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More than a year after the COVID-19 pandemic was declared, the need still exists for accurate, rapid, inexpensive and non-invasive diagnostic methods that yield high specificity and sensitivity towards the current and newly emerging SARS-CoV-2 strains. Compared to the nasopharyngeal swabs, several studies have established saliva as a more amenable specimen type for early detection of SARS-CoV-2. Considering the limitations and high demand for COVID-19 testing, we employed MALDI-ToF mass spectrometry in the analysis of 60 gargle samples from human donors and compared the resultant spectra against COVID-19 status. Several standards, including isolated human serum immunoglobulins, and controls, such as pre-COVID-19 saliva and heat inactivated SARS-CoV-2 virus, were simultaneously analyzed to provide a relative view of the saliva and viral proteome as they would appear in this workflow. Five potential biomarker peaks were established that demonstrated high concordance with COVID-19 positive individuals. Overall, the agreement of these results with RT-qPCR testing on nasopharyngeal swabs was ≥90% for the studied cohort, which consisted of young and largely asymptomatic student athletes. From a clinical standpoint, the results from this pilot study suggest that MALDI-ToF could be used to develop a relatively rapid and inexpensive COVID-19 assay.

To identify significant factors that help predict whether health care personnel (HCP) will test positive for severe acute respiratory coronavirus 2 (SARS-CoV-2).We conducted a prospective cohort study among 7015 symptomatic HCP from March 25, 2020, through November 11, 2020. We analyzed the associations between health care role, contact history, symptoms, and a positive nasopharyngeal swab SARS-CoV-2 polymerase chain reaction test results, using univariate and multivariable modelling.Of the symptomatic HCP, 624 (8.9%) were positive over the study period. On multivariable analysis, having a health care role other than physician or advanced practice provider, contact with family or community member with known or suspected coronavirus disease 2019 (COVID-19), and seven individual symptoms (cough, anosmia, ageusia, fever, myalgia, chills, and headache) were significantly associated with higher adjusted odds ratios for testing positive for SARS-CoV-2. For each increase in symptom number, the odds of testing positive nearly doubled (odds ratio, 1.93; 95% CI, 1.82 to 2.07, P.001).Symptomatic HCP have higher adjusted odds of testing positive for SARS-CoV-2 based on three distinct factors: (1) nonphysician/advanced practice provider role, (2) contact with a family or community member with suspected or known COVID-19, and (3) specific symptoms and symptom number. Differences among health care roles, which persisted after controlling for contacts, may reflect the influence of social determinants. Contacts with COVID-19-positive patients and/or HCP were not associated with higher odds of testing positive, supporting current infection control efforts. Targeted symptom and contact questionnaires may streamline symptomatic HCP testing for COVID-19.

Rapid and widespread diagnostic testing is critical to providing timely patient care and reducing transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently, the Visby Medical COVID-19 point of care (POC) test was granted emergency use authorization (EUA) for qualitative detection of SARS-CoV-2 nucleic acid at the point of care. We evaluated its performance characteristics using residual specimens (n = 100) collected from Mayo Clinic patients using nasopharyngeal (NP) swabs and placed in viral transport media (VTM). The same specimen was tested using both the laboratory reference method (RT-qPCR) and Visby test. The reference methods utilized included a laboratory developed test with EUA (Mayo Clinic Laboratories, Rochester, MN) using the TaqMan assay on a Roche Light Cycler 480 or a commercially available EUA platform (cobas® SARS-CoV-2; Roche Diagnostics, Indianapolis, IN). Positive, negative, and overall percent agreement between the Visby COVID-19 test and the reference method were calculated. Additionally, the limit of detection (LoD) claimed by the manufacturer (1112 copies/mL) was verified with serial dilutions of heat inactivated virus. The Visby COVID-19 test correctly identified 29/30 positive samples and 69/70 negative samples, resulting in an overall concordance of 98.0%, positive percent agreement of 96.7%, and negative percent agreement of 98.6%. The abbreviated LoD experiment showed that the analytical sensitivity of the method is as low as or lower than 500 copies/mL. Our study demonstrated that Visby COVID-19 is well-suited to address rapid SARS-CoV-2 testing needs. It has high concordance with central laboratory-based RT-qPCR methods, a low rate of invalid results, and superior analytical sensitivity to some other EUA POC devices.

