Self-Collection of Saliva Specimens as a Suitable Alternative to Nasopharyngeal Swabs for the Diagnosis of SARS-CoV-2 by RT-qPCR

A nasopharyngeal swab is a sample used for the diagnosis of SARS-CoV-2 infection. Saliva is a sample easier to obtain and the risk of contagion for the professional is lower. This study aimed to evaluate the utility of saliva for the diagnosis of SARS-CoV-2 infection. This prospective study involved 674 patients with suspected SARS-CoV-2 infection. Paired nasopharyngeal and saliva samples were processed by RT-qPCR. Sensitivity, specificity, and kappa coefficient were used to evaluate the results from both samples. We considered the influence of age, symptoms, chronic conditions, and sample processing with lysis buffer. Of the 674 patients, 636 (94.4%) had valid results from both samples. The virus detection in saliva compared to a nasopharyngeal sample (gold standard) was 51.9% (95% CI: 46.3%–57.4%) and increased to 91.6% (95% CI: 86.7%–96.5%) when the cycle threshold (Ct) was ≤ 30. The specificity of the saliva sample was 99.1% (95% CI: 97.0%–99.8%). The concordance between samples was 75% (κ = 0.50; 95% CI: 0.45–0.56). The Ct values were significantly higher in saliva. In conclusion, saliva sample utility is limited for clinical diagnosis, but could be a useful alternative for the detection of SARS-CoV-2 in massive screening studies, when the availability of trained professionals for sampling or personal protection equipment is limited.

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Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems

10.1101/2020.05.26.20099440 ◽

2020 ◽

Author(s):

Henrik Dimke ◽

Sanne L Larsen ◽

Marianne N Skov ◽

Hanne Larsen ◽

Gitte N Hartmeyer ◽

...

Keyword(s):

Low Cost ◽

Rna Extraction ◽

Diagnostic System ◽

Nasopharyngeal Swab ◽

Analytical Sensitivity ◽

Automated Systems ◽

Suitable Alternative ◽

Fully Integrated ◽

Rna Purification ◽

Sensitivity Specificity

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly reached pandemic levels. Sufficient testing for SARS-CoV-2 remains essential for tracking and containing the rapid spread of the virus. However, due to increased global demand, kits and proprietary reagents for RNA extraction are limited, which markedly reduce SARS-CoV-2 testing capabilities in many countries. Here, we explore the use of conventional acid guanidinium thiocyanate-phenol-chloroform (AGPC)-based RNA purification as an alternative to commercial automated systems for detection of SARS-CoV-2 by RT-qPCR. 87 clinical oropharyngeal or nasopharyngeal swab specimens were extracted by AGPC and compared to the commercial platforms, the Maxwell® RSC 48 instrument for automated RNA extraction and the fully integrated diagnostic system, the Cobas®6800 apparatus. Our results show that RNA extracted using the AGPC method is fully comparable to modern automated systems regarding analytical sensitivity, specificity and accuracy with respect to detection of SARS-CoV-2 as evaluated by RT-qPCR. Moreover, we find that the AGPC method is easily scalable and implemented in conventional laboratories. Taken together, these data identify conventional AGPC-based RNA extraction as a low cost and suitable alternative to automated systems for the detection of SARS-CoV-2, when automated systems, kits and reagents are not readily available.

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Outbreak Of Nipah Encephalitis In Greater Faridpur District

Faridpur Medical College Journal ◽

10.3329/fmcj.v5i2.6825 ◽

1970 ◽

Vol 5 (2) ◽

pp. 63-65

Author(s):

MY Ali ◽

SA Fattah ◽

MM Islam ◽

MA Hossain ◽

SY Ali

Keyword(s):

Health Personnel ◽

Viral Encephalitis ◽

Review Article ◽

Personal Protection ◽

Emerging Infections ◽

College Hospital ◽

Personal Protection Equipment ◽

Medical College ◽

History Of ◽

Deadly Disease

Nipah viral encephalitis is one of the fatal re-emerging infections especially in southeast Asia. After its outbreak in Malaysia and Singapore; repeated outbreaks occurred at western part of Bangladesh especially in Faridpur region. Besides, sporadic attacks appear to occur in the country throughout the year. Here two Nipah outbreaks in greater Faridpur district in 2003 and 2004 are described along with brief review on transmission of the virus. Where the history of illness among patients are very much in favour of man to man transmission. Moreover the death of an intern doctor from Nipah encephalitis who was involved in managing such patients in Faridpur Medical College Hospital strongly suggests man to man transmission of this virus. So, aim of this review article to make the health personnel and general people be aware about man to man transmission of virus, so that they can adapt personal protection equipment (PPE) for their protection against this deadly disease. DOI: 10.3329/fmcj.v5i2.6825Faridpur Med. Coll. J. 2010;5(2):63-65

