Nasopharyngeal Swab Collection Research Articles

Perceived distress due to nasopharyngeal swab collection: Correspondence.

Perceived distress due to nasopharyngeal swab collection: Correspondence.

Efficacy of SARS-CoV-2 detection from used surgical masks compared with standard detection method

The real-time reverse transcription-polymerase chain reaction (RT-PCR) test is the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. Proper specimen collection and obtaining a sufficient specimen are the most essential steps for laboratory diagnosis. The nasopharyngeal (NP) swab is recommended as the reference collection method. However, NP swab collection is invasive and uncomfortable for patients and poses some risk to healthcare workers. This study aimed to compare the efficacy of SARS-CoV-2 RNA detection from surgical masks with the NP swab method using RT-PCR testing. Of 269 patients, RT-PCR RNA from NP swabs was detected among 82 patients (30.5%) and was undetected among 187 patients (69.5%). All patients were tested for SARS-CoV-2 RNA from surgical masks. SARS-CoV-2 RNA was detected in 25/82 (30.5%) surgical mask filters, while undetected among 57 (69.5%). For the surgical mask with an average use time of 7.05 h, the sensitivity was 30.5%, the specificity was 100.0%, with positive predictive value of 100.0% and negative predictive value of 76.2%. Therefore, surgical masks could be an alternative non-invasive specimen source for SARS-CoV-2 RT-PCR testing. The results of our study suggest that the test could be employed after wearing surgical masks for at least 8-12 h, with increased sensitivity when used for more than 12 h.

Influenza A, like Omicron SARS-CoV-2, Is Similarly Detected in Saliva or Nasopharyngeal Samples via RT-qPCR.

After the Coronavirus pandemic, the importance of virus surveillance was highlighted, reinforcing the constant necessity of discussing and updating the methods for collection and diagnoses, including for other respiratory viruses. Although the nasopharyngeal swab is the gold-standard sample for detecting and genotyping SARS-CoV-2 and Influenza viruses, its collection is uncomfortable and requires specialized teams, which can be costly. During the pandemic, non-invasive saliva samples proved to be a suitable alternative for SARS-CoV-2 diagnosis, but for Influenza virus the use of this sample source is not recognized yet. In addition, most SARS-CoV-2 comparisons were conducted before the Omicron variant emerged. Here, we aimed to compare Influenza A and Omicron RT-qPCR analysis of nasopharyngeal swabs and saliva self-collection in paired samples from 663 individuals. We found that both nasopharyngeal swab and saliva collection are efficient for the diagnosis of Omicron (including sub-lineages) and for Influenza A, with high sensitivity and accuracy (>90%). The kappa index is 0.938 for Influenza A and 0.905 for SARS-CoV-2. These results showed excellent agreement between the two samples reinforcing saliva samples as a reliable source for detecting Omicron and highlighting saliva as a valid sample source for Influenza detection, considering this cheaper and more comfortable alternative.

Comparison of the safety, effectiveness, and usability of swab robot vs. manual nasopharyngeal specimen collection

BackgroundHealthcare workers face a risk of infection during aerosol-generating procedures, such as nasal swabbing. Robot-assisted nasopharyngeal sampling aims to minimize this risk and reduce stress for healthcare providers. However, its effectiveness and safety require validation. MethodsWe conducted a controlled trial with 80 subjects at two teaching hospitals and compared robot-collected vs manually-collected nasopharyngeal swabs. The primary outcomes included specimen quality and success rate of nasopharyngeal swab collection. We also recorded the pain index, duration of the collection, and psychological stress using a post-collection questionnaire. ResultsDuring the study period, from September 23 to October 27, 2020, 40 subjects were enrolled in both the robotic and manual groups. The cycle threshold (Ct) value for nasopharyngeal specimens was statistically higher in the robotic group compared to the manual group (30.9 vs 28.0, p < 0.01). Both groups had Ct values under 35, indicating good quality specimens. In the robotic group, 3 out of 40 subjects required a second attempt at specimen collection, resulting in a success rate of 92.5 %. Further, although the pain levels were lower in the robotic group, the difference was not statistically significant (2.8 vs 3.6, p = 0.07). The manual group had a shorter sampling time, which was 29 s (201 vs 29, p < 0.05). However, when factoring in the time needed to put on personal protective equipment, the average time for the manual group increased to 251 s (201 vs 251, p < 0.05). Participants' questionnaire results show comparable psychological stress in both groups. Medical staff expressed that using a robot would reduce their psychological stress. ConclusionsWe propose a safe and effective robotic technology for collecting nasopharyngeal specimens without face-to-face contact, which may reduce the stress of physicians and nurses. This technology can also be optimized for efficiency, making it useful in situations where droplet-transmitted infectious diseases are a concern.

