SERS Signature of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs: Towards Perspective COVID-19 Point-of-Care Diagnostics.

In this study, the intrinsic surface-enhanced Raman spectroscopy (SERS)-based approach coupled with chemometric analysis was adopted to establish the biochemical fingerprint of SARS-CoV-2 infected human fluids: saliva and nasopharyngeal swabs. The numerical methods, partial least squares discriminant analysis (PLS-DA) and support vector machine classification (SVMC), facilitated the spectroscopic identification of the viral-specific molecules, molecular changes, and distinct physiological signatures of pathetically altered fluids. Next, we developed the reliable classification model for fast identification and differentiation of negative CoV(-) and positive CoV(+) groups. The PLS-DA calibration model was described by a great statistical value-RMSEC and RMSECV below 0.3 and R2cal at the level of ~0.7 for both type of body fluids. The calculated diagnostic parameters for SVMC and PLS-DA at the stage of preparation of calibration model and classification of external samples simulating real diagnostic conditions evinced high accuracy, sensitivity, and specificity for saliva specimens. Here, we outlined the significant role of neopterin as the biomarker in the prediction of COVID-19 infection from nasopharyngeal swab. We also observed the increased content of nucleic acids of DNA/RNA and proteins such as ferritin as well as specific immunoglobulins. The developed SERS for SARS-CoV-2 approach allows: (i) fast, simple and non-invasive collection of analyzed specimens; (ii) fast response with the time of analysis below 15 min, and (iii) sensitive and reliable SERS-based screening of COVID-19 disease.

Access to SARS-CoV-2 diagnostic tests: are there barriers for the immigrants in Italy?

OBJECTIVES: to describe the epidemiology of SARS-CoV-2 infection in relation with the use of nasal swabs in the immigrant population in Italy, using data from the COVID-19 national surveillance system and to verify if a difference is present comparing natives and immigrant. DESIGN: descriptive study based on longitudinal health-administrative data. SETTING AND PAR TICIPAN TS: general population of six Italian Regions (Piedmont, Lombardy, Veneto, Emilia-Romagna, Tuscany, Lazio) covering about 55% of the resident population and 72% of foreigners' population. MAIN OUTCOME MEASURES: regional rates of access to at least a nasal swab, separately by country of origin. RESULTS: across all the periods, a lower rate in the foreigners' group was observed, with the only exception of the period May-June 2021. Considering separately High Migratory Pressure Countries (HMPCs) and Highly Developed Countries (HDCs), a higher proportion of nasal swabs performed in people coming from HDC with respect to HMPCs and natives was noticed. This observation is consistent in males and females. CONCLUSIONS: during the first wave of the pandemic, Italians have had a higher proportion of nasal swabs compared to migrants across all Regions. This difference disappeared in the following periods, probably due to a major availability of diagnostic tests.

Dynamics of Clinical Symptoms and Secretory Immunoglobulin a in Covid-19 Convalescent Patients

The post-COVID-19 recovery period is characterized by persistence of some symptoms, with immunological alterations being of great importance. Development of preventive measures to normalize mucosal immunity after a coronavirus infection determines the relevance of the current study. The aim was to study dynamics of clinical symptoms and level of secretory immunoglobulin A in individuals after a novel coronavirus infection as well as evaluate effectiveness of using IFN alpha-2b. Materials and methods. A study was conducted with patients aged 18 to 60 years old (n = 130), surveyed 1 to 9 months after post-infection, as well as in apparently healthy individuals lacking COVID-19 (n = 15). Previous novel coronavirus infection and post-COVID manifestations were verified based on medical documentation, complaints, anamnesis data, physical examination and questionnaires. The concentration of salivatory and nasopharyngeal mucosal sIgA was measured dynamically prior to and after administration of local therapy with IFN alpha-2b (gel applied intranasally twice a day for 30 days). Results. The acute period of COVID-19 was characterized by fever, anosmia, severe asthenia (fatigue and weakness), muscle and joint pain. Among the post-COVID manifestations at early period (1-3 months), pain in the joints and muscles (75.0%) as well as elevated body temperature (21.2%) were reliably detected, whereas in the long period (6-9 months) there were revealed dominance with the same frequency of shortness of breath, muscle and joint pain (75.8%, respectively). Based on examination data in healthy subjects, there was determined an arbitrary normal range of secretory IgA in saliva - 6.45 +/- 1.81 mg/ml and nasal swabs - 13.43 +/- 3.24 mg/ml. In the group of patients 1-3 months post-infection, therapy with IFN alpha-2b one month later resulted in significantly increased level of secretory IgA in saliva (from 1.84 +/- 0.28 to 5.78 +/- 1.96 mg/ml) and in nasal swabs (from 28.61 +/- 3.0 to 39.83 +/- 3.85 mg/ml) by more than 3-and 1.5-fold, respectively. In the group of patients without therapy was featured with stably sustained decline in sIgA level up to 9 months after COVID-19. In particular, the level of saliva sIgA ranged from 2.36 +/- 0.56 down to 2.16 +/- 0.66 mg/ml, and in nasal smears - from 15.66 +/- 1.32 to 10.23 +/- 1.07 mg/ml that differed insignificantly compared to baseline level. The rate of respiratory diseases prevailed in this group (27.6% of cases), which fully lacked in the group of topically administered IFN alpha-2b. Conclusion. In the post-COVID period, multiple organ disorders persist and reduced sIgA level is registered. Intranasally applied IFN alpha-2b made possible to normalize sIgA level and prevent accumulation of respiratory infectious pathologies.

