Nucleotide sequence analysis of the S genomic segment of Prospect Hill virus: comparison with the prototype Hantavirus

Abstract

The genomic S RNA segment of Prospect Hill virus (PHV), a member of the Hantavirus genus, was molecularly cloned and the nucleotide sequence of the cDNA determined. The PHV S RNA segment is 1675 nucleotides long. A long open reading frame was identified in the viral complementary-sense RNA that could encode a 433 amino acid (49K) nucleocapsid (N) protein. Comparison with the sequence of the related Hantavirus (Hantaan 76-118) S RNA segment indicated that there was 57% nucleotide sequence homology between the two S RNA segments. A higher degree of conservation in amino acid sequence homology (62%) was observed in the N proteins of these viruses. At the N-terminus 147 of 225 amino acids are homologous, while approximately 82% of the 124 amino acids at the C-terminus are homologous between the two N proteins. The longest stretch of homologous amino acid sequence is found in this region, and is 17 amino acids in length. Also, many of the differences in amino acid sequence between the two N proteins resulted from conservative substitutions. Hydropathy plots of the two N proteins also reveal many similarities including a conserved potential antigenic site. Unlike Hantaan virus, a second smaller overlapping open reading frame was observed in the viral complementary-sense RNA of PHV and could potentially encode a 90 amino acid (10.5K) protein. Our data indicate that the N proteins of PHV and Hantaan virus are closely related despite divergence in the nucleotide sequence of their S RNA segments.