Higher SARS-CoV-2 detection of oropharyngeal compared with nasopharyngeal or saliva specimen for molecular testing: a multicentre randomised comparative accuracy study

BackgroundTesting is critical for detecting SARS-CoV-2 infection, but the best sampling method remains unclear.ObjectivesTo determine whether nasopharyngeal swab (NPS), oropharyngeal swab (OPS) or saliva specimen collection has the highest detection...

A simplified nasopharyngeal swab collection procedure for minimizing patient discomfort while retaining sample quality.

A nasopharyngeal swab (NPS) is the most frequently collected sample type when molecular diagnosis of respiratory viruses, including SARS CoV-2, is required. An optimal collection technique would provide sufficient sample quality for the diagnostic process and would minimize the discomfort felt by the patient. This study compares a simplified NPS collection procedure with only one rotation of the swab to a more standard procedure with five rotations. Swabs were collected from 76 healthy volunteers by the same healthcare professional on 2 consecutive days at a similar hour to minimize variability. The number of Ubiquitin C copy number per sample was measured by real-time quantitative PCR and patient discomfort was assessed by questionnaire. No statistically significant difference (p = 0.15) was observed in the Ubiquitin C copy number per sample between a NPS collected with one rotation (5.2 ± 0.6 log UBC number copies/sample) or five rotations (5.3 ± 0.5 log UBC number copies/sample). However, a statistically significant difference was observed in discomfort between these two procedures, the second being much more uncomfortable. Additional analysis of the results showed a weak correlation between discomfort and the number of human cells recovered (Spearman's rho = 0.202) and greater discomfort in younger people. The results of this study show that a NPS collected with one slow rotation has the same quality as a NPS collected with five rotations. However, the collection time is shorter and, most importantly, less unpleasant for patients.

Perceived distress due to nasopharyngeal swab collection: Correspondence.

Dear Editor, we would like to correspond on the publication “Assessment of perceived distress due to nasopharyngeal swab collection in healthy Indian infants participating in a clinical trial1”. Nasopharyngeal swab collection caused significant distress, which worsened with age, according to Kawade et al.1 The authors concluded that sample collectors should be properly trained, and parents should be encouraged to participate in the procedure.1 We agree that effective clinical specimen collection can lead to a high diagnostic yield and give patients the most comfort. However, regardless of the invasiveness of the treatment, fear of specimen collection is a prevalent problem among pediatric patients.2 Children may experience severe pain, worry, and suffering during a specimen collecting procedure.3, 4 Most young children who had clinical specimens collected reported having a lot of fear before the procedure.3 Children who experienced more moderate to severe pain throughout the specimen collection process were more likely to have high pre-procedural anxiety.4 To lessen the discomfort experienced during the procedure, anxiety-reducing therapies should be investigated.4 To lessen the subjects' worry and terror, a standard quality control for specimen collecting procedure as well as patient preparation is required. The reported distress may have been lessened had the authors applied effective distraction during the procedure. Any distraction method could have been chosen.2 Distraction tactics of any kind have been shown to significantly lower the perception of pain and anxiety.2 Kawade et al. should provide details on the distraction technique(s) used with the children in their study. None.