Evaluation of the ePlex Respiratory pathogen panel 2 to detect viral and bacterial pathogens, including SARS-CoV-2 Omicron in nasopharyngeal swabs

The simultaneous detection and specific identification of multiple pathogens from patients exhibiting respiratory symptoms is important for directing pathogen-specific treatments. The ePlex Respiratory Pathogen Panel 2 (ePlex RP2 panel) is a multiplex molecular test for the qualitative detection of many viral and bacterial pathogens including SARS-CoV-2 in respiratory tract infections. The ePlex RP2 panel received FDA emergency use authorization for nasopharyngeal swab specimens collected in viral transport media. In the evaluation using the ePlex RP2, a total of 67 nasopharyngeal swab specimens were compared to the ePlex RP panel and the CDC 2019-nCoV Real-Time RT-PCR assay as the reference methods. The overall agreement of the ePlex RP2 panel was 100%. The ePlex RP2 panel could detect Omicron BA1 and BA2. The ePlex RP2 panel is a rapid, sensitive and specific "specimen-to-answer" platform to detect simultaneously multiple viruses and bacteria in the upper respiratory tract.Copyright © 2022 The Authors

Anatomical and Vision-Guided Path Generation Method for Nasopharyngeal Swabs Sampling

Due to the global COVID-19 pandemic, there is a strong demand for pharyngeal swab sampling and nucleic acid testing. Research has shown that the positive rate of nasopharyngeal swabs is higher than that of oropharyngeal swabs. However, because of the high complexity and visual obscuring of the interior nasal cavity, it is impossible to obtain the sampling path information directly from the conventional imaging principle. Through the combination of anatomical geometry and spatial visual features, in this paper, we present a new approach to generate nasopharyngeal swabs sampling path. Firstly, this paper adopts an RGB-D camera to identify and locate the subject's facial landmarks. Secondly, the mid-sagittal plane of the subject's head is fitted according to these landmarks. At last, the path of the nasopharyngeal swab movement in the nasal cavity is determined by anatomical geometry features of the nose. In order to verify the validity of the method, the location accuracy of the facial landmarks and the fitting accuracy of mid-sagittal plane of the head are verified. Experiments demonstrate that this method provides a feasible solution with high efficiency, safety and accuracy. Besides, it can solve the problem that the nasopharyngeal robot cannot generate path based on traditional imaging principles. It also provides a key method for automatic and intelligent sampling of nasopharyngeal swabs, and it is of great clinical value to reduce the risk of cross-infection. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

DYNAMICS OF CLINICAL SYMPTOMS AND SECRETORY IMMUNOGLOBULIN A IN COVID-19 CONVALESCENT PATIENTS.

