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Hepatitis C virus F protein sequence reveals a lack of functional constraints and a variable pattern of amino acid substitution

¹ Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
² Cátedra de Hemoterapia, Facultad de Medicina, Av. Italia s/n, Montevideo, Uruguay
³ Instituto de Investigaciones Clínicas, Facultad de Medicina ‘San Fernando’, Universidad Nacional Mayor de San Marcos, Parque de la Medicina, Avenida Grau Cuadra 13 s/n, Lima 01, Peru
⁴ Servicio de Inmunología, Hospital Nacional Edgardo Rebagliati Martins HNERN, Domingo Cueto s/n, Jesús María, Lima 11, Peru

Correspondence
Juan Cristina
cristina{at}cin1.cin.edu.uy

Hepatitis C virus (HCV) is an important human pathogen that affects 170 million people worldwide. The HCV genome is an RNA molecule that is approximately 9·6 kb in length and encodes a polyprotein that is cleaved proteolytically to generate at least 10 mature viral proteins. Recently, a new HCV protein named F has been described, which is synthesized as a result of a ribosomal frameshift. Little is known about the biological properties of this protein, but the possibility that the F protein may participate in HCV morphology or replication has been raised. In this work, the presence of functional constraints in the F protein was investigated. It was found that the rate of amino acid substitutions along the F protein was significantly higher than the rate of synonymous substitutions, and comparisons involving genes that represented independent phylogenetic lineages yielded very different divergence/conservation patterns. The distribution of stop codons in the F protein across all HCV genotypes was also investigated; genotypes 2 and 3 were found to have more stop codons than genotype 1. The results of this work suggest strongly that the pattern of divergence in the F protein is not affected by functional constraints.

The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this work are AJ582128–AJ582131 and AJ781117–AJ781124.

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