SG-APSIC1062: The role of active surveillance in the primary-care setting during a pandemic in Singapore

Objectives: In response to the COVID-19 pandemic, primary care swiftly transformed and re-established patient flow in clinics to red, orange, and green zones based on a set of screening criteria. To further manage the influx of suspected COVID-19 patients and their needs safely, a list of surveillance audit criteria was developed to ensure good infection control standards. Methods: The infection control team prepared the surveillance audit criteria based on recommended CDC/WHO guidelines for pandemic preparedness. These criteria were contextualized to the primary-care polyclinic setting. The surveillance audit criteria were grouped according to their category: screening, triage, early recognition and source control, inventory management of personal protective equipment (PPE), infection control measures in the red zone, precautionary measures during collection of nasopharyngeal swabs and environmental cleaning and disinfection for premises in the red, orange, and green zones, respectively. The infection control liaison nurses in each polyclinic were trained to use the checklist to ensure consistency in interpretation of the criteria. Results: Surveillance audits were conducted biweekly in the first 3 months then monthly once the compliance rate was steady at 90%–100% for all categories. The overall average compliance rate since commencing in March 2020 for all polyclinics was sustained at 90%–100%. Common findings included inappropriate use of PPE (eg, self-contamination during removal of gown or wrong sequence of doffing), inadequate ventilation, and inadequate cleaning processes. All findings were corrected immediately, and staff education was provided. Conclusions: Primary care plays an important role during a pandemic. It is essential that both patients and healthcare workers in the primary care setting are protected from infection risk during a pandemic. Having a good surveillance audit process helps ensure that primary care services can continue for the general population. Surveillance is an essential component of the health system’s response to a pandemic.

Are We Truly Safe? Unfolding the Final Chapters of COVID-19 Walk-Through Booths.

This research proposes a safety strategy for coronavirus disease 2019 (COVID-19) walk-through booths to optimize pandemic preparedness. These booths, designed for respiratory sample collection during the COVID-19 pandemic, effectively reduce infection risk and personal protective equipment-related fatigue among healthcare workers. However, inadequate disinfection and glove management could escalate infection transmission. Using computational fluid dynamics simulations, we analyzed droplet dispersion on booth surfaces and gloves under various wind conditions. Our findings suggest that when setting up COVID-19 walk-through booths, their location should be strategically chosen to minimize the effects of wind. All surfaces of booth gloves must be thoroughly disinfected with a certified disinfectant after nasopharyngeal swab collection. It is also recommended to wear disposable gloves over booth gloves when changing between patient examinations. In wind-affected areas, individuals nearby should not solely rely on the 2-meter distancing rule due to potential droplet spread from walk-through booths. We strongly recommend consistent and proper mask use for effective droplet blocking. Adherence to these guidelines can significantly enhance the safety and efficiency of walk-through booths, particularly in potential future pandemics.

Saliva as a Viable and Simple Alternative to Nasopharyngeal and Oropharyngeal Swabs for COVID-19 Real-Time Reverse Transcriptase Polymerase Chain Reaction