The post-COVID-19 recovery period is characterized by persistence of some symptoms, with immunological alterations being of great importance. Development of preventive measures to normalize mucosal immunity after a coronavirus infection determines the relevance of the current study. The aim was to study dynamics of clinical symptoms and level of secretory immunoglobulin A in individuals after a novel coronavirus infection as well as evaluate effectiveness of using IFNalpha-2b. Materials and methods. A study was conducted with patients aged 18 to 60 years old (n = 130), surveyed 1 to 9 months after post-infection, as well as in apparently healthy individuals lacking COVID-19 (n = 15). Previous novel coronavirus infection and post-COVID manifestations were verified based on medical documentation, complaints, anamnesis data, physical examination and questionnaires. The concentration of salivatory and nasopharyngeal mucosal sIgA was measured dynamically prior to and after administration of local therapy with IFNalpha-2b (gel applied intranasally twice a day for 30 days). Results. The acute period of COVID-19 was characterized by fever, anosmia, severe asthenia (fatigue and weakness), muscle and joint pain. Among the post-COVID manifestations at early period (1-3 months), pain in the joints and muscles (75.0%) as well as elevated body temperature (21.2%) were reliably detected, whereas in the long period (6-9 months) there were revealed dominance with the same frequency of shortness of breath, muscle and joint pain (75.8%, respectively). Based on examination data in healthy subjects, there was determined an arbitrary normal range of secretory IgA in saliva - 6.45+/-1.81 mg/ml and nasal swabs - 13.43+/-3.24 mg/ml. In the group of patients 1-3 months post-infection, therapy with IFNalpha-2b one month later resulted in significantly increased level of secretory IgA in saliva (from 1.84+/-0.28 to 5.78+/-1.96 mg/ml) and in nasal swabs (from 28.61+/-3.0 to 39.83+/-3.85 mg/ml) by more than 3- and 1.5-fold, respectively. In the group of patients without therapy was featured with stably sustained decline in sIgA level up to 9 months after COVID-19. In particular, the level of saliva sIgA ranged from 2.36+/-0.56 down to 2.16+/-0.66 mg/ml, and in nasal smears - from 15.66+/-1.32 to 10.23+/-1.07 mg/ml that differed insignificantly compared to baseline level. The rate of respiratory diseases prevailed in this group (27.6% of cases), which fully lacked in the group of topically administered IFNalpha-2b. Conclusion. In the post-COVID period, multiple organ disorders persist and reduced sIgA level is registered. Intranasally applied IFNalpha-2b made possible to normalize sIgA level and prevent accumulation of respiratory infectious pathologies.Copyright © 2022 Saint Petersburg Pasteur Institute. All rights reserved.

COVID-19: Test, Test and Test.

A new virus was identified in late December 2019 when China reported the first cases of pneumonia in Wuhan, and a global COVID-19 pandemic followed. The world was not late to respond, with a number of sweeping measures ranging from social distancing protocols, stringent hygienic practices, and nation-wide lockdowns, as well as COVID-19 testing campaigns in an attempt to prevent the transmission of the disease and contain the pandemic. Currently, different types of diagnostic testing have been adopted globally, such as nucleic acid detection tests, immunological tests and imaging approaches; however, real-time reverse transcriptase-polymerase chain reaction (RT-PCR) remains the "gold standard" for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pre-analytical factors, such as specimen selection and collection, are crucial for RT-PCR, and any suboptimal collection may contribute to false-negative results. Herein, we address some of the specimen types that have been used in molecular detection methods for COVID-19. However, the pandemic is still evolving, and information might change as more studies are conducted.

Dental calculus - An emerging bio resource for past SARS CoV2 detection, studying its evolution and relationship with oral microflora.

The most grievous threat to human health has been witnessed worldwide with the recent outbreak of Corona virus disease 2019 (COVID-19). There is mounting evidence available regarding theconnect of COVID -19 and oral cavity, particularly periodontal disease. The current review provides an update on the diagnostic potential of dental calculus and how this bio resource may help in providing us huge amount of diagnostic regarding the causative virus. Contemporary standard method of diagnosis via nasopharyngeal swabs (NPS) is tedious, may enhance the risk of aerosol contamination by inducing sneezing and detects the presence of active infection only.However,dental calculus being a mineralized deposit serves as a reservoir for biomoleculesand provides detection of past SARS CoV2 infection. Further, the abundance of information that can be obtained from this remarkable mineralized deposit on teeth regarding the viral genome, its evolution and interactions with the oral microflora shall enhance the understanding of the viral disease process and its connection with the periodontal disease. Additional diagnostic information, which may be obtained from this simple bio reservoir can complement the contemporary diagnostic strategies adopted in the management of COVID-19pandemic and enhance our existing knowledge for developing improvised novel approaches to mitigate the effects of mutated variants of the infectious agent.

Validation of 3D-Printed Swabs for Sampling in SARS-CoV-2 Detection: A Pilot Study.

