Molecular characterization and expression of glycoprotein gene of Hantavirus R22 strain isolated from Rattus norvegicus in China

Genetic characterisation of a Hantavirus isolated from a laboratory-acquired infection

Seoul (SEO) viruses belong to the Hantavirus genus (family Bunyaviridae), cause the moderate form of haemorrhagic fever with renal syndrome, and have been associated with laboratory-acquired infections in many countries. To investigate the pedigree of an isolate, designated IR461, which was obtained from a laboratory-acquired infection in a UK research institute, we determined the nucleotide sequences of the small (S) and medium (M) genome segments. In addition, we determined the sequences of the S segments of two Chinese isolates (R22 and L99) and an American isolate (Tchoupitoulas [TCH]). The S segments range within 1769-1785 nucleotides in length and showed identities of >88% in nucleotide sequence and 97% in amino acid sequence to those of published S segment sequences. The M RNA segment of IR461 is 3651 nucleotides long and shows >84% identity at the nucleotide level and >98% at the amino acid level to the M segments of other SEO viruses. These data confirm that SEO viruses show the least diversity within the Hantavirus genus. Phylogenetic analyses of the sequences showed geographic clustering of the Chinese SEO viruses, and that IR461 was more closely related to SEO viruses isolated in the New World than to those from the Far East.

Evolutionary diversification of protein-coding genes of hantaviruses

Phylogenetic analyses of the S:, M, and L: genes of the hantaviruses (Bunyaviridae: Hantavirus) revealed three well-differentiated clades corresponding to viruses parasitic on three subfamilies (Murinae, Arvicolinae, and Sigmodontinae) of the rodent family Muridae. In rooted trees of M: and L: genes, the viruses with hosts belonging to Murinae formed an outgroup to those with hosts in Arvicolinae and Sigmodontinae. This phylogeny corresponded with a phylogeny of the murid subfamilies based on mitochondrial cytochrome b sequences, supporting the hypothesis that hantaviruses have coevolved with their mammalian hosts at least since the common ancestor of these three subfamilies, which probably occurred about 50 MYA. The nucleocapsid protein (encoded by the S: gene) differentiated among the viruses parasitic on the three subfamilies in such a way that a high frequency of amino acid residue charge changes occurred in a hypervariable (HV) portion of the molecule, and nonsynonymous nucleotide differences causing amino acid charge changes in the HV region occurred significantly more frequently than expected under random substitution. Along with evidence that at least in some hantaviruses the HV region is a target for host antibodies and the known importance of charged residues in determining antibody epitopes, these results suggest that changes in the HV region may represent adaptation to host-specific characteristics of the immune response.

Nucleotide sequence and phylogenetic analysis of the medium (M) genomic RNA segments of three hantaviruses isolated in China

The medium (M) genome segment of hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins. G1 and G2, as a precursor protein in the complementary sense RNA. We determined the nucleotide sequences of the M genome segments of three Chinese hantavirus isolates, a Hantaan-type (HTN) virus designated A9 and two Seoul-type (SEO) viruses designated L99 and HB55, and compared them to those of other HTN or SEO viruses isolated in Eastern Asia. The M segment of A9 is 3616 nucleotides in length and shows 99.5% identity at the nucleotide level and 99.1% identity at the amino acid level to that of the Chinese HTN isolate HV114. The M segments of L99 and HB55 are 3652 nucleotides in length, one nucleotide longer than the M segments of other sequenced SEO isolates such as SEO 80-39, SR-11, and Biken-1. The Chinese SEO isolates showed 95% nucleotide sequence identity and 99% amino acid sequence identity to SEO 80-39. We also sequenced a 736 nucleotides region of the M genome segment of another Chinese SEO isolate, R22, which revealed errors in the published data. Phylogenetic analysis of the available sequences indicated that both the Chinese HTN- and SEO-type viruses form lineages distinct from those of the isolates from other parts of Eastern Asia.

Comparison of nucleotide sequences of M genome segments among Seoul virus strains isolated from eastern Asia

The nucleotide sequences of the M genome segments of three Seoul virus strains (KI strains) which were isolated from urban rats inhabiting the same enzootic focus between 1983 and 1988 were compared. The viral cDNAs were amplified by PCR and were directly sequenced. The nucleotide sequences of KI strains were extremely homologous regardless of isolation year (less than 10 substitutions in 3651 nucleotides, less than 4 substitutions in 1133 amino acids). In addition, the nucleotide sequence of the KI strain isolated in 1983 (KI-83-262) was also quite similar to that of other Seoul viruses, which were isolated from laboratory rats in Japan (strain SR-11, 98.1% and B-1 strain, 96.5%), from an urban rat in Korea (Seoul 80-39, 96.5%) and from an urban rat in China (R22 strain, 93.4%). All possible N-glycosylation sites in the deduced amino acid sequences were conserved among all Seoul viruses examined. The nucleotide and amino acid sequences of Seoul virus strains were highly conserved although they were isolated from various districts of eastern Asia. These results indicate the genetic stability of Seoul virus strains maintained under a natural environment and the homology of Seoul viruses isolated from various districts of eastern Asia. The relationship among Seoul virus strains isolated from eastern Asia was compared by phylogenetic analysis.