Comparison of Saliva and Mid-Turbinate Swabs for Detection of COVID-19

BackgroundSaliva is an attractive sample for detecting SARS-CoV-2 because it is easy to collect and minimally invasive. However, contradictory reports exist concerning the sensitivity of saliva versus nasal swabs.MethodsWe recruited and followed close contacts of COVID-19 cases for up to 14 days from their last exposure and collected self-reported symptoms, mid-turbinate swabs (MTS) and saliva every two or three days. Ct values and frequency of viral detection by MTS and saliva were compared. Logistic regression was used to estimate the probability of detection by days since symptom onset for the two sample types.ResultsWe enrolled 58 contacts who provided a total of 200 saliva and MTS sample pairs; 14 contacts (13 with symptoms) had one or more positive samples. Overall, saliva and MTS had similar rates of viral detection (p=0.78). Although Ct values for saliva were significantly greater than for MTS (p=0.014), Cohen’s Kappa demonstrated substantial agreement (κ=0.83). However, sensitivity varied significantly with time relative to symptom onset. Early in the course of infection (days -3 to 2), saliva had 12 times (95%CI: 1.2, 130) greater likelihood of detecting viral RNA compared to MTS. After day 2, there was a non-significant trend to greater sensitivity using MTS samples.ConclusionSaliva and MTS specimens demonstrated high agreement, making saliva a suitable alternative to MTS nasal swabs for COVID-19 detection. Furthermore, saliva was more sensitive than MTS early in the course of infection, suggesting that it may be a superior and cost-effective screening tool for COVID-19.Key PointsSaliva is more sensitive in detecting symptomatic cases of COVID-19 than MTS early in the course of infection.Saliva performs best in the pre-symptomatic period.Saliva and MTS demonstrated high agreement making saliva a suitable and cost-effective COVID-19 screening tool.

No Evidence of SARS-CoV-2 Among Flies or Cockroaches in COVID-19 Positive Households

Background:The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a pandemic of coronavirus disease (COVID-19), which continues to cause infections and mortality worldwide. SARS-CoV-2 is transmitted primarily via the respiratory route and has experimentally been found to be stable on surfaces for multiple days. Flies (Diptera) and other arthropods mechanically transmit several pathogens, including turkey coronavirus. A previous experimental study demonstrated house flies, Musca domestica, can mechanically transmit SARS-CoV-2, but the ability of flies in general to acquire and deposit this virus in natural settings has not been explored. The purpose of this study was to explore the possibility of mechanical transmission of SARS-CoV-2 by peridomestic insects and their potential as a xenosurveillance tool for detection of the virus.Methods:In order to optimize chances of viral detection, flies were trapped in homes where at least one confirmed human COVID-19 case(s) resided. Sticky and liquid baited fly traps were deployed inside and outside of the homes of SARS-CoV-2 human cases in Brazos, Bell, and Montgomery Counties, from June to September 2020. Flies from sticky traps were identified, pooled by taxa, homogenized, and tested for the presence of SARS-CoV-2 RNA using qRT-PCR. Liquid traps were drained, and the collected fluid similarly tested after RNA concentration. Experimental viral detection pipeline and viral inactivation were confirmed in a Biosafety Level 3 lab. As part of a separate ongoing study, companion animals in the home were sampled and tested for SARS-CoV-2 on the same day of insect trap deployment.Results:We processed the contents of 133 insect traps from 44 homes, which contained over 1,345 individual insects of 11 different Diptera families and Blattodea.These individuals were grouped into 243 pools, and all tested negative for SARS-CoV-2 RNA. Dead flies exposed to SARS-CoV-2 in a BSL3 lab were processed using the same methods and viral RNA was detected by RT-PCR. Fourteen traps in seven homes were deployed on the day that cat or dog samples tested positive for SARS-CoV-2 RNA by nasal, oral, body, or rectal samples.Conclusions:This study presents evidence that biting and non-biting flies are not likely to contribute to mechanical transmission of SARS-CoV-2 or be useful in xenosurveillance for SARS-CoV-2.