In this pilot study, we characterize and evaluate 3D-printed swabs for the collection of nasopharyngeal and oropharyngeal secretion samples for the SARS-CoV-2 detection. Swabs are made with the fused deposition modeling technique using the biopolymer polylactic acid (PLA) which is a medical-grade, biodegradable and low-cost material. We evaluated six swabs with mechanical tests in a laboratory and in an Adult Human Simulator performed by healthcare professionals. We proved the adequacy of the PLA swab to be used in the gold standard reverse transcriptase-polymerase chain reaction (qRT-PCR) for viral RNA detection. Then, we did in vitro validation for cell collection using the 3D-printed swabs and RNA extraction for samples from 10 healthy volunteers. The 3D-printed swabs showed good flexibility and maneuverability for sampling and at the same time robustness to pass into the posterior nasopharynx. The PLA did not interfere with the RNA extraction process and qRT-PCR test. When we evaluated the expression of the reference gene (RNase P) used in the SARS-CoV-2 detection, the 3D-printed swabs showed good reproducibility in the threshold cycle values (Ct = 23.5, range 19-26) that is comparable to control swabs (Ct = 24.7, range 20.8-32.6) with p value = 0.47. The 3D-printed swabs demonstrated to be a reliable, and an economical alternative for mass use in the detection of SARS-CoV-2.

DYNAMICS OF CLINICAL SYMPTOMS AND SECRETORY IMMUNOGLOBULIN A IN COVID-19 CONVALESCENT PATIENTS.

The post-COVID-19 recovery period is characterized by persistence of some symptoms, with immunological alterations being of great importance. Development of preventive measures to normalize mucosal immunity after a coronavirus infection determines the relevance of the current study. The aim was to study dynamics of clinical symptoms and level of secretory immunoglobulin A in individuals after a novel coronavirus infection as well as evaluate effectiveness of using IFNalpha-2b. Materials and methods. A study was conducted with patients aged 18 to 60 years old (n = 130), surveyed 1 to 9 months after post-infection, as well as in apparently healthy individuals lacking COVID-19 (n = 15). Previous novel coronavirus infection and post-COVID manifestations were verified based on medical documentation, complaints, anamnesis data, physical examination and questionnaires. The concentration of salivatory and nasopharyngeal mucosal sIgA was measured dynamically prior to and after administration of local therapy with IFNalpha-2b (gel applied intranasally twice a day for 30 days). Results. The acute period of COVID-19 was characterized by fever, anosmia, severe asthenia (fatigue and weakness), muscle and joint pain. Among the post-COVID manifestations at early period (1-3 months), pain in the joints and muscles (75.0%) as well as elevated body temperature (21.2%) were reliably detected, whereas in the long period (6-9 months) there were revealed dominance with the same frequency of shortness of breath, muscle and joint pain (75.8%, respectively). Based on examination data in healthy subjects, there was determined an arbitrary normal range of secretory IgA in saliva - 6.45+/-1.81 mg/ml and nasal swabs - 13.43+/-3.24 mg/ml. In the group of patients 1-3 months post-infection, therapy with IFNalpha-2b one month later resulted in significantly increased level of secretory IgA in saliva (from 1.84+/-0.28 to 5.78+/-1.96 mg/ml) and in nasal swabs (from 28.61+/-3.0 to 39.83+/-3.85 mg/ml) by more than 3- and 1.5-fold, respectively. In the group of patients without therapy was featured with stably sustained decline in sIgA level up to 9 months after COVID-19. In particular, the level of saliva sIgA ranged from 2.36+/-0.56 down to 2.16+/-0.66 mg/ml, and in nasal smears - from 15.66+/-1.32 to 10.23+/-1.07 mg/ml that differed insignificantly compared to baseline level. The rate of respiratory diseases prevailed in this group (27.6% of cases), which fully lacked in the group of topically administered IFNalpha-2b. Conclusion. In the post-COVID period, multiple organ disorders persist and reduced sIgA level is registered. Intranasally applied IFNalpha-2b made possible to normalize sIgA level and prevent accumulation of respiratory infectious pathologies. Copyright © 2022 Saint Petersburg Pasteur Institute. All rights reserved.

