Differentiation of strains of tick-borne encephalitis virus by means of RNA-DNA hybridization

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Abstract
Cloned cDNA and synthetic deoxyoligonucleotides, complementary to various parts of the genomic RNA of tick-borne encephalitis virus (TBEV), strain Sofjin, were used to distinguish between strains of TBEV and other flaviviruses. The cDNA probe hybridized with strains of TBEV and related flaviviruses of the TBE complex except for Powassan virus, and it did not react with flaviviruses of the Japanese encephalitis and dengue subgroups. Viruses of the TBE complex and some strains of TBEV were differentiated from TBEV strain Sofjin by the thermal stability of RNA-DNA hybrids. Negishi and louping-ill viruses were the most closely related to TBEV strain Sofjin, among viruses of the TBE complex. Eight strains of TBEV isolated in different geographical areas from different sources were tested by dot-hybridization with 11 deoxyoligonucleotide probes. The probes revealed genetic variations among strains of TBEV. The pattern of hybridization correlated with the source of virus strains: TBEV strains isolated from TBE patients reacted with more probes than strains isolated from ticks. Within a group of epidemic strains of TBEV there was a correlation between the geographical area of isolation and similarity to TBEV strain Sofjin.