Identification and characterization of codon usage pattern and influencing factors in HFRS-causing hantaviruses

Frontiers in Immunology

Immunology

Abu Bakar¹  Fatima Noor²  Muhammad Shareef Masoud²  Usman Ali Ashfaq²  Muhammad Qasim²  Abdulrahman Alshammari³  Metab Alharbi³  Muhammad Shahid Riaz⁴ 

[1] Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan;Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan;Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia;School of Dentistry, University of Maryland, Baltimore, MD, United States;

关键词: hemorrhagic fever with renal syndrome;    hantavirus;    RSCU;    ENC;    mutation;    selection;   

DOI  :  10.3389/fimmu.2023.1131647

 received in 2022-12-25, accepted in 2023-06-22,  发布年份 2023

来源: Frontiers

【 摘 要 】

Hemorrhagic fever with renal syndrome (HFRS) is an acute viral zoonosis carried and transmitted by infected rodents through urine, droppings, or saliva. The etiology of HFRS is complex due to the involvement of viral factors and host immune and genetic factors which hinder the development of potential therapeutic solutions for HFRS. Hantaan virus (HTNV), Dobrava-Belgrade virus (DOBV), Seoul virus (SEOV), and Puumala virus (PUUV) are predominantly found in hantaviral species that cause HFRS in patients. Despite ongoing prevention and control efforts, HFRS remains a serious economic burden worldwide. Furthermore, recent studies reported that the hantavirus nucleocapsid protein is a multi-functional protein and plays a major role in the replication cycle of the hantavirus. However, the precise mechanism of the nucleoproteins in viral pathogenesis is not completely understood. In the framework of the current study, various in silico approaches were employed to identify the factors influencing the codon usage pattern of hantaviral nucleoproteins. Based on the relative synonymous codon usage (RSCU) values, a comparative analysis was performed between HFRS-causing hantavirus and their hosts, suggesting that HTNV, DOBV, SEOV, and PUUV, were inclined to evolve their codon usage patterns that were comparable to those of their hosts. The results indicated that most of the overrepresented codons had AU-endings, which revealed that mutational pressure is the major force shaping codon usage patterns. However, the influence of natural selection and geographical factors cannot be ignored on viral codon usage bias. Further analysis also demonstrated that HFRS causing hantaviruses adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts. To our knowledge, no study to date reported the factors influencing the codon usage pattern within hantaviral nucleoproteins. Thus, the proposed computational scheme can help in understanding the underlying mechanism of codon usage patterns in HFRS-causing hantaviruses which lend a helping hand in designing effective anti-HFRS treatments in future. This study, although comprehensive, relies on in silico methods and thus necessitates experimental validation for more solid outcomes. Beyond the identified factors influencing viral behavior, there could be other yet undiscovered influences. These potential factors should be targets for further research to improve HFRS therapeutic strategies.

【 授权许可】

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Copyright © 2023 Noor, Ashfaq, Bakar, Qasim, Masoud, Alshammari, Alharbi and Riaz