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Register a new userAnalysis of the SARS-CoV-2 outbreak in Rio Grande do Sul / Brazil
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Christian S. Perone
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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.
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The aim of this paper is to analyse the evolution of the COVID-19 pandemic in Rio Grande do Sul by applying graph-theoretical tools, particularly spectral clustering techniques, on weighted graphs defined on the set of 167 municipalities in the state with population 10,000 or more, which are based on data provided by government agencies and other sources. To respond to this outbreak, the state has adopted a system by which pre-determined regions are assigned flags on a weekly basis, and different measures go into effect according to the flag assigned. Our results suggest that considering a flexible approach to the regions themselves might be a useful additional tool to give more leeway to cities with lower incidence rates, while keeping the focus on public safety. Moreover, simulations show the dampening effect of isolation on the dissemination of the disease.
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.
Viral transmission pathways have profound implications for public safety; it is thus imperative to establish a complete understanding of viable infectious avenues. Mounting evidence suggests SARS-CoV-2 can be transmitted via the air; however, this has not yet been demonstrated. Here we quantitatively analyze virion accumulation by accounting for aerosolized virion emission and destabilization. Reported superspreading events analyzed within this framework point towards aerosol mediated transmission of SARS-CoV-2. Virion exposure calculated for these events is found to trace out a single value, suggesting a universal minimum infective dose (MID) via aerosol that is comparable to the MIDs measured for other respiratory viruses; thus, the consistent infectious exposure levels and their commensurability to known aerosol-MIDs establishes the plausibility of aerosol transmission of SARS-CoV-2. Using filtration at a rate exceeding the destabilization rate of aerosolized SARS-CoV-2 can reduce exposure below this infective dose.
The development and authorization of COVID-19 vaccines has provided the clearest path forward to eliminate community spread hence end the ongoing SARS-CoV-2 pandemic. However, the limited pace at which the vaccine can be administered motivates the question, to what extent must we continue to adhere to social intervention measures such as mask wearing and social distancing? To address this question, we develop a mathematical model of COVID-19 spread incorporating both vaccine dynamics and socio-epidemiological parameters. We use this model to study two important measures of disease control and eradication, the effective reproductive number $R_t$ and the peak intensive care unit (ICU) caseload, over three key parameters: social measure adherence, vaccination rate, and vaccination coverage. Our results suggest that, due to the slow pace of vaccine administration, social measures must be maintained by a large proportion of the population until a sufficient proportion of the population becomes vaccinated for the pandemic to be eradicated. By contrast, with reduced adherence to social measures, hospital ICU cases will greatly exceed capacity, resulting in increased avoidable loss of life. These findings highlight the complex interplays involved between vaccination and social protective measures, and indicate the practical importance of continuing with extent social measures while vaccines are scaled up to allow the development of the herd immunity needed to end or control SARS-CoV-2 sustainably.
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