Introduction: Attributable to the difficulties in specimen collection, discomfort and symptoms caused on by Nasopharyngeal (NPS) and Oropharyngeal Swab (OPS) collection, and significant risk to Healthcare Workers (HCW), evaluation of an alternative specimen for the diagnosis of Coronavirus Disease 2019 (COVID-19) is required. Saliva specimen could be an alternative specimen with many advantages over NPS and OPS, however little is known about how well it performs this purpose. Aim: The present study was conducted to assess the efficacy of saliva as a viable and simple alternative specimen to NPS and OPS for COVID-19 Real-Time reverse transcriptase Polymerase Chain Reaction (rRT-PCR). Materials and Methods: The present cross-sectional study was conducted in the Department of Microbiology, SGT Medical College Hospital and Research Institute, Haryana, India, from July 2020 to December 2020. A total of 60 symptomatic and 20 asymptomatic COVID-19 patients were recruited for the study and specimen viz., saliva, NPS and OPS were collected at four different sampling points i.e., on day 1, 5, 7 and 14 after confirmation of COVID-19 rRT-PCR test positivity. Data obtained from the study was analysed and expressed as median, frequency, interquartile range and Chi-square test was done for comparison of categorical variables. Results: Majority of the patients in symptomatic hospitalised COVID-19 patients were males (n=49, 81.7%) and remaining were females (n=11, 18.3%) and in asymptomatic group 8 (40%) were males and 12 (60%) were females. Saliva was the most sensitive specimen (74.2%), followed by NPS, Naso Oropharyngeal Swab (NOPS) with 70.8% each and OPS (65.8%) for detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in symptomatic patients at four different sampling points. Comparable findings were also observed in specimens obtained from asymptomatic individuals as well. In addition, the viral load was also highest in saliva sample, as measured by Cycle Threshold (CT)-value. Across all specimen types, high viral load (lower CT-values) was observed during the early period of infection. Majority of the study participants reported discomfort during NPS and OPS collection (90% and 85%, respectively), lacrimation, sneezing and gag reflex being the most commonly reported induced symptoms. Conclusion: In the present study, saliva could be a viable and alternate specimen for COVID-19 diagnosis due to its ease in sample collection, specimen stability and reduced risk of transmission of infection due to droplets.

1953. Immune responses, viral shedding, and COVID-19 symptom burden from breakthrough SARS-CoV-2 infection in a 2:1 randomized, double-blind, placebo-controlled Phase 3 study of AZD1222 (ChAdOx1 nCoV-19) vaccination