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Eye in COVID-19: A Brief Review

Pakistan Journal of Ophthalmology ◽

10.36351/pjo.v36i3.1040 ◽

2020 ◽

Vol 36 (3) ◽

Author(s):

Muhammad Mohsin Ali ◽

Qudsia Anwar Dar ◽

Zahid Kamal ◽

Alishba Khan

Keyword(s):

Infection Control ◽

Respiratory Symptoms ◽

Literature Search ◽

Control Measures ◽

Transmission Route ◽

Ocular Manifestation ◽

Personal Protection ◽

Personal Protection Equipment ◽

Ocular Manifestations ◽

Infection Control Measures

This is a brief review covering the currently available literature on ocular manifestations of COVID-19, andprevention strategies for ophthalmologists. A literature search was carried out of Pubmed, Google Scholar andWHO database of publications on COVID. Keywords used in the search were eye, ocular manifestations,ophthalmology, COVID-19, nCoV-2019, and coronavirus disease. All available articles were reviewed and thosepertinent to the study topic were included. Considering the dearth of information available, ophthalmology journals were also searched separately for relevant articles. Major ocular manifestation of COVID reported in literature is red eye, which usually presents before the onset of respiratory symptoms. Since the eye can be a possible transmission route for SARS-CoV-2, infection control measures should be undertaken by ophthalmologists, including use of personal protection equipment and eye/face covering. A framework for structuring ophthalmological services during the COVID pandemic is also presented in this review.

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Pre-Procedural COVID-19 Nasopharyngeal Swab Has Good Concordance with Bronchoalveolar Lavage in Patients at Low Risk for Viral Infection

Respiration ◽

10.1159/000514928 ◽

2021 ◽

pp. 1-5

Author(s):

Catherine L. Oberg ◽

Reza Ronaghi ◽

Erik E. Folch ◽

Colleen L. Channick ◽

Tao He ◽

...

Keyword(s):

Bronchoalveolar Lavage ◽

Low Risk ◽

Lower Airway ◽

Nasopharyngeal Swab ◽

Symptom Screening ◽

The World ◽

Good Concordance ◽

Sensitivity Specificity ◽

Overall Reliability ◽

Rule Out

Background: The coronavirus disease 2019 (COVID-19) pandemic has drastically affected hospital and operating room (OR) workflow around the world as well as trainee education. Many institutions have instituted mandatory preoperative SARS-CoV-2 PCR nasopharyngeal swab (NS) testing in patients who are low risk for COVID-19 prior to elective cases. This method, however, is challenging as the sensitivity, specificity, and overall reliability of testing remains unclear. Objectives: The objective of this study was to assess the concordance of a negative NS in low risk preoperative patients with lower airway bronchoalveolar lavage (BAL) specimens obtained from the same patients. Methods: We prospectively sent intraoperative lower airway BAL samples collected within 48 h of a negative mandatory preoperative NS for SARS-CoV-2 PCR testing. All adult patients undergoing a scheduled bronchoscopic procedure for any reason were enrolled, including elective and nonelective cases. Results: One-hundred eighty-nine patients were included. All BAL specimens were negative for SARS-CoV-2 indicative of 100% concordance between testing modalities. Conclusions: These results are promising and suggest that preoperative nasopharyngeal SARS-CoV-2 testing provides adequate screening to rule out active COVID-19 infection prior to OR cases in a population characterized as low risk by negative symptom screening. This information can be used for both pre-procedural screening and when reintroducing trainees into the workforce.

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Frequency of nasopharyngeal swab collection and positivity for SARS-CoV-2 infection in the population of the Italian province of Udine with and without chronic conditions

Health Policy ◽

10.1016/j.healthpol.2020.12.009 ◽

2020 ◽

Author(s):

Francesca Valent ◽

Giada Mazzilis ◽

Anna Doimo ◽

Corrado Pipan

Keyword(s):

Chronic Conditions ◽

Nasopharyngeal Swab ◽

Italian Province

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Income, wealth and use of personal protection equipment in the Mekong Delta

Environmental Science and Pollution Research ◽

10.1007/s11356-021-13449-w ◽

2021 ◽

Author(s):

Matteo Migheli

Keyword(s):

