem Samuel Surja ◽

Enty Tjoa ◽

...

Keyword(s):

Target Genes ◽

Local Population ◽

Rna Extraction ◽

Human Saliva ◽

Attractive Alternative ◽

Rt Pcr ◽

Sampling Device ◽

Agreement Rate ◽

Extraction Step ◽

Oropharyngeal Swab

Saliva as a sample matrix has been an attractive alternative for the detection of SARS-CoV-2. However, due to potential variability in collection and processing steps, it is recommended to evaluate a proposed workflow amongst the local population. Here, we aim to validate collection and treatment of human saliva as a direct specimen for RT-qPCR based detection of SARS-CoV-2 in Indonesia. We demonstrated that SARS-CoV-2 target genes were detected in saliva specimen and remained stable for five days refrigerated or room temperature storage. The method of processing saliva specimen described in this report is free from RNA-extraction step, thereby reduces cost, time, and manpower required for processing samples. The developed method was validated for use on three COVID-19 RT-PCR kits commercially available. Our developed method achieved 85% agreement rate when compared to paired nasopharyngeal and oropharyngeal swab specimens (NPOP). With the assistance of a specimen sampling device, QuickSpit(TM), collection was found to be more convenient for individuals and improved agreement rate to 90%.

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