Determining the rate of infectious disease testing through contagion potential

Abstract

The emergence of new strains, varying in transmissibility, virulence, and presentation, makes the existing epidemiological statistics an inadequate representation of COVID-19 contagion. Asymptomatic individuals continue to act as carriers for the elderly and immunocompromised, making the timing and extent of vaccination and testing extremely critical in curbing contagion. In our earlier work, we proposed contagion potential (CP) as a measure of the infectivity of an individual in terms of their contact with other infectious individuals. Here we extend the idea of CP at the level of a geographical region (termed a zone). We estimate CP in a spatiotemporal model based on infection spread through social mixing as well as SIR epidemic model optimization, under varying conditions of virus strains, reinfection, and superspreader events. We perform experiments on the real daily infection dataset at the country level (Italy and Germany) and state level (New York City, USA). Our analysis shows that CP can effectively assess the number of untested (and asymptomatic) infected and inform the necessary testing rates. Finally, we show through simulations that CP can trace the evolution of the infectivity profiles of zones due to the combination of inter-zonal mobility, vaccination policy, and testing rates in real-world scenarios.

Mortality-Associated Sars-Cov-2 Genomic Variants From Patients Hospitalized for Severe Pneumonia in Aguascalientes, Mexico From 2020 to 2023

“…The viral genome typically encodes four structural proteins: Spike (s), envelope (E), membrane (M), and nucleocapsid (N), along with numerous non-structural proteins and multiple accessory proteins [Ren et al, 2020]. 4 Now recognized as Severe acute respiratory coronavirus 2 (SARS-CoV-2), it is a highly contagious virus that caused the COVID-19 pandemic disease that brought the world to a standstill, with a primary reproduction number (Ro), which depends on several factors, including the circulating variant, therefore, for Delta the Ro was 3.2 and for Omicron it was 9.5, which also depends on the population density, the mobility patterns, social interactions, and vaccination policies (Roy S, et al, 2023).…”

“…Now recognized as Severe acute respiratory coronavirus 2 (SARS-CoV-2), it is a highly contagious virus that caused the COVID-19 pandemic disease that brought the world to a standstill, with a primary reproduction number (Ro), which depends on several factors, including the circulating variant, therefore, for Delta the Ro was 3.2 and for Omicron it was 9.5, which also depends on the population density, the mobility patterns, social interactions, and vaccination policies (Roy S, et al, 2023). It is a single-stranded positive RNA virus with a length of 29,891 nucleotides, encoding 9,860 amino acids.…”