Low Income ◽

Mekong Delta ◽

Developed Countries ◽

Household Wealth ◽

Protective Equipment ◽

Personal Protection ◽

Personal Protection Equipment ◽

Management Techniques ◽

Using Data ◽

Developing And Developed Countries

AbstractBoth in developing and developed countries, farmers often do not protect themselves adequately, especially when applying agrochemicals that are dangerous for their health. The issue is relevant because insufficient protection is between the causes leading to intoxication of farmers and workers who handle these products. The literature suggests that both lack of training and information and low income may explain why, especially in developing countries, protective equipment is under-used. Using data from the Mekong Delta, this study addresses the issue of whether income and household wealth may help explaining the use of incomplete protections against pesticides. The results suggest that income, more than wealth, is a reason why Vietnamese farmers operating in the Mekong Delta fail in using adequate protections. In particular, the data suggest that they may prefer to divert resources to increasing the production of their fields or to buying goods that may be used both as protection and as everyday garments. This behaviour leads to underinvestment in some important protective goods. Possible public interventions to mitigate the problem are suggested; in particular, the promotion of integrated pest management techniques could be useful.

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Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

Viruses ◽

10.3390/v13040615 ◽

2021 ◽

Vol 13 (4) ◽

pp. 615

Author(s):

Allen Wing-Ho Chu ◽

Cyril Chik-Yan Yip ◽

Wan-Mui Chan ◽

Anthony Chin-Ki Ng ◽

Dream Lok-Sze Chan ◽

...

Keyword(s):

Nucleic Acid ◽

High Throughput ◽

Rna Extraction ◽

Nasopharyngeal Swab ◽

Acid Extraction ◽

Rt Pcr ◽

Nucleic Acid Extraction ◽

Suitable Alternative ◽

Pcr Inhibitors ◽

Pcr Targeting

SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFYTM) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS® easyMAG®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors.

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Comparison of saliva with healthcare workers- and patient-collected swabs in the diagnosis of COVID-19 in a large cohort

BMC Infectious Diseases ◽

10.1186/s12879-021-06343-w ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Mitnala Sasikala ◽

Yelamanchili Sadhana ◽

Ketavarapu Vijayasarathy ◽

Anand Gupta ◽

Sarala Kumari Daram ◽

...

Keyword(s):

Healthcare Workers ◽

Early Stage ◽

Cost Effective ◽

Hospitalized Patients ◽

Detection Sensitivity ◽

Nasopharyngeal Swab ◽

Predictive Values ◽

Qrt Pcr ◽

Asymptomatic Patients ◽

Sensitivity Specificity

Abstract Background A considerable amount of evidence demonstrates the potential of saliva in the diagnosis of COVID-19. Our aim was to determine the sensitivity of saliva versus swabs collected by healthcare workers (HCWs) and patients themselves to assess whether saliva detection can be offered as a cost-effective, risk-free method of SARS-CoV-2 detection. Methods This study was conducted in a hospital involving outpatients and hospitalized patients. A total of 3018 outpatients were tested. Of these, 200 qRT-PCR-confirmed SARS-CoV-2-positive patients were recruited for further study. In addition, 101 SARS-CoV-2-positive hospitalized patients with symptoms were also enrolled in the study. From outpatients, HCWs collected nasopharyngeal swabs (NPS), saliva were obtained. From inpatients, HCWs collected swabs, patient-collected swabs, and saliva were obtained. qRT-PCR was performed to detect SARS-CoV-2 by TAQPATH assay to determine the sensitivity of saliva detection. Sensitivity, specificity and positive/negative predictive values (PPV, NPV) of detecting SARS-CoV-2 were calculated using MedCalc. Results Of 3018 outpatients (asymptomatic: 2683, symptomatic: 335) tested by qRT-PCR, 200 were positive (males: 140, females: 60; aged 37.9 ± 12.8 years; (81 asymptomatic, 119 symptomatic). Of these, saliva was positive in 128 (64%); 39 of 81 asymptomatic (47%),89 of 119 symptomatic patients (74.8%). Sensitivity of detection was 60.9% (55.4–66.3%, CI 95%), with a negative predictive value of 36%(32.9–39.2%, CI 95%).Among 101 hospitalized patients (males:65, females: 36; aged 53.48 ± 15.6 years), with HCW collected NPS as comparator, sensitivity of saliva was 56.1% (47.5–64.5, CI 95%), specificity 63.5%(50.4–75.3, CI95%) with PPV of 77.2% and NPV of 39.6% and that of self-swab was 52.3%(44–60.5%, CI95%), specificity 56.6% (42.3–70.2%, CI95%) with PPV 77.2% and NPV29.7%. Comparison of positivity with the onset of symptoms revealed highest detection in saliva on day 3 after onset of symptoms. Additionally, only saliva was positive in 13 (12.8%) hospitalized patients. Conclusion Saliva which is easier to collect than nasopharyngeal swab is a viable alternate to detect SARS-COV-2 in symptomatic patients in the early stage of onset of symptoms. Although saliva is currently not recommended for screening asymptomatic patients, optimization of collection and uniform timing of sampling might improve the sensitivity enabling its use as a screening tool at community level.