Abstract Background Breakthrough infections post-COVID-19 vaccination increase with waning immunity and typically produce milder disease than infections in unvaccinated individuals. We investigated immuno-virologic responses and COVID-19 symptom burden upon breakthrough infection in participants from a Phase 3 study of 2-dose primary series AZD1222 vaccination (NCT04516746) to explore disease attenuation. Methods Study participants who experienced protocol-defined COVID-19 symptoms initiated a series of illness visits over 28 days with collection of sera, nasopharyngeal (NP) swabs and saliva samples (SS), and documentation of symptoms (data-cut off: July 30, 2021). For baseline-seronegative participants with PCR-confirmed SARS-CoV-2 infection ≥15 days after dose 2 of AZD1222 or placebo we assessed: anti-SARS-CoV-2 spike (S), nucleocapsid (N) and neutralizing antibody (Ab) titers by multiplex immunoassay and SARS-CoV-2 pseudovirus assay in sera; viral load by quantitative RT-PCR in NP swabs; and viral shedding by qualitative and quantitative RT-PCR in SS. Data were stratified by age and SARS-CoV-2 variant, and time since primary series dose 2. Results Illness Day 1 (ILL-D1) S Ab GMTs in AZD1222 vaccinees were similar to peak GMTs seen 14 days after dose 2 of AZD1222 and were higher vs placebo at all timepoints. The magnitude of S Ab response differed by age: median GMTs were lower at ILL-D1 and higher at ILL-D14 in vaccinees aged ≥65 vs 18–64 years (Fig.1). ILL-D1 overall, SARS-CoV-2 ancestral, alpha, and epsilon variant viral load titers in NP swabs were lower in vaccinees vs placebo (Fig 2). Mean viral load in NP swabs and viral shedding titers in SS were lower in vaccinees vs placebo at all timepoints. Vaccinees reported fewer COVID-19 symptoms than placebo participants, and experienced shorter symptom duration, particularly for fatigue and difficulty breathing. Figure 1. SARS-CoV-2 spike IgG antibody titers upon SARS-CoV-2 infection by participant age in AZD1222 vaccinees and placebo recipients during illness visits Figure 2. Quantification of viral load (nasopharyngeal swabs quantitative viral titer) by SARS-CoV-2 variant at Illness Visit Day 1 Conclusion Improved S Ab responses, lower viral loads, and reduced symptom burden upon breakthrough infection in vaccinees vs placebo recipients, suggest that robust recall responses to AZD1222 vaccination may attenuate COVID-19 disease severity and duration. These findings alongside data on cellular immune responses to breakthrough infection will inform understanding of protective immunity to SARS-CoV-2 infection. Disclosures Magdalena E. Sobieszczyk, MD, MPH, Bill and Melinda Gates Foundation: Grant/Research Support|Gilead Sciences: Grant/Research Support|Janssen Global Services, LLC: Grant/Research Support|Merck: Grant/Research Support|National Institute of Allergy and Infectious Diseases (NIAID): Grant/Research Support|National Institutes of Health (NIH): Grant/Research Support|Sanofi Pasteur Inc.: Grant/Research Support Ann R. Falsey, MD, BioFire Diagnostics: Grant/Research Support|Janssen: Grant/Research Support|Merck, Sharp and Dohme: Grant/Research Support|Novavax: Advisor/Consultant|Pfizer: Grant/Research Support Anne F. Luetkemeyer, MD, AstraZeneca: Grant/Research Support|Gilead Sciences: Grant/Research Support Grant C. Paulsen, MD, AstraZeneca: Grant/Research Support|Moderna: Grant/Research Support|Pfizer: Grant/Research Support Sharon A. Riddler, MD, National Institute of Allergy and Infectious Diseases (NIAID): Grant/Research Support|National Institutes of Health (NIH): Grant/Research Support|Novimmune: Advisor/Consultant Merlin L. Robb, MD, Walter Reed Army Institute of Research: Advisor/Consultant Charlotte-Paige M. Rolle, MD, MPH, Gilead Sciences: Board Member|Gilead Sciences: Grant/Research Support|Gilead Sciences: Honoraria|Janssen: Board Member|ViiV Healthcare: Board Member|ViiV Healthcare: Grant/Research Support|ViiV Healthcare: Honoraria|Vindico CME: Honoraria Beverly E. Sha, MD, Gilead Sciences: Grant/Research Support|MATEC: Honoraria|University of Chicago: Grant/Research Support|US Government: Grant/Research Support Bahar Ahani, BSC, AstraZeneca: Employee|AstraZeneca: Stocks/Bonds Anastasia A. Aksyuk, PhD, AstraZeneca: Employee|AstraZeneca: Stocks/Bonds Himanshu Bansal, MS, AstraZeneca: Employee|AstraZeneca: Stocks/Bonds Justin A. Green, MD, AstraZeneca: Employee|AstraZeneca: Stocks/Bonds Brett Jepson, MS, AstraZeneca: Contractor via Cytel Jill Maaske, MD, AstraZeneca: Employee|AstraZeneca: Stocks/Bonds Kathryn Shoemaker, MS, AstraZeneca: Employee|AstraZeneca: Stocks/Bonds Stephanie Sproule, MMath, AstraZeneca: Contractor via Joule/System One Ann Marie Stanley, PhD, AstraZeneca: Employee|AstraZeneca: Stocks/Bonds Deidre Wilkins, BSC, AstraZeneca: Employee|AstraZeneca: Stocks/Bonds Tonya L. Villafana, PhD, MPH, AstraZeneca: Employee|AstraZeneca: Stocks/Bonds Elizabeth J. Kelly, PhD, AstraZeneca: Employee|AstraZeneca: Stocks/Bonds.

Difference in CT RT-PCR Value of SARS-COV-2 on VTM Non-inactivated with VTM Inavtivated

Nasopharyngeal swab collection for SARS-CoV-2 examination by RT-PCR requires Viral Transport Medium (VTM) using VTM non-activated and inactivated. This study determined the difference in CT values for SARS CoV-2 RT-PCR examination in non-activated VTM and inactivated VTM. This study is a comparative analytical study with a cross-sectional method using 20 confirmed positive samples for SARS-CoV-2 at RSU. Dr. Suyoto was analyzed by the T-Independent test (N gene) and Mann-Whitney test (ORF1ab gene) using SPSS with α=0.05. The results showed that VTM non-inactivated had a mean CT value of the N gene 33.56 ± 1.39 and the ORF1ab gene 35.4 ± 1.94, while VTM inactivated had an average CT value of 32.24 ± 1.44 for the N and ORF1ab gene 33.93 ± 3.22. Statistical analysis was tested by the T-independent test (N gene), and the Mann Whitney test (ORF1ab gene) between the use of VTM non-inactivated and VTM inactivated in the SARS CoV-2 RT-PCR examination, obtained p-value 0.05 with a mean difference the results of Ct gene n (p=0.006) and gene ORF1ab (p=0.028). This indicated a difference in the mean C CT value of the SARS CoV-2 RT-PCR examination in non-activated VTM and inactivated VTM.

