In 1999, a total of 447 TBE cases confirmed by enzyme immunoassay were reported in Novosibirsk Region (Figure 1). Nine (2.0%) patients died; 72.9% of cases occurred in the city of Novosibirsk or its suburbs. The deaths of eight of these patients were associated with a pronounced hemorrhagic syndrome; symptoms included massive gastrointestinal bleedings and multiple hemorrhages in mucosa and internal organs. Four of the patients who died resided in the Toguchin District; the remainder lived in districts located near Novosibirsk (Figure 1). A total of 371 and 358 cases of TBEV infection confirmed by enzyme immunoassay and reverse transcriptase-polymerase chain reaction (RT-PCR) were reported in 2000 and 2001, respectively. In 2001, the mortality rate increased to 3.6%. Surveillance for TBEV during the summers of 2000 and 2001 identified no new cases of TBE with the hemorrhagic syndrome. This lack might be ascribed to the decrease in TBE incidence during this period, the change in the circulation of TBEV strains, and an unusual weather pattern during May and June.

We found no published reports describing a hemorrhagic disease caused by TBEV, although hemorrhagic manifestation is typical for tick-borne flaviviruses, including Omsk hemorrhagic fever virus (OHFV), Alkhurma virus, and Kyasanur Forest disease virus (9). Cases of OHFV occur occasionally in the Novosibirsk Region. Most cases result from the direct contact of a human with a muskrat, which was introduced in Siberia in 1928 (10,11), and most occur in the Ust’ Tarka District (Figure 1), located on the western border of the Novosibirsk Region (12). We found that hemorrhagic TBE emerged in the Toguchin district, located on the eastern border of the Novosibirsk Region, approximately 500 km from the Ust’ Tarka District. We found no cases of TBE in the central districts of the Novosibirsk Region, where the lakes and marshes make an unfavorable environment for the spread of this virus. The discovery of hemorrhagic TBE in the eastern part of the Novosibirsk Region is probably not related to the OHFV found in the far western part of the region.

By reviewing all available medical records, we retrospectively analyzed the eight cases of fatal hemorrhagic TBE infection. Diagnoses were confirmed serologically by testing for specific antiviral immunoglobulin M antibodies. All cases occurred in June and July 1999 after patients were bitten by ticks; the latent period was from 5 to 26 days (average 12.8). The ages of the patients ranged from 44 to 69 years. Disease onset included typical TBE clinical symptoms such as fever, myalgia, and malaise, followed by pronounced viral encephalitis accompanied by loss of consciousness, pareses, and paralyses. Hemorrhagic symptoms developed as massive gastrointestinal bleeding and local hemorrhages on mucosa and skin. The first sign of the hemorrhagic syndrome was erythrocytes in urine on day 7 of the infection, which is not usual for TBE infection. Common central nervous system manifestations occurred 3 days later. Patients died 2−3 days after the massive hemorrhagic syndrome developed, despite intensive treatment. The average time of death was 16 days after illness onset. Autopsies showed the pronounced hemorrhagic syndrome and viral encephalitis. Our retrospective screening of medical records from 1999 did not produce any evidence of a milder hemorrhagic syndrome in the rest of the case-patients.

Since hemorrhagic TBE has not been described previously, our objective was to determine the genotype of the virus. However, only six brain tissue samples from the fatal cases were available at the time this study was initiated. Archival samples of formalin-fixed brain tissue from the fatal hemorrhagic cases were collected in March 2000 and stored at −70°C. These samples had been stored for 8 to 9 months in 10% formaldehyde solution at room temperature at the pathology laboratory of the First Municipal Clinical Infectious Hospital of Novosibirsk. Viral RNA was isolated from formalin-fixed brain tissue by using the modified protocol described by Masuda et al. (13) and Coombs et al. (14). The RT-PCR system (GeneAmp RNA PCR Kit, Perkin-Elmer, Branchburg, NJ) was developed for detection of TBEV. RT-PCR primers were designed by using conserved DNA regions encoding gene E of TBEV, strain 205: 5′-TGCACACAYYTGGAAAACAGGGA-3′ (TBE913F), 5′-TGGCCACTTTTCAGGTGGTACTTGGTTCC-3′ (TBE1738R). The sense primer 5′-CAGAGTGATCGAGGCTGGGGYAA-3′ (TBE1192F) and antisense primer 5′-AACACTCCAGTCTGGTCTCCRAGGTTGTA-3′ (1669R) were used for second round of PCR.

Nucleotide sequences of E gene fragment PCR products (1,192–1,661 bp) of TBEV strains were determined by using a Beckman sequencing kit and Beckman CEQ2000XL DNA Analysis System (Beckman Coulter, Inc., Fullerton, CA) according to manufacturer’s instructions. These samples were used to isolate RNA and generate cDNA fragments corresponding to positions 1,192−1,669 bp of protein E gene by using nested RT-PCR. The amplification products were sequenced. We submitted these sequences to GenBank (accession nos. AF540029–AF540034).

The homologic values between the nucleotide sequences of protein E fragment of hemorrhagic TBEV, Siberian, and Far Eastern TBEV subtypes are shown in Table 1. The nucleotide sequences of hemorrhagic TBEV strains show approximately the same degree of homology (82%) with protein E gene of different strains of Siberian subtype (strains Lesopark-11, Eltsovka-2, and Vasilchnenko isolated near Novosibirsk) and 94% homology with the Far Eastern subtype. The typical phylogenetic tree with support values is shown in Figure 2. Because hemorrhagic TBEV strains clustered with the Far Eastern subtype of TBEV, we associated them with the Far Eastern subtype.

The amino acid sequence of hemorrhagic TBE has higher homology with the Far Eastern subtype (98%) than with the Siberian subtype (96%). We identified 13 different amino acid mutations in six sequenced fragments of protein E (Table 2). These mutations were not previously described for TBEV; however, most of them (except 121C, 244L, and 249A) were found among other flaviviruses. Cysteine 121 is highly conserved among all flaviviruses since it is involved in maintaining the protein E 3D structure through a disulfide bridge with cysteine 92. Substituting cysteine 121 for glycine in the Koltsovo 31 TBEV variant might cause dramatic changes in protein E structure and function.

Long-term surveillance in Siberia indicates that persons with TBEV infection have relatively mild fever; death occurs in 1% of patients (2). The high incidence of TBE in Western Siberia is attributed to the active circulation of Siberian TBEV variants (3,6,7). By sequencing a fragment of protein E, we found these variants grouped to a separate subtype (Siberian). Overall, 75 protein E sequences of TBEV variants isolated in 1952 to 2002 in different regions of Russia were published. Of these virus isolates, 46 were collected directly in the suburbs of Novosibirsk (8). Our study showed that Siberian variants have approximately 78% to 81% homology in protein E genes with the Far Eastern TBEV subtype.

Our sequencing data showed that the genome of hemorrhagic TBEV variants differs from already known Siberian TBEV and OHFV strains. Variants of hemorrhagic TBEV show the highest degree of homology with the Far Eastern subtype, represented by prototype strains 205 and Sofiin. This finding supports our hypothesis that a relationship exists between the occurrence of unusual clinical disease and emergence of new TBEV variants in the Novosibirsk Region.