EVIDENCE OF TRUNCATED E1 PROTEINS IN WILD-TYPE VENEZUELAN EQUINE ENCEPHALITIS VIRUS

N.L. Forrester, Ph.D., X. Liang, S.C. Weaver, Ph.D.

Department of Pathology, UTMB

Introduction: The presence of quasispecies or intra-host variation within viruses is thought to increase the ability of the virus to adapt and alter to changes in the environment whether external pressures or within the host. Whilst intra-host variation has been demonstrated to play an important role in many viral infections [e.g. HIV and Hepatitis C virus (HCV)], the importance of such variation in arboviruses (Arthropod-borne viruses) is as yet unknown. Additionally, it is known that arboviruses appear to have a lower evolutionary rate than other viruses in part because the mosquito acts as a limiting factor on viral evolution. Objective: These experiments were undertaken to determine the degree of variation present in a wild-type strain of VEEV IE, so that this could be used as a base line in further experiments. Method: An original isolate of VEEV IE strain MX01-32 was used for total RNA extraction. A reverse-transcription step was performed using random hexamers to prevent bias in the amplification step. The genome was amplified in overlapping 1000bp fragments using primers designed to amplify all IE strains. The resulting fragments were cloned into a vector and 48 clones amplified and sequenced for all PCR fragments. Results: Variation was found as expected across the genome, in general point mutations were observed with occasional deletions, ranging from single nucleotide deletions to much larger deletions. Surprisingly multiple deletions were observed in the 5’ region of the E1 gene ranging from 30bp to 150bp. Summary: Variation in the genome was as expected for most of the genome, with point mutations and occasional deletions. However, the number of deletions in the 5’ regions of the E1 gene was not expected and is likely to affect the structure and function of the E1 gene. Further work is required to determine if these deletions are maintained after additional replication of the virus. Supported by The James W. McLaughlin Fellowship Fund.