Difference in CT RT-PCR Value of SARS-COV-2 on VTM Non-inactivated with VTM Inavtivated

Nasopharyngeal swab collection for SARS-CoV-2 examination by RT-PCR requires Viral Transport Medium (VTM) using VTM non-activated and inactivated. This study determined the difference in CT values for SARS CoV-2 RT-PCR examination in non-activated VTM and inactivated VTM. This study is a comparative analytical study with a cross-sectional method using 20 confirmed positive samples for SARS-CoV-2 at RSU. Dr. Suyoto was analyzed by the T-Independent test (N gene) and Mann-Whitney test (ORF1ab gene) using SPSS with α=0.05. The results showed that VTM non-inactivated had a mean CT value of the N gene 33.56 ± 1.39 and the ORF1ab gene 35.4 ± 1.94, while VTM inactivated had an average CT value of 32.24 ± 1.44 for the N and ORF1ab gene 33.93 ± 3.22. Statistical analysis was tested by the T-independent test (N gene), and the Mann Whitney test (ORF1ab gene) between the use of VTM non-inactivated and VTM inactivated in the SARS CoV-2 RT-PCR examination, obtained p-value 0.05 with a mean difference the results of Ct gene n (p=0.006) and gene ORF1ab (p=0.028). This indicated a difference in the mean C CT value of the SARS CoV-2 RT-PCR examination in non-activated VTM and inactivated VTM.

Evaluation of Four Fully Integrated Molecular Assays for the Detection of Respiratory Viruses during the Co-Circulation of SARS-CoV-2, Influenza and RSV.

Background: The clinical presentation of viral respiratory infections is unspecific. We assessed the performances of two new RT-PCR, the Idylla™ SARS-CoV-2 and the Idylla™ SARS-CoV2/Flu/RSV, and two isothermal amplification assays, the ID NOW COVID and the ID NOW influenza A & B 2. Methods: The study was conducted in two parts: (i) the Idylla™ assays were assessed using a collection of nasopharyngeal swabs which were positive for various respiratory viruses. (ii) The performances of the four assays were assessed prospectively: all of the symptomatic patients admitted to the emergency department from 10 to 21 December were enrolled. Results: (i) All of the SARS-CoV-2 false negatives with the Idylla™ assays had a Ct value greater than 30 with the reference RT-PCR. No cross-reactivity was identified. (ii) Overall, 218 patients were enrolled. The respective prevalences of SARS-CoV-2, influenza A, and RSV were 19.8%, 4.8%, and 3.2%. All of the assays were 100% specific. The sensitivity of SARS-CoV-2 detection was 97.7%, 82.5%, and 86.3% for the Idylla™ SARS-CoV2, the Idylla™ SARS-CoV2/Flu/RSV, and the ID NOW COVID-19, respectively. For influenza A, it was 90.0% for the Idylla™ SARS-CoV2/Flu/RSV and 80.0% for the ID NOW Influenza. Discussion. All of the assays are suitable for testing patients with respiratory symptoms. False negatives should be considered, and the test should be repeated regarding the context.

A Folding-Based Electrochemical Aptasensor for the Single-Step Detection of the SARS-CoV-2 Spike Protein.

