Comprehensive analysis of codon usage patterns of porcine deltacoronavirus and its host adaptability

Abstract

The porcine deltacoronavirus (PDCoV) is a newly discovered pig enteric coronavirus that can infect cells from various species. In Haiti, PDCoV infections in children with acute undifferentiated febrile fever were recently reported. Considering the great potential of inter‐species transmission of PDCoV, we performed a comprehensive analysis of codon usage patterns and host adaptation profiles of 54 representative PDCoV strains with the spike (S) gene. Phylogenetic analysis of the PDCoV S gene indicates that the PDCoV strains can be divided into five genogroups. We found a certain codon usage bias existed in the S gene, in which the synonymous codons are often ended with U or A. Heat map analysis revealed that all the PDCoV strains shared a similar codon usage trend. The PDCoV S gene with a dN/dS ratio lower than 1 reveals a negative selection on the PDCoV S gene. Neutrality analysis showed that natural selection is the dominant force in shaping the codon usage bias of the PDCoV S gene. Unexpectedly, host adaptation analysis reveals a higher adaptation level of PDCoV to Homo sapiens and Gallus gallus than to Sus scrofa. Compared to the USA lineage, the PDCoV strains in the Early China lineage and Thailand lineage were less adapted to their hosts, which indicates that the evolutionary process plays an important role in the adaptation ability of PDCoV. These findings of this study add to our understanding of PDCoV's evolution, adaptability, and inter‐species transmission.

Comprehensive codon usage analysis of the African Swine Fever Virus

“…The ENC, an absolute measure of CUB, was 52.80, indicating that ASFV has a low codon usage bias (>45) (Hemert et al, 2016). This result aligns with those for PDCoV (ENC = 52.69) (Peng et al, 2022), SARS-CoV-2 (ENC = 45.38) (Hou, 2020), PEDV (ENC = 47.91) (Chen et al, 2014), MERS-CoV (ENC = 49.82) (Chen et al, 2017), and other viruses.…”

“…Numerous DNA and RNA viruses exhibit CUB, with some, such as the Hepatitis A Virus, showing significant bias (ENC = 39.78) (Andrea et al, 2011;Bera et al, 2017). In contrast, other viruses, such as PDCoV (ENC = 52.69) (Peng et al, 2022), SARS-CoV-2 (ENC = 45.38) (Hou, 2020), PEDV (ENC = 48.04) (Yu et al, 2021a), CHIKV (ENC = 55.56) (Butt et al, 2014), ZIKV (ENC = 53.32) (Wang et al, 2016), Classical Swine Fever Virus (ENC = 51.7) (Tao et al, 2009), H7N9 Influenza A Virus (ENC = 51) (Sun et al, 2020), and Bluetongue (ENC = 57.9) (Yao et al, 2020), display weak codon usage bias.…”

Reverse Genetics Systems for Emerging and Re-Emerging Swine Coronaviruses and Applications

“…CoV infection is initiated by the interaction between S protein and specific cellular receptors; this biological process largely determines a CoV s host spectrum and tissue tropism. Phylogenetic analysis reveals that PDCoV is closely related to sparrow CoV HKU17, which supports the hypothesis that PDCoV evolved from avian deltacoronavirus [16,78]. Niu et al constructed chimeric PDCoVs that harbor the S protein of HKU17 (icPDCoV-SHKU17) or the RBD of ISU73347 (icPDCoV-RBDISU) [79].…”

Attenuation of a Highly Pathogenic Porcine Deltacoronavirus Strain CZ2020 by a Serial Passage In Vitro

“…Te molecular mechanism for PDCoV attenuation is not fully elucidated yet, and this is the frst study to attenuate a virulent PDCoV strain via a serial passage in vitro. Based on the heterogenicity analysis of the spike gene, the PDCoV strains from Tailand, Laos, and Vietnam formed a separate lineage [21]. Currently, the pathogenicity of various PDCoV strains was diferent, and it seems that the Tailand-lineage PDCoV strains showed higher pathogenicity than other lineage strains [22].…”