Implementation of the Lean methodology for the optimization of Covid-19 testing points: the experience of Piove di Sacco

During the outbreak of SARS-CoV-2 the need to optimize the operations inside the Italian NHS has rapidly grown. This L'otteniissue was particularly significant for the management of swab testing hubs. Some tools from the Lean methodology toolbox has been implemented in a Veneto region's swab testing hub to map the process, collect data and define effective actions for user flow improvement. Users' average transit time has been reduced by 73% for molecular tests and by 42% for antigen tests. In addition, errors during the check-in have been zeroed and staff satisfaction level has been increased. The importance to meet challenges with agility, the effectiveness of an iterative approach and the relevance of the cross collaboration are the main learnings of this experience. © 2022 Authors. All rights reserved.

Nasal swab is a good alternative sample for detecting SARS-CoV-2 with rapid antigen test: A meta-analysis.

BACKGROUND: We aim to determine if nasal samples have equivalent detection sensitivity to nasopharyngeal swabs for RAT and evaluate the diagnostic accuracy of nasal swabs with RAT. METHODS: PubMed and Web of Science were searched for eligible studies published before August 23, 2022. A bivariate random effects model was used to perform the quantitative synthesis. RESULTS: The pooled sensitivity, pooled specificity, positive likelihood ratio, negative likelihood ratio, and summary AUC on nasal swabs with RAT were 0.81 (95% CI, 0.77-0.85), 1.00 (95% CI: 0.99-1.00), 0.97 (95% CI, 0.95-0.98), 298.91 (95% CI, 144.71-617.42) and 0.19 (95% CI, 0.15-0.23), respectively. WHO required RAT kits to perform with a sensitivity of 0.80 and a specificity of 0.97, nasal swabs (0.81) achieved the required sensitivity while nasopharyngeal swabs (0.75) did not. The symptomatic population yielded higher pooled sensitivity than the asymptomatic population (0.86 versus 0.71), with a pooled sensitivity of 0.90 for five days of symptom onset. CONCLUSION: Nasal sampling had a great performance and yielded a high sensitivity in detecting SARS-CoV-2 using RAT, we believe that RAT performed with nasal swabs is a good alternative for detecting SARS-CoV-2, especially early in the onset of symptoms.

Implementation of MRSA Nasal Swabs as an Antimicrobial Stewardship Intervention to Decrease Anti-MRSA Therapy in COVID-19 Infection.

In the early stages of treating patients with SARS-CoV-2, limited information was available to guide antimicrobial stewardship interventions. The COVID-19 Task Force and Antimicrobial Stewardship Committee, at a 988-bed academic medical center, implemented the use of methicillin-resistant Staphylococcus aureus (MRSA) nasal swab polymerase chain reaction (PCR) testing to assist with the de-escalation of anti-MRSA therapy in patients with suspected superimposed bacterial pneumonia in COVID-19. A retrospective study was conducted to evaluate the impact of MRSA nasal swab PCR testing on the rate of anti-MRSA therapy between 13 April 2020 and 26 July 2020. A total of 122 patients were included in the analysis. Of the patients included in the final analysis, 58 (47.5%) had anti-MRSA therapy discontinued and 41 (33.6%) avoided anti-MRSA therapy completely due to a negative swab result. With the implementation of MRSA nasal swab PCR testing in COVID-19 patients, anti-MRSA therapy was reduced in 81% of patients in this study. In patients who continued with anti-MRSA therapy, nasal swabs were either positive for MRSA or an alternative indication for anti-MRSA therapy was noted. Only three patients in the cohort had MRSA identified in a sputum culture, all of whom had anti-MRSA therapy continued. MRSA nasal swab PCR testing may serve as an effective antimicrobial stewardship tool in COVID-19 pneumonia.

The Effect of Disinfectants on the SARS-CoV-2 RNA Detection in Swabs from Various Surfaces.

The COVID-19 pandemic has spread rapidly around the world; some countries have introduced controls on imported products, including testing for viral nucleic acids. In this work, the influence of disinfectants for treating various SARS-CoV-2-contaminated surfaces on the detection of viral RNA fragments in swabs from these surfaces was analyzed using quantitative RT-PCR. Quaternary ammonium salt, hydrogen peroxide, 1-propanol, and sodium salt of dichloroisocyanuric acid, as well as ultraviolet irradiation, were tested as such disinfecting agents. Our results show that without exposure to disinfectants, viral RNA can be detected on the surface of all examined materials for at least 3 days. UV irradiation or irrigation with a disinfectant containing 0.2% active chlorine had the greatest effect on the decontamination of nonporous surfaces as measured by RT-PCR of swabs from these surfaces. Irrigation with disinfectants of porous surfaces (cardboard) had practically no effect on the detection of SARS-CoV-2 RNA by RT-PCR.

