Identification of a Functional Small Noncoding RNA of African Swine Fever Virus.

Laura E M Dunn,Alasdair Ivens,Christopher L Netherton,Philippa M Beard,David A G Chapman,Joanna L Shisler

doi:10.1128/jvi.01515-20

Abstract

African swine fever virus (ASFV) causes a lethal hemorrhagic disease of domestic pigs, against which no vaccine is available. ASFV has a large, double-stranded DNA genome that encodes over 150 proteins. Replication takes place predominantly in the cytoplasm of the cell and involves complex interactions with host cellular components, including small noncoding RNAs (sncRNAs). A number of DNA viruses are known to manipulate sncRNA either by encoding their own or disrupting host sncRNA. To investigate the interplay between ASFV and sncRNAs, a study of host and viral small RNAs extracted from ASFV-infected primary porcine macrophages (PAMs) was undertaken. We discovered that ASFV infection had only a modest effect on host miRNAs, with only 6 miRNAs differentially expressed during infection. The data also revealed 3 potential novel small RNAs encoded by ASFV, ASFVsRNA1-3. Further investigation of ASFVsRNA2 detected it in lymphoid tissue from pigs with ASF. Overexpression of ASFVsRNA2 led to an up to 1-log reduction in ASFV growth, indicating that ASFV utilizes a virus-encoded small RNA to disrupt its own replication.IMPORTANCE African swine fever (ASF) poses a major threat to pig populations and food security worldwide. The disease is endemic to Africa and Eastern Europe and is rapidly emerging into Asia, where it has led to the deaths of millions of pigs in the last 12 months. The development of safe and effective vaccines to protect pigs against ASF has been hindered by lack of understanding of the complex interactions between ASFV and the host cell. We focused our work on characterizing the interactions between ASFV and sncRNAs. Although comparatively modest changes to host sncRNA abundances were observed upon ASFV infection, we discovered and characterized a novel functional ASFV-encoded sncRNA. The results from this study add important insights into ASFV host-pathogen interactions. This knowledge may be exploited to develop more effective ASFV vaccines that take advantage of the sncRNA system.

Highlights

African swine fever virus (ASFV) causes a lethal hemorrhagic disease of domestic pigs, against which no vaccine is available
We found that virulent ASFV infection of primary porcine macrophages had only a small impact on host miRNAs, with only 6 out of 178 identified porcine miRNAs differentially expressed over a 16-h time period
To investigate if ASFV shares the ability of vaccinia virus (VACV) to induce miRNA polyadenylation and decay, porcine alveolar macrophages (PAMs) were infected with the pathogenic ASFV Benin 97/1 strain and Vero cells were infected with the Vero cell-adapted ASFV strain, Ba71v

Summary

Introduction

African swine fever virus (ASFV) causes a lethal hemorrhagic disease of domestic pigs, against which no vaccine is available. Replication takes place predominantly in the cytoplasm of the cell and involves complex interactions with host cellular components, including small noncoding RNAs (sncRNAs). Eukaryotic cells produce multiple classes of sncRNA, including microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), and endogenous small interfering RNAs (siRNAs) [12]. These sncRNAs are involved in many biological processes, including apoptosis, differentiation, stress response, and immune activation [13]. Virus-encoded miRNAs have been identified in a number of DNA virus families, including Herpesviridae, Polyomaviridae, Iridoviridae, Ascoviridae, Baculoviridae, and the Adenoviridae [14] These miRNAs play a variety of roles, including cell proliferation regulation, control of apoptosis, and modulation of host immunity [15]. An interesting example is the herpes simplex virus 1 (HSV-1)-encoded non-miRNA small RNAs (LAT sRNA1 and sRNA1) that regulate productive infection and inhibit apoptosis [18]

Methods

Results

Conclusion