MVSE: An R‐package that estimates a climate‐driven mosquito‐borne viral suitability index

Abstract

Viruses, such as dengue, Zika, yellow fever and chikungunya, depend on mosquitoes for transmission. Their epidemics typically present periodic patterns, linked to the underlying mosquito population dynamics, which are known to be driven by natural climate fluctuations. Understanding how climate dictates the timing and potential of viral transmission is essential for preparedness of public health systems and design of control strategies. While various alternative approaches have been proposed to estimate local transmission potential of such viruses, few open‐source, ready to use and freely available software tools exist. We developed the Mosquito‐borne Viral Suitability Estimator (MVSE) software package for the R programming environment. MVSE estimates the index P, a novel suitability index based on a climate‐driven mathematical expression for the basic reproductive number of mosquito‐borne viruses. By accounting for local humidity and temperature, as well as viral, vector and human priors, the index P can be estimated for specific host and viral species in different regions of the globe. We describe the background theory, empirical support and biological interpretation of the index P. Using real‐world examples spanning multiple epidemiological contexts, we further demonstrate MVSE's basic functionality, research and educational potentials.

Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic

“…We then used the R package MVSE and entomological and epidemiological priors documented in the literature (Supplementary Table 1 ) to calculate daily transmission potential, from which we calculated weekly means for the duration of our study period 17 . We found that the model was reasonably robust to a range of priors for each of the parameters and therefore elected to use short human incubation and infectious period estimates to inform the model.…”

Characterising West Nile virus epidemiology in Israel using a transmission suitability index

“…[37]). Mathematical details can be found in our recent publication introducing the theory, practice and free R package that estimates the index P [33].…”

“…The main results can be reproduced by estimating index P with the freely available Mosquito-borne Viral Suitability Estimator (MVSE) R package (code as provided in Supplementary Text S2 section 3.13 of [33]), using the Israeli meteorological data as input and the priors listed in the Table. The MVSE is freely available at https://sourceforge.net/projects/mvse/. In the Supplement, we include minimal code that estimates the index P from the Israeli meteorological stations included in this study.…”

“…Suitability measures are an increasingly common, data-driven practice in mosquito-borne disease epidemiology, relying on meteorological variables as drivers of mosquito population dynamics and virusmosquito transmission efficiency [23,24,35]. We have validated the suitability index P in previous research, by successfully characterising the transmission potential of Aedes-borne pathogens, such as dengue virus in Brazil and Myanmar, Zika, dengue and chikungunya viruses in Honduras [33,36], and Zika virus in the Amazon region [34].…”

“…In this study we set out to characterise in detail the transmission potential of WNV in Israel using a mosquito-borne suitability measure termed the index P [33,34]. Suitability measures are an increasingly common, data-driven practice in mosquito-borne disease epidemiology, relying on meteorological variables as drivers of mosquito population dynamics and virusmosquito transmission efficiency [23,24,35].…”