Evaluation of the Rapid Antigen Detection Test for Diagnosing SARS-CoV-2 during the COVID-19 Pandemic: Experience from a Centralized Isolation Site in Shanghai, China.

Rapid and reliable diagnosis is important for the management of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid antigen detection test (RADT) is a rapid, inexpensive, and easy method. Several studies have reported that RADTs performed well in many countries; however, very few studies have been reported in China. In this study, we assessed the performance of the RADT (Ediagnosis COVID-19 antigen test kit). This study was conducted in a centralized isolation site in Shanghai and enrolled 716 patients with COVID-19 and 203 noninfected participants. Nasopharyngeal swabs from all participants were collected on the same day and tested using the RADT and real-time reverse transcription-PCR (RT-PCR). The performance of the RADT was evaluated in different scenarios, such as threshold cycle (CT) values, symptomatic phase, and symptoms on the day of testing. The results demonstrated that the sensitivity for patients with CT values lower than 20 was 96.55% (95% confidence interval [CI], 87.05 to 99.4). The sensitivities were 78.4% (95% CI, 69.96 to 85.05) for participants within 5 days after the first RT-PCR-positive result and 90.77% (95% CI, 80.34 to 96.19) within 5 days after symptom onset. Moreover, the sensitivity of the RADT was more than 80% for patients with symptoms on the day of testing, including fever (89.29%), cough (86.84%), stuffy nose (92.59%), runny nose (92%), sore throat (81.25%), and muscle pain (80.77%), especially for those with upper respiratory tract symptoms. The specificity of the RADT was good in all scenarios. During the SARS-CoV-2 epidemic, Ediagnosis performed excellently in individuals with a higher viral load (evidenced by lower CT values), individuals in the early symptomatic phase, and especially those with upper respiratory tract symptoms. IMPORTANCE RADTs have demonstrated excellent performance in many counties for screening SARS-CoV-2 infection, but very few studies have been conducted in China. The performance of RADTs is largely related to different real-life scenarios. In our study, the performance of the RADT was evaluated in different scenarios, such as CT values, symptomatic phase, and symptoms on the day of testing. The results demonstrated that Ediagnosis (an RADT made in China) performed excellently for individuals with a higher viral load (evidenced by lower CT values), individuals in the early symptomatic phase, and especially those with upper respiratory tract symptoms.

Manufacturing Expansion of COVID-19 Foam Testing Swabs

The outbreak of COVID-19 in early 2020 caused the demand for foam-tipped swabs, required for COVID-19 testing, to skyrocket. There were only two major manufacturers of foam-tipped swabs worldwide. The only US producer of COVID-19 foam-tipped testing swabs was Puritan of Guilford, Maine with a capacity of < 10M swabs per month. Puritan's existing capacity was nowhere near the 10's of millions needed. The U.S. Government utilized the provisions enacted under the Defense Production Act to award a $73M agreement to Puritan on 23 April 2020 to expand capacity to produce an additional 20M foam-tipped swabs per month. Puritan was faced with daunting supply-chain and workforce challenges to increase their production capability within the 90 day deadline during a pandemic. In spite of the challenges, Puritan met the objectives set by the agreement and delivered the additional capacity on time. © 2022 MANTECH 2022. All rights reserved.

COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya.

Background: The Basic Science Laboratory (BSL) of the Kenya Medical Research Institute/Walter Reed Project in Kisumu, Kenya addressed mass testing challenges posed by the emergent coronavirus disease 2019 (COVID-19) in an environment of global supply shortages. Before COVID-19, the BSL had adequate resources for disease surveillance and was therefore designated as one of the testing centres for COVID-19. Intervention: By April 2020, the BSL had developed stringent safety procedures for receiving and mass testing potentially infectious nasal specimens. To accommodate increased demand, BSL personnel worked in units: nucleic acid extraction, polymerase chain reaction, and data and quality assurance checks. The BSL adopted procedures for tracking sample integrity and minimising cross-contamination. Lessons learnt: Between May 2020 and January 2022, the BSL tested 63 542 samples, of which 5375 (8.59%) were positive for COVID-19; 1034 genomes were generated by whole genome sequencing and deposited in the Global Initiative on Sharing All Influenza Data database to aid global tracking of viral lineages. At the height of the pandemic (August and November 2020, April and August 2021 and January 2022), the BSL was testing more than 500 samples daily, compared to 150 per month prior to COVID-19. An important lesson from the COVID-19 pandemic was the discovery of untapped resilience within BSL personnel that allowed adaptability when the situation demanded. Strict safety procedures and quality management that are often difficult to maintain became routine. Recommendations: A fundamental lesson to embrace is that there is no 'one-size-fits-all' approach and adaptability is the key to success.

