Positive epistasis between viral polymerase and the 3′ untranslated region of its genome reveals the epidemiologic fitness of dengue virus

Ayesa Syenina,Subhash G Vasudevan,Milly M Choy,Eng Eong Ooi,Hwee Cheng Tan,Colin Cheng,Tanamas Siriphanitchakorn,Esther Shuyi Gan,Dhanasekaran Vijaykrishna

doi:10.1073/pnas.1919287117

Abstract

Dengue virus (DENV) is a global health threat, causing repeated epidemics throughout the tropical world. While low herd immunity levels to any one of the four antigenic types of DENV predispose populations to outbreaks, viral genetic determinants that confer greater fitness for epidemic spread is an important but poorly understood contributor of dengue outbreaks. Here we report that positive epistasis between the coding and noncoding regions of the viral genome combined to elicit an epidemiologic fitness phenotype associated with the 1994 DENV2 outbreak in Puerto Rico. We found that five amino acid substitutions in the NS5 protein reduced viral genomic RNA (gRNA) replication rate to achieve a more favorable and relatively more abundant subgenomic flavivirus RNA (sfRNA), a byproduct of host 5'-3' exoribonuclease activity. The resulting increase in sfRNA relative to gRNA levels not only inhibited type I interferon (IFN) expression in infected cells through a previously described mechanism, but also enabled sfRNA to compete with gRNA for packaging into infectious particles. We suggest that delivery of sfRNA to new susceptible cells to inhibit type I IFN induction before gRNA replication and without the need for further de novo sfRNA synthesis could form a "preemptive strike" strategy against DENV.

Highlights

Dengue virus (DENV) is a global health threat, causing repeated epidemics throughout the tropical world
To systemically define the amino acid substitutions that could have contributed to the emergence of PR2B in 1994, we conducted ancestral state reconstruction on the codon phylogenies of all DENV2s isolated from Puerto Rico dating as far back as 1981
This was done by first estimating the tree topology using the maximum likelihood (ML) method using the general timereversible (GTR) nucleotide substitution model in Randomized Axelerated Maximum Likelihood (RaXML v. 8) [16] and subsequently estimating genetic distances and ancestral sequences using phylogenetic analysis by maximum likelihood (PAML), version 4 [17]

Summary

Introduction

Dengue virus (DENV) is a global health threat, causing repeated epidemics throughout the tropical world. Several outbreaks have occurred in areas where new DENV strains emerged and displaced endemic strains without a change in either viral serotype or genotype Such instances have been observed in Sri Lanka [4], Puerto Rico [5], Singapore [6], Vietnam [7], Nicaragua [8], Taiwan [9], and Brazil [10]. To gain insight into genetic determinants of epidemiologic fitness, we have taken advantage of the 1994 dengue outbreak in Puerto Rico In this outbreak, sequence data of the DENV genome revealed the emergence of a clade of DENV2 (PR2B clade) in 1994 that displaced another DENV2 clade (PR1) that had circulated endemically before the outbreak [5]. This will allow for better implementation of control measures to intercept impending outbreaks before many lives are affected

Methods

Results

Conclusion