Global discovery of human-infective RNA viruses: A modelling analysis.

Mark E. J. Woolhouse,Bram A. D. van Bunnik,Feifei Zhang,Margo Chase-Topping,Liam Brierley,Chuan-Guo Guo,Stephen Morse

doi:10.1371/journal.ppat.1009079

Abstract

RNA viruses are a leading cause of human infectious diseases and the prediction of where new RNA viruses are likely to be discovered is a significant public health concern. Here, we geocoded the first peer-reviewed reports of 223 human RNA viruses. Using a boosted regression tree model, we matched these virus data with 33 explanatory factors related to natural virus distribution and research effort to predict the probability of virus discovery across the globe in 2010-2019. Stratified analyses by virus transmissibility and transmission mode were also performed. The historical discovery of human RNA viruses has been concentrated in eastern North America, Europe, central Africa, eastern Australia, and north-eastern South America. The virus discovery can be predicted by a combination of socio-economic, land use, climate, and biodiversity variables. Remarkably, vector-borne viruses and strictly zoonotic viruses are more associated with climate and biodiversity whereas non-vector-borne viruses and human transmissible viruses are more associated with GDP and urbanization. The areas with the highest predicted probability for 2010-2019 include three new regions including East and Southeast Asia, India, and Central America, which likely reflect both increasing surveillance and diversity of their virome. Our findings can inform priority regions for investment in surveillance systems for new human RNA viruses.

Highlights

Since the first identification of a virus in humans—yellow fever virus in 1901—viruses have been recognised as a leading cause of human infectious diseases [1]
By using a machine learning method, we found that the virus discovery was driven by a combination of variables describing socio-economic level, land use, climate and biodiversity, with GDP and GDP growth found to be the two leading predictors
We predicted the probability of virus discovery in 2010– 2019 across the globe, and identified three new areas (East and Southeast Asia, India, and Central America) in addition to the historical high-risk areas

Summary

Introduction

Since the first identification of a virus in humans—yellow fever virus in 1901—viruses have been recognised as a leading cause of human infectious diseases [1]. A virus is identified through investigation of the aetiology of a human disease (e.g. yellow fever virus [11], measles virus [12]), some have been identified during active virus discovery programmes (e.g. rotavirus C [13], parechovirus B [14]). Viruses such as hepatitis delta virus [15] and Highlands J virus [16] were discovered by chance, as incidental findings as part of a disease investigation

Methods

Results

Discussion

Conclusion