Historical Isolates of Semliki Forest and Chikungunya Viruses and Their Virological Characteristic, Whole-Genome Sequences, and Phylogeny

The purpose of the study was to analyze alphavirus isolates collected in Uganda and Tanzania in the period preceding their global spread dating back to the middle of the last century. We supposed that analysis of their genomes could help to learn more about the specific features and the direction of molecular evolution of alphaviruses in the modern world. Archival samples of Chikungunya (CHIKV) and Semliki Forest (SFV) viruses were revived by cultivation in the Vero E6 cells. Isolates were identified by RT-PCR followed by sequencing. Whole genome sequences were obtained by NGS and used for phylogenetic analysis. The presence of two representatives of the Alphavirus genus, namely, CHIKV and SFV, was observed in the studied archival CHIKV sample. Only SFV was found in the archival sample from 1942. All isolates were capable of highly efficient replication in the C6/36, Vero E6, 293, and SPEV cell cultures showing the development of cytopathological effects and were able to produce pathomorphological changes typical of these alphaviruses in mice. Whole genome sequences have been obtained for these viruses and analyzed. Studied isolates clustered with the typical African CHIKV and SFV strains. These isolates may be attributed to the oldest known SFV and CHIKV strains dating back to 1942 and 1953 preserved in laboratory collections. The archival CHIKV isolate was genotyped as an ECSA variant, the modern representatives of which are associated with the global spread of CHIKV in recent decades. Semliki Forest and Chikungunya virus isolates were revived from archival laboratory samples presumably dating back to 1942 and 1953, and their virological characterization was carried out, followed by genotyping and phylogenetic analysis of their whole-genome sequences.