Retrospective epidemiological analysis of SARS-CoV-2 wastewater surveillance and case notifications data – New South Wales, Australia, 2020

This epidemiological study analysed SARS-CoV-2 wastewater surveillance and case notifications data to inform evidence-based public health action in NSW. We investigated measures of association between SARS-CoV-2 RNA fragments detected in wastewater samples (n=100) and case notifications (n=1,367, as rates per 100,000 population) within wastewater catchment areas (n=6); and evaluated the performance of wastewater testing as a population-level diagnostic tool. Furthermore, we modelled SARS-CoV-2 RNA fragment detection in wastewater given the case notification rate using logistic regression. The odds of a viral detection in wastewater samples increased by a factor of 5.68 (95% CI: 1.51–32.1, P=0.004) with rates of one or more notified cases within a catchment. The diagnostic specificity of wastewater viral detection results was 0.88 (95% CI: 0.69–0.97); the overall diagnostic sensitivity was 0.44 (95% CI: 0.33–0.56). The probability of a viral detection result in wastewater exceeded 50% (95% CI: 36–64%) once the case rate within a catchment exceeded 10.5. Observed results suggest that in a low prevalence setting, wastewater viral detections are a more reliable indicator of the presence of recent virus shedding cases in a catchment, than non-detect results are of the absence of cases in a catchment.

Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism

Lichen thalli are formed through the symbiotic association of a filamentous fungus and photosynthetic green alga and/or cyanobacterium. Recent studies have revealed lichens also host highly diverse communities of secondary fungal and bacterial symbionts, yet few studies have examined the viral component within these complex symbioses. Here, we describe viral biodiversity and functions in cyanolichens collected from across North America and Europe. As current machine-learning viral-detection tools are not trained on complex eukaryotic metagenomes, we first developed efficient methods to remove eukaryotic reads prior to viral detection and a custom pipeline to validate viral contigs predicted with three machine-learning methods. Our resulting high-quality viral data illustrate that every cyanolichen thallus contains diverse viruses that are distinct from viruses in other terrestrial ecosystems. In addition to cyanobacteria, predicted viral hosts include other lichen-associated bacterial lineages and algae, although a large fraction of viral contigs had no host prediction. Functional annotation of cyanolichen viral sequences predicts numerous viral-encoded auxiliary metabolic genes (AMGs) involved in amino acid, nucleotide, and carbohydrate metabolism, including AMGs for secondary metabolism (antibiotics and antimicrobials) and fatty acid biosynthesis. Overall, the diversity of cyanolichen AMGs suggests that viruses may alter microbial interactions within these complex symbiotic assemblages.

Serological Testing Reveals the Hidden COVID-19 Burden among Health Care Workers Experiencing a SARS-CoV-2 Nosocomial Outbreak

We describe the results of testing frontline health care workers, from a hospital in Japan that had experienced a COVID-19 outbreak, for SARS-CoV-2-specific antibodies. Antibody testing revealed that a surprising 42% of overlooked COVID-19 diagnoses occurred when case detection relied solely on PCR-based viral detection.

Validation of a direct-to-PCR COVID-19 detection protocol utilizing mechanical homogenization: A model for reducing resources needed for accurate testing

Efficient and effective viral detection methodologies are a critical piece in the global response to COVID-19, with PCR-based nasopharyngeal and oropharyngeal swab testing serving as the current gold standard. With over 100 million confirmed cases globally, the supply chains supporting these PCR testing efforts are under a tremendous amount of stress, driving the need for innovative and accurate diagnostic solutions. Herein, the utility of a direct-to-PCR method of SARS-CoV-2 detection grounded in mechanical homogenization is examined for reducing resources needed for testing while maintaining a comparable sensitivity to the current gold standard workflow of nasopharyngeal and oropharyngeal swab testing. In a head-to-head comparison of 30 patient samples, this initial clinical validation study of the proposed homogenization-based workflow demonstrated significant agreeability with the current extraction-based method utilized while cutting the total resources needed in half.

Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism

Lichen thalli are formed through the symbiotic association of a filamentous fungus and photosynthetic green alga and/or cyanobacterium. Recent studies have revealed lichens also host highly diverse communities of secondary fungal and bacterial symbionts, yet few studies have examined the viral component within these complex symbioses. Here, we describe viral biodiversity and functions in cyanolichens collected from across North America and Europe. As current machine learning viral-detection tools are not trained on complex eukaryotic metagenomes, we first developed efficient methods to remove eukaryotic reads prior to viral detection and a custom pipeline to validate viral contigs predicted with three machine-learning methods. Our resulting high-quality viral data illustrate that every cyanolichen thallus contains diverse viruses that are distinct from viruses in other terrestrial ecosystems. In addition to cyanobacteria, predicted viral hosts include other lichen-associated bacterial lineages and algae, although a large fraction of viral contigs had no host prediction. Functional annotation of cyanolichen viral sequences reveals numerous viral-encoded auxiliary metabolic genes (AMGs) involved in amino acid, nucleotide, and carbohydrate metabolism, including AMGs for secondary metabolism (antibiotics and antimicrobials) and fatty acid biosynthesis. Overall, the diversity of cyanolichen AMGs suggests that viruses may alter microbial interactions within these complex symbiotic assemblages.