Efficient and timely testing has taken center stage in the management, control, and monitoring of the current COVID-19 pandemic. Simple, rapid, cost-effective diagnostics are needed that can complement current polymerase chain reaction-based methods and lateral flow immunoassays. Here, we report the development of an electrochemical sensing platform based on single-walled carbon nanotube screen-printed electrodes (SWCNT-SPEs) functionalized with a redox-tagged DNA aptamer that specifically binds to the receptor binding domain of the SARS-CoV-2 spike protein S1 subunit. Single-step, reagentless detection of the S1 protein is achieved through a binding-induced, concentration-dependent folding of the DNA aptamer that reduces the efficiency of the electron transfer process between the redox tag and the electrode surface and causes a suppression of the resulting amperometric signal. This aptasensor is specific for the target S1 protein with a dissociation constant (KD) value of 43 ± 4 nM and a limit of detection of 7 nM. We demonstrate that the target S1 protein can be detected both in a buffer solution and in an artificial viral transport medium widely used for the collection of nasopharyngeal swabs, and that no cross-reactivity is observed in the presence of different, non-target viral proteins. We expect that this SWCNT-SPE-based format of electrochemical aptasensor will prove useful for the detection of other protein targets for which nucleic acid aptamer ligands are made available.

Assessment of Virological Contributions to COVID-19 Outcomes in a Longitudinal Cohort of Hospitalized Adults.

BackgroundWhile several demographic and clinical correlates of coronavirus disease 2019 (COVID-19) outcome have been identified, their relationship to virological and immunological parameters remains poorly defined.MethodsTo address this, we performed longitudinal collection of nasopharyngeal swabs and blood samples from a cohort of 58 hospitalized adults with COVID-19. Samples were assessed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load, viral genotype, viral diversity, and antibody titer. Demographic and clinical information, including patient blood tests and several composite measures of disease severity, was extracted from electronic health records.ResultsSeveral factors, including male sex, higher age, higher body mass index, higher 4C Mortality score, and elevated lactate dehydrogenase levels, were associated with intensive care unit admission. Of all measured parameters, only the retrospectively calculated median Deterioration Index score was significantly associated with death. While quantitative polymerase chain reaction cycle threshold (Ct) values and genotype of SARS-CoV-2 were not significantly associated with outcome, Ct value did correlate positively with C-reactive protein levels and negatively with D-dimer, lymphocyte count, and antibody titer. Intrahost viral genetic diversity remained constant through the disease course and resulted in changes in viral genotype in some participants.ConclusionsUltimately, these results suggest that worse outcomes are driven by immune dysfunction rather than by viral load and that SARS-CoV-2 evolution in hospital settings is relatively constant over time.

Cerebrospinal fluid rhinorrhea following COVID-19 nasal swab testing: case report

The COVID-19 pandemic has led to widespread adoption of screening tests to quickly and accurately diagnose disease. Nasopharyngeal swab tests are among the most common utilized. We present a case of a 58 year old female who suffered a cerebrospinal fluid leak from a bony defect in the sphenoid sinus immediately following a pre-procedural COVID screening test with subsequent development of meningitis. Providers should be aware of this potential risk of nasopharyngeal swab collection. Alternate COVID screening tests may be considered in patients with a history of sinonasal or cranial base surgery.

Detection of coronavirus disease 2019 in patients presenting with influenza-like illness

Introduction Coronavirus disease 2019 (COVID-19), a global public health emergency, has brought life to an unprecedented near-standstill. So many respiratory viruses including the new pandemic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can be attributed to influenza-like illnesses (ILIs). The differentiation of different respiratory viruses based on symptoms and clinical examination is very difficult without testing for a specific virus. All ILI patients should undergo COVID-19 testing as per WHO revised strategies and Indian Medical Council Research guidelines.Objectives To assess the prevalence of SARS-CoV-2 infection in patients with ILIs during the present pandemic.Patients and methods A prospective study was conducted in a dedicated COVID-19 hospital, Bengaluru. All ILI patients visiting the Victoria Hospital underwent nasopharyngeal and oropharyngeal swab collection and were tested for SARS-CoV-2 as per the Indian Medical Council Research-approved protocol.Results In all, 12 062 patients attended the fever clinic in Victoria Hospital attached to Bangalore Medical College and Research Institute. Out of them, 1167 (12.67%) patients presented with ILI. Of the studied patients, 873 (78%) patients were under 50 years. Male patients constituted 67.09% of the study population. In the present study, 337 (30.55%) of the patients with ILI tested positive to SARS-CoV-2 antigen. Nearly 2/3rd of SARS-CoV-2-positive ILI patients were males and below 50 years. The positive rate of SARS-CoV-2 was higher in the noncontainment zone than the containment zones of ILI patients although statistically not significant (P=0.09).Conclusion Thirty percent of ILI patients were SARS-CoV-2 positive. Majority of SARS-CoV-2 positive tested ILI patients were men under the age of 50 years.