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Detection of influenza virus in rectal swabs of patients admitted in hospital for febrile illnesses in Thailand

SAGE Open Medicine ◽

10.1177/2050312121989631 ◽

2021 ◽

Vol 9 ◽

pp. 205031212198963

Author(s):

Artit Sangkakam ◽

Pasin Hemachudha ◽

Abhinbhen W Saraya ◽

Benjamard Thaweethee-Sukjai ◽

Thaniwan Cheun-Arom ◽

...

Keyword(s):

Influenza Virus ◽

Gastrointestinal Tract ◽

Hospital Stay ◽

Rectal Swab ◽

Average Length ◽

Gastrointestinal Symptoms ◽

Virus Detection ◽

Length Of Hospital Stay ◽

Nasopharyngeal Swab ◽

Influenza Virus Detection

Introduction: Influenza virus favours the respiratory tract as its primary site of host entry and replication, and it is transmitted mainly via respiratory secretions. Nasopharyngeal swab is the gold standard specimen type for influenza detection, but several studies have also suggested that the virus replicates in the human gastrointestinal tract. Methods: A retrospective study was conducted on all patients positive for influenza virus and initially recruited as part of the PREDICT project from 2017 to 2018. The objectives of the study were to investigate whether rectal swab could aid in improving influenza detection, and if there was any correlation between gastrointestinal disturbances and severity of infection, using length of hospital stay as an indicator of severity. Results: Of the 51 influenza-positive patients, 12 had detectable influenza virus in their rectal swab. Among these 12 rectal swab positive patients, influenza virus was not detected in the nasopharyngeal swab of three of them. Gastrointestinal symptoms were observed for 28.2% patients with a negative rectal swab negative and 25.0% patients with a positive rectal swab. Average length of hospital stay was 4.2 days for rectal swab positive group and 3.7 days for rectal swab negative group. This difference was not statistically significant (p = 0.288). Conclusions: There is no correlation between influenza virus detection in rectal swab and gastrointestinal disturbances or disease severity, and there is currently insufficient evidence to support replicative ability in the gastrointestinal tract.

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Sources of SARS-CoV-2 and Other Microorganisms in Dental Aerosols

Journal of Dental Research ◽

10.1177/00220345211015948 ◽

2021 ◽

pp. 002203452110159

Author(s):

A.P. Meethil ◽

S. Saraswat ◽

P.P. Chaudhary ◽

S.M. Dabdoub ◽

P.S. Kumar

Keyword(s):

Infection Control ◽

Dental Treatment ◽

Quantitative Polymerase Chain Reaction ◽

The United States ◽

Control Measures ◽

Personal Protection ◽

Personal Protection Equipment ◽

Linear Discriminant ◽

16S Sequencing ◽

Asymptomatic Patients

On March 16, 2020, 198,000 dentists in the United States closed their doors to patients, fueled by concerns that aerosols generated during dental procedures are potential vehicles for transmission of respiratory pathogens through saliva. Our knowledge of these aerosol constituents is sparse and gleaned from case reports and poorly controlled studies. Therefore, we tracked the origins of microbiota in aerosols generated during ultrasonic scaling, implant osteotomy, and restorative procedures by combining reverse transcriptase quantitative polymerase chain reaction (to identify and quantify SARS-CoV-2) and 16S sequencing (to characterize the entire microbiome) with fine-scale enumeration and source tracking. Linear discriminant analysis of Bray-Curtis dissimilarity distances revealed significant class separation between the salivary microbiome and aerosol microbiota deposited on the operator, patient, assistant, or the environment ( P < 0.01, analysis of similarities). We also discovered that 78% of the microbiota in condensate could be traced to the dental irrigant, while saliva contributed to a median of 0% of aerosol microbiota. We also identified low copy numbers of SARS-CoV-2 virus in the saliva of several asymptomatic patients but none in aerosols generated from these patients. Together, the bacterial and viral data encourage us to conclude that when infection control measures are used, such as preoperative mouth rinses and intraoral high-volume evacuation, dental treatment is not a factor in increasing the risk for transmission of SARS-CoV-2 in asymptomatic patients and that standard infection control practices are sufficiently capable of protecting personnel and patients from exposure to potential pathogens. This information is of immediate urgency, not only for safe resumption of dental treatment during the ongoing COVID-19 pandemic, but also to inform evidence-based selection of personal protection equipment and infection control practices at a time when resources are stretched and personal protection equipment needs to be prioritized.

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