Severe acute respiratory virus syndrome 2 (SARS-CoV-2) has led to a worldwide pandemic. Early studies in solid organ transplant (SOT) recipients suggested a wide variety of presentations, however, there remains a paucity of robust data in this population. We conducted a systematic review and meta-analysis of SOT recipients with SARS-CoV-2 infection from January 1st t October 9th, 2020. Pooled incidence of symptoms, treatments and outcomes were assessed. Two hundred and fifteen studies were included for systematic review and 60 for meta-analysis. We identified 2,772 unique SOT recipients including 1,500 kidney, 505 liver, 141 heart and 97 lung. Most common presenting symptoms were fever and cough in 70.2% and 63.8% respectively. Majority (81%) required hospital admission. Immunosuppressive medications, especially antimetabolites, were decreased in 76.2%. Hydroxychloroquine and interleukin six antagonists were administered in59.5% and 14.9% respectively, while only few patients received remdesivir and convalescent plasma. Intensive care unit admission was 29% from amongst hospitalized patients. Only few studies reported secondary infections. Overall mortality was 18.6%. Our analysis shows a high incidence of hospital admission in SOT recipients with SARS-CoV-2 infection. As management of SARS-CoV-2 continues to evolve, long-term outcomes among SOT recipients should be assessed in future studies., Highlights • High rate of hospital and ICU admission amongst SOT recipients with COVID-19 • Fever maybe absent in up to 30% of SOT recipients with COVID-19. • Majority of centers held anti-metabolites in SOT patients with COVID-19. • Overall mortality in SOT recipients with COVID-19 was 20%.

Background : South Africa was the African country with the most recorded cases of SARS-CoV-2 during 2020, experiencing 2 waves of infection. During the first wave, diagnostics were largely based on reverse transcription-linked PCR (RT-PCR). The Abbott PanBio antigen test was deployed during the 2nd wave which may have been driven by emergence of the B.1.351 variant. At the time of evaluation in mid-November 2020, B.1.351 was the dominant circulating virus in Nelson Mandela Bay, in the Eastern Cape Province. Methods : Used PanBio antigen swabs (collected from patients with genetically characterised virus) were first validated as suitable for PCR. A prospective study was then undertaken to evaluate assay performance in the field. Testing was conducted at mobile community testing centres on 677 ambulant patients. Used swabs were kept and tested by RT-PCR. Results : During initial validation, used swabs in proprietary lysis buffer were found to be suitable for PCR and secondly, the PB assay reliably detected patients infected with B.1.351. In the field study, of 146 RT-PCR positive individuals, 101 were RTD positive in the clinic. The RTD had a sensitivity of 69.2% (95%CI 61.4, 75.8) and specificity of 99.0% (95%CI 98.8, 99.3). Sensitivity was dependent on the amount of viral RNA in clinical samples, as reflected by the PCR cycle threshold (CT) value. Conclusions : The assay reliably detected B.1.351 infections in ambulatory ill patients during initial validation and in field testing. In the field, assay sensitivity was >90% in patients with high viral loads who are expected to be most infectious. Negative and positive predictive values were also >90%.

Background The respiratory illness identified as coronavirus disease 2019 (COVID-19) has resulted in a pandemic illness that has changed the face of healthcare. As the COVID-19 pandemic continues, patients have continued to require neurosurgical interventions, and the endoscopic endonasal approach for surgery has continued to be a mainstay treatment of pituitary tumors and anterior skull base lesions. Methods We sought to highlight the current lack of recommendations regarding testing protocols for neurosurgical patients. Results We implemented a novel testing protocol for our patient populations at increased risk and have proposed a model that can be used at other institutions to mitigate the risk of complications associated with some forms of COVID-19 testing. Conclusion Patients with anterior skull base defects may be at risk with current COVID-19 testing protocols, and may benefit from alternative specimen collection strategies.

Since the outbreak of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the control of virus spread has remained challenging given the pitfalls of the current diagnostic tests. Nevertheless, RNA amplification techniques have been the gold standard among other diagnostic methods for monitoring clinical samples for the presence of the virus. In the current paper, we review the shortcomings and strengths of RT-PCR (real-time polymerase chain reaction) techniques for diagnosis of coronavirus disease (COVID)-19. We address the repercussions of false-negative and false-positive rates encountered in the test, summarize approaches to improve the overall sensitivity of this method. We discuss the barriers to the widespread use of the RT-PCR test, and some technical advances, such as RT-LAMP (reverse-transcriptase-loop mediated isothermal amplification). We also address how other molecular techniques, such as immunodiagnostic tests can be used to avoid incorrect interpretation of RT-PCR tests.

Here, we retrospectively analyzed the comparative results of 182 paired dry nasopharyngeal swabs tested by Abbott ID NOW and nasopharyngeal swabs in viral transport medium by real-time RT-PCR methods. While the overall agreement was 96.2%, we found that of 15 samples that were tested positive with RT-PCR methods, 7 were missed by ID NOW, resulting in a false-negative rate of 47%.