Sinonasal Lobular Capillary Hemangioma After Continuous Self-tests for COVID-19: A Case Report and Review of the Literature.

Sinonasal lobular capillary hemangiomas (LCH) are rare benign vascular lesions commonly arising from the nasal septum. Nasopharyngeal, nasal mid-turbinate, and anterior nasal swabbing is the preferred method of screening for coronavirus disease-2019 (COVID-19). Herein, we present a case of a sinonasal LCH in a child after continuous self-tests for COVID-19, with an anterior nasal swab. The child presented with a well-defined red mass in the anterior part of the nasal septum, which was removed endoscopically. Histopathology revealed a LCH. This is the first report of a complication other than epistaxis with the use of an anterior nasal swab. Our literature review identified 32 studies reporting complications of COVID-19 screening. Cerebrospinal fluid leaks and foreign body retention are the most common ones. A proper specimen collection technique and a quick patient history with an emphasis on risk factors are the best practices to prevent complications from COVID-19 screening.

Performance & clinical utility of oropharyngeal versus nasopharyngeal swabs in COVID-19.

Background & objectives: The oropharyngeal (OP) and nasopharyngeal (NP) swab samples are the most recommended clinical specimens for detecting SARS-CoV-2 in an individual through the quantitative real-time reverse-transcriptase-polymerase chain reaction (rRT-PCR) method. The primary objective of this study was to compare the performance of NP and OP swabs for the diagnosis of COVID-19 among 2250 concomitant samples (1125 NP + 1125 OP) using rRT-PCR test. Methods: This study was conducted at a tertiary care hospital in southern India. The study compared the specificity and efficacy of the two samples (NP & OP swabs) in 1125 individuals suspected having COVID-19 infection. The rRT-PCR values from all the samples were compared based on gender, age group and viral load. The differences between unmatched proportion and matched proportion were analysed. Agreement between the two methods was assessed using Kappa statistic. Absolute sensitivity, specificity, positive and negative predictive values (PPV and NPV) for OP and NP swabs were analysed. Results: The study identified a fair degree of agreement between OP and NP swabs in diagnosis of COVID-19 (kappa = 0.275, P <0.001). There was also a fair degree of agreement between NP and OP swabs irrespective of gender, age or duration of symptoms. NP swabs had better sensitivity and NPV as compared to OP swabs, however, specificity and PPV were 100 per cent for both. Interpretation & conclusions: The present study showed that both OP and NP swabs had similar sensitivity and specificity for predicting the presence of SARS-CoV-2.

Survival and detection of SARS-CoV-2 variants on dry swabs post storage.

COVID-19 has resulted in nearly 598 million infections and over 6.46 million deaths since the start of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in 2019. The rapid onset of the pandemic, combined with the emergence of viral variants, crippled many health systems particularly from the perspective of coping with massive diagnostic loads. Shortages of diagnostic kits and capacity forced laboratories to store clinical samples resulting in huge backlogs, the effects of this on diagnostic pickup have not been fully understood. Herein, we investigated the impact of storing SARS-CoV-2 inoculated dry swabs on the detection and viability of four viral strains over a period of 7 days. Viral load, as detected by qRT-PCR, displayed no significant degradation during this time for all viral loads tested. In contrast, there was a ca. 2 log reduction in viral viability as measured by the tissue culture infectious dose (TCID) assay, with 1-3 log viable virus detected on dry swabs after 7 days. When swabs were coated with 102 viral copies of the Omicron variant, no viable virus was detected after 24 hours following storage at 4°C or room temperature. However there was no loss of PCR signal over 7 days. All four strains showed comparable growth kinetics and survival when cultured in Vero E6 cells. Our data provide information on the viability of SARS-CoV-2 on stored swabs in a clinical setting with important implications for diagnostic pickup and laboratory processing protocols. Survival after 7 days of SARS-CoV-2 strains on swabs with high viral loads may impact public health and biosafety practices in diagnostic laboratories.