Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples.

Genetic analysis of intra-host viral populations provides unique insight into pre-emergent mutations that may contribute to the genotype of future variants. Clinical samples positive for SARS-CoV-2 collected in California during the first months of the pandemic were sequenced to define the dynamics of mutation emergence as the virus became established in the state. Deep sequencing of 90 nasopharyngeal samples showed that many mutations associated with the establishment of SARS-CoV-2 globally were present at varying frequencies in a majority of the samples, even those collected as the virus was first detected in the US. A subset of mutations that emerged months later in consensus sequences were detected as subconsensus members of intra-host populations. Spike mutations P681H, H655Y, and V1104L were detected prior to emergence in variant genotypes, mutations were detected at multiple positions within the furin cleavage site, and pre-emergent mutations were identified in the nucleocapsid and the envelope genes. Because many of the samples had a very high depth of coverage, a bioinformatics pipeline, "Mappgene", was established that uses both iVar and LoFreq variant calling to enable identification of very low-frequency variants. This enabled detection of a spike protein deletion present in many samples at low frequency and associated with a variant of concern.

SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection.

Wastewater-based epidemiology (WBE) is a popular tool for the early indication of community spread of infectious diseases. WBE emerged as an effective tool during the COVID-19 pandemic and has provided meaningful information to minimize the spread of infection. Here, we present a combination of analyses using the correlation of viral gene copies with clinical cases, sequencing of wastewater-derived RNA for the viral mutants, and correlative analyses of the viral gene copies with the bacterial biomarkers. Our study provides a unique platform for potentially using the WBE-derived results to predict the spread of COVID-19 and the emergence of new variants of concern. Further, we observed a strong correlation between the presence of SARS-CoV-2 and changes in the microbial community of wastewater, particularly the significant changes in bacterial genera belonging to the families of Lachnospiraceae and Actinomycetaceae. Our study shows that microbial biomarkers could be utilized as prediction tools for future infectious disease surveillance and outbreak responses. Overall, our comprehensive analyses of viral spread, variants, and novel bacterial biomarkers will add significantly to the growing body of literature on WBE and COVID-19.

Performance of three-dimensional printed nasopharyngeal swabs for COVID-19 testing.

ABSTRACT: At the start of the COVID-19 pandemic, the US faced nationwide shortages of nasopharyngeal swabs due to both overwhelmed supply chains and an increase in demand. To address this shortfall, multiple 3D printed swabs were ultimately produced and sold for COVID-19 testing. In this work, we present a framework for mechanical and functional bench-testing of nasopharyngeal swabs using standard and widely available material testing equipment. Using this framework, we offer a comprehensive, quantitative comparison of the 3D printed swabs to benchmark their performance against traditional flocked swabs. The test protocols were designed to emulate the clinical use of the nasopharyngeal swabs and to evaluate potential failure modes. Overall, the 3D printed swabs performed comparably to, or outperformed, the traditional swabs in all mechanical tests. While traditional swabs outperformed some of the new 3D printed swabs in terms of sample uptake and retention, similar amounts of RNA were recovered from both 3D printed and traditional swabs.

Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline.

A rapid response is necessary to contain emergent biological outbreaks before they can become pandemics. The novel coronavirus (SARS-CoV-2) that causes COVID-19 was first reported in December of 2019 in Wuhan, China and reached most corners of the globe in less than two months. In just over a year since the initial infections, COVID-19 infected almost 100 million people worldwide. Although similar to SARS-CoV and MERS-CoV, SARS-CoV-2 has resisted treatments that are effective against other coronaviruses. Crystal structures of two SARS-CoV-2 proteins, spike protein and main protease, have been reported and can serve as targets for studies in neutralizing this threat. We have employed molecular docking, molecular dynamics simulations, and machine learning to identify from a library of 26 million molecules possible candidate compounds that may attenuate or neutralize the effects of this virus. The viability of selected candidate compounds against SARS-CoV-2 was determined experimentally by biolayer interferometry and FRET-based activity protein assays along with virus-based assays. In the pseudovirus assay, imatinib and lapatinib had IC50 values below 10 µM, while candesartan cilexetil had an IC50 value of approximately 67 µM against Mpro in a FRET-based activity assay. Comparatively, candesartan cilexetil had the highest selectivity index of all compounds tested as its half-maximal cytotoxicity concentration 50 (CC50) value was the only one greater than the limit of the assay (>100 µM).

Quantitative Fit Evaluation of N95 Filtering Facepiece Respirators and Coronavirus Inactivation Following Heat Treatment.

Reuse of filtering facepiece respirators (FFRs, commonly referred to as N95s) normally meant for single use has become common in healthcare facilities due to shortages caused by the COVID-19 pandemic. Here, we report that murine hepatitis coronavirus initially seeded on FFR filter material is inactivated (6 order of magnitude reduction as measured by median tissue culture infective dose, TCID50) after dry heating at 75°C for 30 min. We also find that the quantitative fit of FFRs after heat treatment at this temperature, under dry conditions or at 90% relative humidity, is not affected by single or 10 heating cycles. Previous studies have reported that the filtration efficiency of FFRs is not negatively impacted by these heating conditions. These results suggest that thermal inactivation of coronaviruses is a potentially rapid and widely deployable method to reuse N95 FFRs in emergency situations where reusing FFRs is a necessity and broad-spectrum sterilization is unavailable. However, we also observe that a radiative heat source (e.g. an exposed heating element) results in rapid qualitative degradation of the FFR. Finally, we discuss differences in the results reported here and other recent studies investigating heat as a means to recycle FFRs. These differences suggest that while our repeated decontamination cycles do not affect FFR fit, overall wear time and the number of donning/doffing cycles are important factors that likely degrade FFR fit and must be investigated further.