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

Background & Aims Although coronavirus disease 2019 (COVID-19) is characterized by fever and respiratory symptoms, some patients have no or mild symptoms. Severe acute respiratory syndrome-coronavirus (SARS-CoV-2) has been detected in feces of patients. We investigated gastrointestinal symptoms and shedding of virus into feces of patients with asymptomatic or mild COVID-19. Methods We collected data from 46 patients (median age, 26 y; 46% men) with asymptomatic or mild COVID-19 (without fever and pneumonia) and prolonged respiratory shedding of SARS-CoV-2, quarantined from April 4, 2020, through April 24, 2020, in Korea. Respiratory specimens included upper respiratory specimens (nasopharyngeal and oropharyngeal swabs) and lower respiratory specimens (sputum), and were collected twice per week. The median interval between COVID-19 diagnosis to the start of fecal sample collection was 37 days (range, 29–41 d); 213 stool specimens were collected from 46 patients. We used real-time reverse-transcription polymerase chain reaction to detect SARS-CoV-2 in the respiratory and fecal specimens. Results Gastrointestinal manifestations were observed in 16 of the 46 patients (35%); diarrhea was the most common (15%), followed by abdominal pain (11%), dyspepsia (11%), and nausea (2%). Virus RNA was detected in feces from 2 patients without gastrointestinal symptoms (4%). Mean cycle threshold values from the time of quarantine to the time of fecal collection tended to be lower in patients with virus detected in fecal samples than in patients without virus in fecal samples (29.91 vs 33.67 in the first week, 29.47 vs 35.71 in the fifth week, respectively). Shedding of virus into feces persisted until day 50 after diagnosis; fecal samples began to test negative before or at approximately the time that respiratory specimens also began to test negative. Conclusions In an analysis of fecal and respiratory specimens from patients with COVID-19 in quarantine in Korea, we found that the gastrointestinal tract could be a route of transmission of SARS-CoV-2 even in patients with asymptomatic or mild disease, with no gastrointestinal symptoms. The viral load of the respiratory specimens appears be related to shedding of the virus into feces in this group of patients.

Isothermal nucleic acid amplification methods can potentially shorten the amount of time required to diagnose influenza. We developed and evaluated a novel isothermal nucleic acid amplification method, RT-SIBA to rapidly detect and differentiate between influenza A and B viruses in a single reaction tube. The performance of the RT-SIBA Influenza assay was compared with two established RT-PCR methods. The sensitivities of the RT-SIBA, RealStar RT-PCR, and CDC RT-PCR assays for the detection of influenza A and B viruses in the clinical specimens were 98.8%, 100%, and 89.3%, respectively. All three assays demonstrated a specificity of 100%. The average time to positive result was significantly shorter with the RT-SIBA Influenza assay (90 min). The method can be run using battery-operated, portable devices with a small footprint and therefore has potential applications in both laboratory and near-patient settings., Highlights • We developed and evaluated novel isothermal nucleic acid amplification method for the rapid detection and differentiation of influenza A and B viruses in human respiratory specimens. • The method displayed high level of sensitivity and specificity and correlated well with those of the reference methods. • The method detected influenza virus within 20 minutes and can potentially be used in near patient or field setting.

Graphical abstract, More than a year after the SARS-CoV-2 pandemic, the Coronavirus disease 19 (COVID-19) is still a major global challenge for scientists to understand the different dimensions of infection and find ways to prevent, treat, and develop a vaccine. On January 30, 2020, the world health organization (WHO) officially announced this new virus as an international health emergency. While many biological and mechanisms of pathogenicity of this virus are still unclear, it seems that cytokine storm resulting from an immune response against the virus is considered the main culprit of the severity of the disease. Despite many global efforts to control the SARS-CoV-2, several problems and challenges have been posed in controlling the COVID-19 infection. These problems include the various mutations, the emergence of variants with high transmissibility, the short period of immunity against the virus, the possibility of reinfection in people improved, lack of specific drugs, and problems in the development of highly sensitive and specific vaccines. In this review, we summarized the results of the current trend and the latest research studies on the characteristics of the structure and genome of the SARS-CoV- 2, new mutations and variants of SARS-CoV-2, pathogenicity, immune response, virus diagnostic tests, potential treatment, and vaccine candidate.

We describe 4 children (11–17 years in age) at our institution with acute appendicitis in the setting of SARS-CoV-2 infection, suggesting a possible association. Providers should consider testing for this infection in patients with severe gastrointestinal symptoms, in order to take appropriate transmission based precautions, until more is understood.

Background Human metapneumovirus (hMPV) is prevalent in children, the elderly and immunocompromised individuals, but available epidemiological data is limited. Objectives (1) To develop and validate a real-time PCR method for hMPV diagnosis. (2) To determine the percentage of hMPV in respiratory specimens from the community and its association with outbreaks in our geographic area. (3) To provide epidemiological data in terms of age distribution, seasonality and co-infections. Study design A real-time PCR assay was designed for detection of hMPV lineages A and B. Prospective testing for hMPV over a 22-month period was then undertaken. Results The real-time PCR was sensitive and specific for detection of both lineages of hMPV. hMPV was detected in 9.5% ( n =8239) of the specimens and 25% of the outbreaks ( n =100) tested. The hMPV-positive patients ranged in age from 18 days to 99 years with a median age of 24 months. The number of positive samples peaked during the winter months of December, January and February. A high rate of co-infections was noted in the samples tested. Conclusions hMPV is common in the community and is associated with outbreaks. Including hMPV in routine testing improves etiological diagnosis of acute respiratory infections.