SARS-CoV-2 Total and Subgenomic RNA Viral Load in Hospitalized Patients (preprint)

Understanding viral load in patients infected with SARS-CoV-2 is critical to epidemiology and infection control. Previous studies have demonstrated that SARS-CoV-2 RNA can be detected for many weeks after symptom onset. The clinical significance of this finding is unclear and, in most patients, likely does not represent active infection. There are, however, patients who shed infectious virus for weeks. Detection of subgenomic RNA transcripts expressed by SARS-CoV-2 has been proposed to represent productive infection and may be a tractable marker for monitoring infectivity. Here, we use RT-PCR to quantify total and subgenomic nucleocapsid (N) and envelope (E) transcripts in 190 SARS-CoV-2 positive samples collected on hospital admission. We relate these findings to duration of symptoms. We find that all transcripts decline at the same rate; however, subgenomic E becomes undetectable before other transcripts. In Kaplan-Meier analysis the median duration of symptoms to a negative test is 14 days for sgE and 25 days for sgN. There is a linear decline in subgenomic RNA compared to total RNA suggesting subgenomic transcript copy number is highly dependent on copy number of total transcripts. The mean difference between total N and subgenomic N is 16-fold (4.0 cycles) and the mean difference between total E and sub-genomic E is 137-fold (7.1 cycles). This relationship is constant over duration of symptoms allowing prediction of subgenomic copy number from total copy number. Although Subgenomic E is undetectable at a time that may more closely reflect the duration of infectivity, its utility in determining active infection may be no more useful than a copy number threshold determined for total transcripts.

Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States (preprint)

The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.

Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts (preprint)

Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified a viral load threshold that minimizes false positives. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.

Humidity and deposition solution play a critical role in virus inactivation by heat treatment on N95 respirators (preprint)

Supply shortages of N95 respirators during the coronavirus disease 2019 (COVID-19) pandemic have motivated institutions to develop feasible and effective N95 respirator reuse strategies. In particular, heat decontamination is a treatment method that scales well and can be implemented in settings with variable or limited resources. Prior studies using multiple inactivation methods, however, have often focused on a single virus under narrowly defined conditions, making it difficult to develop guiding principles for inactivating emerging or difficult-to-culture viruses. We systematically explored how temperature, humidity, and virus deposition solutions impact the inactivation of viruses deposited and dried on N95 respirator coupons. We exposed four virus surrogates across a range of structures and phylogenies, including two bacteriophages (MS2 and phi6), a mouse coronavirus (murine hepatitis virus, MHV), and a recombinant human influenza A virus subtype H3N2 (IAV), to heat treatment for 30 minutes in multiple deposition solutions across several temperatures and relative humidities (RH). We observed that elevated RH was essential for effective heat inactivation of all four viruses tested. For heat treatments between 72{degrees}C and 82{degrees}C, RH greater than 50% resulted in > 6-log10 inactivation of bacteriophages and RH greater than 25% resulted in > 3.5-log10 inactivation of MHV and IAV. Furthermore, deposition of viruses in host cell culture media greatly enhanced virus inactivation by heat and humidity compared to other deposition solutions such as phosphate buffered saline, phosphate buffered saline with bovine serum albumin, and human saliva. Past and future heat treatment methods or technologies must therefore explicitly account for deposition solutions as a factor that will strongly influence observed virus inactivation rates. Overall, our data set can inform the design and validation of effective heat-based decontamination strategies for N95 respirators and other porous surfaces, especially for emerging or low-titer viruses that may be of immediate public health concern such as SARS-CoV-2. ImportanceShortages of personal protective equipment, including N95 respirators, during the coronavirus disease 2019 (COVID-19) pandemic have highlighted the need to develop effective decontamination strategies for their reuse. This is particularly important in healthcare settings for reducing exposure to respiratory viruses, like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19. Although several treatment methods are available, a widely accessible strategy will be necessary to combat shortages on a global scale. We demonstrate that the combination of heat and humidity inactivates viruses similar in structure to SARS-CoV-2, namely MS2, phi6, influenza A virus, and mouse coronavirus, after deposition on N95 respirators, and achieves the United States Food and Drug Administration guidelines to validate N95 respirator decontamination technologies. We further demonstrate that depositing viruses onto surfaces when suspended in culture media can greatly enhance observed inactivation, adding caution to how heat and humidity treatments methods are validated.

Validation of N95 filtering facepiece respirator decontamination methods available at a large university hospital (preprint)

ImportanceFiltering facepiece respirators, including N95 masks, are a critical component of infection prevention in hospitals. Due to unprecedented shortages in N95 respirators, many healthcare systems have explored reprocessing of N95 respirators. Data supporting these approaches are lacking in real hospital settings. In particular, published studies have not yet reported an evaluation of multiple viruses, bacteria, and fungi along with respirator filtration and fit in a single, full-scale study. ObjectiveWe initiated a full-scale study to evaluate different N95 FFR decontamination strategies and their impact on respirator integrity and inactivating multiple microorganisms, with experimental conditions informed by the needs and constraints of the hospital. MethodsWe explored several reprocessing methods using new 3M 1860 N95 respirators, including dry (<10% relative humidity) and moist (62-66% relative humidity) heat (80-82 {degrees}C) in the drying cycle of industrial instrument washers, ethylene oxide (EtO), pulsed xenon UV (UV-PX), hydrogen peroxide gas plasma (HPGP), and vaporous hydrogen peroxide (VHP). Respirator samples were treated and analyzed for biological indicator inactivation using four viruses (MS2, phi6, influenza A virus, murine hepatitis virus), three bacteria (Escherichia coli, Staphylococcus aureus, Geobacillus stearothermophilus), and the fungus Aspergillus niger. The impact of different application media was also evaluated. In parallel, decontaminated respirators were evaluated for filtration integrity and fit. ResultsVHP resulted in >2 log10 inactivation of all tested biological indicators. The combination of UV-PX + moist heat resulted in >2 log10 inactivation of all biological indicators except G. stearothermohphilus. Greater than 95% filtration efficiency was maintained following 2 (UV-PX + <10% relative humidity heat) or 10 (VHP) cycles of treatment, and proper fit was also preserved. UV-PX + dry heat was insufficient to inactivate all biological indicators. Although very effective at virus decontamination, HPGP resulted in decreased filtration efficiency after 3 cycles, and EtO treatment raised potential toxicity concerns. The observed inactivation of viruses with UV-PX, heat, and hydrogen peroxide treatments varied as a function of which culture media (PBS buffer or DMEM) they were deposited in. Conclusions and RelevanceHigh levels of biological indicator inactivation were achieved following treatment with either moist heat or VHP. These same treatments did not significantly impact mask filtration or fit. Hospitals have a variety of scalable options to safely reprocess N95 masks. Beyond value in the current Covid-19 pandemic, the broad group of microorganisms and conditions tested make these results relevant in potential future pandemic scenarios.