Salivary biomarkers in COVID-19 patients.

The use of salivary biomarkers in diagnosis, treatment, and overall prognosis of coronavirus disease 2019 (COVID-19) has been developed recently. Salivary biomarkers are extremely promising as they are fast to obtain and involve noninvasive collection of specimens. Monitoring patients in real time is necessary in this pandemic. Saliva is another biofluid with major advantages at the molecular level. Methods that detect viral presence in the host secretions measure the current infection by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), whereas the detection of human antibodies against SARS-CoV-2 evaluates the past exposure to the virus. There is an urgent need to increase the active research for the detection of SARS-CoV-2 in saliva because diagnostics may provide a reliable and cost-effective method and is suitable for the fast and early detection of COVID-19 infection. Salivary biomarkers have a potential to be a vital guide in determining coronavirus disease. Many people still do not get results of COVID-19 tests due to imbalance between supply and demand at large testing centers. The use of saliva has various advantages compared to collection of nasopharyngeal swabs. New techniques should be developed for detecting salivary biomarkers that help in diagnosis of COVID-19.

373. Household transmission of SARS-CoV-2 B.1.1.7 lineage –2 U.S. States, 2021

BackgroundIn December 2020, B.1.1.7 lineage of SARS-CoV-2 was first detected in the United States and has since become the dominant lineage. Previous investigations involving B.1.1.7 suggested higher rates of transmission relative to non-B.1.1.7 lineages. We conducted a household transmission investigation to determine the secondary infection rates (SIR) of B.1.1.7 and non-B.1.1.7 SARS-CoV-2 lineages. MethodsFrom January–April 2021, we enrolled members of households in San Diego County, CA, and Denver, CO metropolitan area (Tri-County), with a confirmed SARS-CoV-2 infection in a household member with illness onset date in the previous 10 days. CDC investigators visited households at enrollment and 14 days later at closeout to obtain demographic and clinical data and nasopharyngeal (NP) samples on all consenting household members. Interim visits, with collection of NP swabs, occurred if a participant became symptomatic during follow-up. NP samples were tested for SARS-CoV-2 using TaqPath™ RT-PCR test, where failure to amplify the spike protein results in S-Gene target failure (SGTF) may indicate B.1.1.7 lineage. Demographic characteristics and SIR were compared among SGTF and non-SGTF households using two-sided p-values with chi-square tests; 95% confidence intervals (CI) were calculated with Wilson score intervals.Results552 persons from 151 households were enrolled. 91 (60%) households were classified as SGTF, 57 (38%) non-SGTF, and 3 (2%) indeterminant. SGTF and non-SGTF households had similar sex distribution (49% female and 52% female, respectively; P=0.54) and age (median 30 years, interquartile range (IQR 14–47) and 31 years (IQR 15–45), respectively). Hispanic people accounted for 24% and 32% of enrolled members of SGTF and non-SGTF households, respectively (p=0.04). At least one secondary case occurred in 61% of SGTF and 58% of non-SGTF households (P=0.66). SIR was 52% (95%[CI] 46%-59%) for SGTF and 45% (95% CI 37%-53%) for non-SGTF households (P=0.18). ConclusionSIRs were high in both SGTF and non-SGTF households; our findings did not support an increase in SIR for SGTF relative to non-SGTF households in this setting. Sequence confirmed SARS-CoV-2 samples will provide further information on lineage specific SIRs.Disclosures All Authors: No reported disclosures