Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections.

Archana Jadhav,Lele Zhao,Sebastian E Ramos-Onsins,Venugopal Nair,Weiwei Liu,Luca Ferretti,Chan Ding

doi:10.3390/v12111305

Abstract

Newcastle disease virus (NDV) infections are well known to harbour quasispecies, due to the error-prone nature of the RNA polymerase. Quasispecies variants in the fusion cleavage site of the virus are known to significantly change its virulence. However, little is known about the genomic patterns of diversity and selection in NDV viral swarms. We analyse deep sequencing data from in vitro and in vivo NDV infections to uncover the genomic patterns of diversity and the signatures of selection within NDV swarms. Variants in viruses from in vitro samples are mostly localised in non-coding regions and 3′ and 5′ untranslated regions (3′UTRs or 5′UTRs), while in vivo samples contain an order of magnitude more variants. We find different patterns of genomic divergence and diversity among NDV genotypes, as well as differences in the genomic distribution of intra-host variants among in vitro and in vivo infections of the same strain. The frequency spectrum shows clear signatures of intra-host purifying selection in vivo on the matrix protein (M) coding gene and positive or diversifying selection on nucleocapsid (NP) and haemagglutinin-neuraminidase (HN). The comparison between within-host polymorphisms and phylogenetic divergence reveals complex patterns of selective pressure on the NDV genome at between- and within-host level. The M sequence is strongly constrained both between and within hosts, fusion protein (F) coding gene is under intra-host positive selection, and NP and HN show contrasting patterns: HN RNA sequence is positively selected between hosts while its protein sequence is positively selected within hosts, and NP is under intra-host positive selection at the RNA level and negative selection at the protein level.

Highlights

RNA viruses often have high mutation rates due to the error-prone nature of RNA polymerases [1,2].Inside a host, viral RNA polymerases induce roughly 10−4 mutations per nucleotide copied due to low fidelity, and this may result in the formation of a viral swarm, i.e., a pool of similar genotypes differing only by a handful of mutations [1,2]
Later, infected chicken embryo fibroblast (CEF) cells were cultured in 2% foetal bovine serum (FBS) containing Dulbecco’s modified Eagle’s medium (DMEM) and cells were harvested before
LaSota and the highly pathogenic Herts/33 [25], as well as from different tissues such as trachea [28], lung [27], and spleen [26] harvested from in vivo experiments on Leghorn and Fayoumi chickens infected with LaSota

Summary

Introduction

Viral RNA polymerases induce roughly 10−4 mutations per nucleotide copied due to low fidelity, and this may result in the formation of a viral swarm, i.e., a pool of similar genotypes differing only by a handful of mutations [1,2]. This is a distinctive pattern of intra-host genetic variability. Viruses 2020, 12, 1305 in organisms with high mutation rates In viral infections, this is frequently related to quasispecies dynamics, with complex interactions between the viruses in the swarm [1,2]. NDV belongs to the Orthoavulavirus genus of the Avulavirinae subfamily in the Paramyxoviridae family of the Mononegavirales order [7]

Methods

Results

Conclusion