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Register a new userWhat is the potential for a second peak in the evolution of SARS-CoV-2 in emerging and developing economies? Insights from a SIRASD model considering the informal economy
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We study the potential scenarios from a Susceptible-Infected-Recovered-Asymptomatic-Symptomatic-Dead (SIRASD) model. As a novelty, we consider populations that differ in their degree of compliance with social distancing policies following socioeconomic attributes that are observed in emerging and developing countries. Considering epidemiological parameters estimated from data of the propagation of SARS-CoV-2 in Brazil -- where there is a significant stake of the population making their living in the informal economy and thus prone to not follow self-isolation -- we assert that if the confinement measures are lifted too soon, namely as much as one week of consecutive declining numbers of new cases, it is very likely the appearance of a second peak. Our approach should be valid for any country where the number of people involved in the informal economy is a large proportion of the total labor force. In summary, our results point out the crucial relevance of target policies for supporting people in the informal economy to properly comply with preventive measures during the pandemic.
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A number of epidemics, including the SARS-CoV-1 epidemic of 2002-2004, have been known to exhibit superspreading, in which a small fraction of infected individuals is responsible for the majority of new infections. The existence of superspreading implies a fat-tailed distribution of infectiousness (new secondary infections caused per day) among different individuals. Here, we present a simple method to estimate the variation in infectiousness by examining the variation in early-time growth rates of new cases among different subpopulations. We use this method to estimate the mean and variance in the infectiousness, $beta$, for SARS-CoV-2 transmission during the early stages of the pandemic within the United States. We find that $sigma_beta/mu_beta gtrsim 3.2$, where $mu_beta$ is the mean infectiousness and $sigma_beta$ its standard deviation, which implies pervasive superspreading. This result allows us to estimate that in the early stages of the pandemic in the USA, over 81% of new cases were a result of the top 10% of most infectious individuals.
SARS-CoV-2 causing COVID-19 disease has moved rapidly around the globe, infecting millions and killing hundreds of thousands. The basic reproduction number, which has been widely used and misused to characterize the transmissibility of the virus, hides the fact that transmission is stochastic, is dominated by a small number of individuals, and is driven by super-spreading events (SSEs). The distinct transmission features, such as high stochasticity under low prevalence, and the central role played by SSEs on transmission dynamics, should not be overlooked. Many explosive SSEs have occurred in indoor settings stoking the pandemic and shaping its spread, such as long-term care facilities, prisons, meat-packing plants, fish factories, cruise ships, family gatherings, parties and night clubs. These SSEs demonstrate the urgent need to understand routes of transmission, while posing an opportunity that outbreak can be effectively contained with targeted interventions to eliminate SSEs. Here, we describe the potential types of SSEs, how they influence transmission, and give recommendations for control of SARS-CoV-2.
The COVID-19 pandemic has lead to a worldwide effort to characterize its evolution through the mapping of mutations in the genome of the coronavirus SARS-CoV-2. Ideally, one would like to quickly identify new mutations that could confer adaptive advantages (e.g. higher infectivity or immune evasion) by leveraging the large number of genomes. One way of identifying adaptive mutations is by looking at convergent mutations, mutations in the same genomic position that occur independently. However, the large number of currently available genomes precludes the efficient use of phylogeny-based techniques. Here, we establish a fast and scalable Topological Data Analysis approach for the early warning and surveillance of emerging adaptive mutations based on persistent homology. It identifies convergent events merely by their topological footprint and thus overcomes limitations of current phylogenetic inference techniques. This allows for an unbiased and rapid analysis of large viral datasets. We introduce a new topological measure for convergent evolution and apply it to the GISAID dataset as of February 2021, comprising 303,651 high-quality SARS-CoV-2 isolates collected since the beginning of the pandemic. We find that topologically salient mutations on the receptor-binding domain appear in several variants of concern and are linked with an increase in infectivity and immune escape, and for many adaptive mutations the topological signal precedes an increase in prevalence. We show that our method effectively identifies emerging adaptive mutations at an early stage. By localizing topological signals in the dataset, we extract geo-temporal information about the early occurrence of emerging adaptive mutations. The identification of these mutations can help to develop an alert system to monitor mutations of concern and guide experimentalists to focus the study of specific circulating variants.
This article contains a series of analyses done for the SARS-CoV-2 outbreak in Rio Grande do Sul (RS) in the south of Brazil. These analyses are focused on the high-incidence cities such as the state capital Porto Alegre and at the state level. We provide methodological details and estimates for the effective reproduction number $R_t$, a joint analysis of the mobility data together with the estimated $R_t$ as well as ICU simulations and ICU LoS (length of stay) estimation for hospitalizations in Porto Alegre/RS.
Solar UV$-$C photons do not reach Earths surface, but are known to be endowed with germicidal properties that are also effective on viruses. The effect of softer UV$-$B and UV$-$A photons, which copiously reach the Earths surface, on viruses are instead little studied, particularly on single$-$stranded RNA viruses. Here we combine our measurements of the action spectrum of Covid$-$19 in response to UV light, Solar irradiation measurements on Earth during the SARS$-$CoV$-$2 pandemics, worldwide recorded Covid$-$19 mortality data and our Solar$-$Pump diffusive model of epidemics to show that (a) UV$-$B$/$A photons have a powerful virucidal effect on the single$-$stranded RNA virus Covid$-$19 and that (b) the Solar radiation that reaches temperate regions of the Earth at noon during summers, is sufficient to inactivate 63perc of virions in open$-$space concentrations (1.5 x 103 TCID50$/$mL, higher than typical aerosol) in less than 2 min. We conclude that the characteristic seasonality imprint displayed world$-$wide by the SARS$-$Cov$-$2 mortality time$-$series throughout the diffusion of the outbreak (with temperate regions showing clear seasonal trends and equatorial regions suffering, on average, a systematically lower mortality), might have been efficiently set by the different intensity of UV$-$B$/$A Solar radiation hitting different Earths locations at different times of the year. Our results suggest that Solar UV$-$B$/$A play an important role in planning strategies of confinement of the epidemics, which should be worked out and set up during spring$/$summer months and fully implemented during low$-$solar$-$irradiation periods.
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