Estimating the potential need and impact of SARS-CoV-2 test-and-treat programs with oral antivirals in low-and-middle-income countries (preprint)

Oral antivirals can potentially reduce the burden of COVID-19. However, low SARS-CoV-2 clinical testing rates in many low- and middle-income countries (LMICs) (mean <10 tests/100,000 people/day, July 2022) makes the development of effective test- and-treat programs challenging. Here, we used an agent-based model to investigate how testing rates and strategies could affect development of test- and-treat programs in three representative LMICs. We find that at <10 tests/100,000 people/day, test- and-treat programs are unlikely to have any impact on the public health burden of COVID-19. At low effective transmission rates ( R t ≤ 1.2), increasing to 100 tests/100,000 people/day and allowing uncapped distribution of antivirals to LMICs (estimate = 26,000,000-90,000,000 courses/year for all LMICs), could avert up to 65% of severe cases, particularly in countries with older populations. For higher R t , significant reductions in severe cases are only possible by substantially increasing testing rates or restricting clinical testing to those with higher risk of severe disease.

Impacts of the COVID-19 pandemic on future seasonal influenza epidemics (preprint)

Summary Seasonal influenza viruses typically cause annual epidemics worldwide infecting 5-15% of the human population 1 . However, during the first two years of the COVID-19 pandemic, seasonal influenza virus circulation was unprecedentedly low with very few reported infections 2 . The lack of immune stimulation to influenza viruses during this time, combined with waning antibody titres to previous influenza virus infections, could lead to increased susceptibility to influenza in the coming seasons and to larger and more severe epidemics when infection prevention measures against COVID-19 are relaxed 3,4 . Here, based on serum samples from 165 adults collected longitudinally before and during the pandemic, we show that the waning of antibody titres against seasonal influenza viruses during the first two years of the pandemic is likely to be negligible. Using historical influenza virus epidemiological data from 2003-2019, we also show that low country-level prevalence of each influenza subtype over one or more years has only small impacts on subsequent epidemic size. These results suggest that the risks posed by seasonal influenza viruses remained largely unchanged during the first two years of the COVID-19 pandemic and that the sizes of future seasonal influenza virus epidemics will likely be similar to those observed before the pandemic.

Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA (preprint)

COVID-19 patients shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. In our benchmarking study, we recommend a standardized protocol for the preservation, extraction and detection of viral RNA from stool. This protocol includes a preservative, viral RNA extraction steps, and PCR-based quantification methods to maximize yield and detection of SARS-CoV-2 RNA. Our protocol takes advantage of commercially available reagents and equipment to maximize ease of access and consistency across studies. Additionally, we apply an attenuated bovine coronavirus vaccine as a spike-in control, and synthetic RNA standards to improve standardization and reliability of the assay. While we recommend both ddPCR and RT-qPCR-based assays, we acknowledge that ddPCR may be prohibitively expensive due to the necessity of specialized equipment and reagents. This protocol was developed with a focus on SARS-CoV-2 RNA, but may apply to other coronaviruses as well. We estimate that this protocol takes between 6 to 8 hours total to quantify the viral RNA load in a fecal sample.

Standardized and optimized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA (preprint)

COVID-19 patients shed SARS-CoV-2 viral RNA in their stool, sometimes well after they have cleared their respiratory infection. This feature of the disease may be significant for patient health, epidemiology, and diagnosis. However, to date, methods to preserve stool samples from COVID patients, and to extract and quantify viral RNA concentration have yet to be optimized. We sought to meet this urgent need by developing and benchmarking a standardized protocol for the fecal detection of SARS-CoV-2 RNA. We test three preservative conditions for their ability to yield detectable SARS-CoV-2 RNA: OMNIgene-GUT, Zymo DNA/RNA shield kit, and the most common condition, storage without any preservative. We test these in combination with three extraction kits: the QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. Finally, we also test the utility of two detection methods, ddPCR and RT-qPCR, for the robust quantification of SARS-CoV-2 viral RNA from stool. We identify that the Zymo DNA/RNA shield collection kit and the QiaAMP viral RNA mini kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR assays. We also demonstrate key features of experimental design including the incorporation of appropriate controls and data analysis, and apply these techniques to effectively extract viral RNA from fecal samples acquired from COVID-19 outpatients enrolled in a clinical trial. Finally, we recommend a comprehensive methodology for future preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.