Comprehensive Analysis of Codon Usage on Porcine Astrovirus.

Huiguang Wu,Jingwen Zhao,Chunxiao Mou,Zhengyu Bao,Zhenhai Chen

doi:10.3390/v12090991

Abstract

Porcine astrovirus (PAstV), associated with mild diarrhea and neurological disease, is transmitted in pig farms worldwide. The purpose of this study is to elucidate the main factors affecting codon usage to PAstVs. Phylogenetic analysis showed that the subtype PAstV-5 sat at the bottom of phylogenetic tree, followed by PAstV-3, PAstV-1, PAstV-2, and PAstV-4, indicating that the five existing subtypes (PAstV1-PAstV5) may be formed by multiple differentiations of PAstV ancestors. A codon usage bias was found in the PAstVs-2,3,4,5 from the analyses of effective number of codons (ENC) and relative synonymous codon usage (RSCU). Nucleotides A/U are more frequently used than nucleotides C/G in the genome CDSs of the PAstVs-3,4,5. Codon usage patterns of PAstV-5 are dominated by mutation pressure and natural selection, while natural selection is the main evolutionary force that affects the codon usage pattern of PAstVs-2,3,4. The analyses of codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) showed the codon usage similarities between the PAstV and animals might contribute to the broad host range and the cross-species transmission of astrovirus. Our results provide insight into understanding the PAstV evolution and codon usage patterns.

Highlights

Porcine astroviruses (PAstVs), comprising five distinct lineages (PAstV1-PAstV5), are highly prevalent in both diarrheic and clinically healthy pigs [1,2,3]
Of the eight CpU dinucleotides-containing codons, eight CpU dinucleotides-containing codons, five codons (GCU, CUU, CCU, UCU, and ACU) were five codons (GCU, CUU, CCU, UCU, and ACU) were preferentially used in PAstV-2. These results preferentially used in PAstV-2. These results indicated that dinucleotide abundance influences the indicated that dinucleotide abundance influences the codon usage bias of the four subtypes of PAstVs
These results indicate that mutation pressure and natural selection led to the codon usage bias of the

Summary

Introduction

Porcine astroviruses (PAstVs), comprising five distinct lineages (PAstV1-PAstV5), are highly prevalent in both diarrheic and clinically healthy pigs [1,2,3]. Co-infection of individual pigs with several lineages of PAstVs has been observed [9]. Both PAstV-2 and PAstV-5 have been identified in the brains of newborn piglets with congenital tremors [10]. PAstV-2 and PAstV4 were simultaneously detected in the blood samples of apparently healthy domestic pigs, while the coexistence of PAstV-2, PAstV-4, and PAstV-5 has been observed in porcine fecal samples collected from the same farms [9,11]

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