Full-length genome analysis of Calovo strains of Batai orthobunyavirus (Bunyamwera serogroup): implications to taxonomy.

Batai virus (BATV) is a poorly studied arthropod-borne virus belonging to the genus Orthobunyavirus (Bunyamwera serogroup) within the family Bunyaviridae. It has been associated with human influenza-like febrile illness in several Asian, African, and European countries. Calovo virus (CVOV), isolated in 1960 in Slovakia, has been classified as BATV based on high antigenic similarity, and since then both CVOV and BATV were used as synonyms. In order to fully clarify the phylogenetic relationships between CVOV, BATV, and other members of the Bunyamwera serogroup, we performed whole genome sequencing of four CVOV strains isolated in Europe and phylogenetic analyses of all related viruses. The nucleocapsid protein, encoded by the S genomic segment, contains 233 amino acids, 60 of which, putatively critical for protein function, are conserved. Within the CVOV polyprotein encoded by the M genomic segment, putative cleavage sites, N-glycosylation sites, and seven transmembrane regions were identified. The RNA-dependent RNA polymerase, encoded by the L genome segment, exhibits conservation of the three regions known to be conserved among bunyavirus and arenavirus L proteins. Phylogenetic analyses of all three genomic segments of selected orthobunyaviruses clearly revealed that European and Asian/African strains of BATV are phylogenetically different and form two distinct lineages, indicating the existence of two different genotypes of BATV, tentatively named European genotype (with CVOV as a type strain) and Afro-Asian genotype (with BATV as a type strain) of BATV.

The variability of the large genomic segment of Tahyna orthobunyavirus and an all-atom exploration of its anti-viral drug resistance.

Tahyna virus (TAHV), a member of the Bunyaviridae family (California complex), is an important but neglected human mosquito-borne pathogen. The virus genome is composed of three segments, i.e., small (S), medium (M), and large (L). Previous studies on genetic variability of viruses within the California complex were focused on S and M segments, but the L segment remains relatively unstudied. To assess the genetic variation and the relation to virus phenotype we analyzed the L segment sequences of biologically diverse TAHV strains isolated in the Czech Republic and Slovakia. Phylogenetic analysis covering all available sequences of the L segment of TAHV clearly revealed two distinguished lineages, tentatively named as "European" and "Asian". The L segment strains within the European lineage are highly conserved (identity 99.3%), whilst Asian strains are more genetically diverse (identity 97%). Based on sequence comparison with other bunyaviruses, several non-synonymous nucleotide substitutions unique for TAHV in the L segment were identified. We also identified specific residue substitutions in the endonuclease domain of TAHV compared with the La Crosse virus. Since the endonuclease domain of the La Crosse virus has been resolved, we employed an all energy landscape algorithm to analyze the ligand migration of a viral polymerase inhibitor. This allowed us to demonstrate, at the atomic level, that this viral polymerase inhibitor randomly explored the specific residue substitutions in the endonuclease domain of the TAHV L segment.

Detection of mosquito-only flaviviruses in Europe.

The genus Flavivirus, family Flaviviridae, includes a number of important arthropod-transmitted human pathogens such as dengue viruses, West Nile virus, Japanese encephalitis virus and yellow fever virus. In addition, the genus includes flaviviruses without a known vertebrate reservoir, which have been detected only in insects, particularly in mosquitoes, such as cell fusing agent virus, Kamiti River virus, Culex flavivirus, Aedes flavivirus, Quang Binh virus, Nakiwogo virus and Calbertado virus. Reports of the detection of these viruses with no recognized pathogenic role in humans are increasing in mosquitoes collected around the world, particularly in those sampled in entomological surveys targeting pathogenic flaviviruses. The presence of six potential flaviviruses, detected from independent European arbovirus surveys undertaken in the Czech Republic, Italy, Portugal, Spain and the UK between 2007 and 2010, is reported in this work. Whilst the Aedes flaviviruses, detected in Italy from Aedes albopictus mosquitoes, had already been isolated in Japan, the remaining five viruses have not been reported previously: one was detected in Italy, Portugal and Spain from Aedes mosquitoes (particularly from Aedes caspius), one in Portugal and Spain from Culex theileri mosquitoes, one in the Czech Republic and Italy from Aedes vexans, one in the Czech Republic from Aedes vexans and the last in the UK from Aedes cinereus. Phylogenetic analysis confirmed the close relationship of these putative viruses to other insect-only flaviviruses.

Nucleotide variability of Tahyna virus (Bunyaviridae, Orthobunyavirus) small (S) and medium (M) genomic segments in field strains differing in biological properties.

Tahyna virus (TAHV), a mosquito-borne bunyavirus (California group), is frequently associated with inapparent or influenza-like (Valtice fever) infections in humans, rarely leading to atypical pneumonia or meningitis. Field TAHV strains exhibit a high variability in their biological properties with respect to virulence for laboratory mouse, temperature-sensitivity or character of plaques in cell culture. In consideration of the variations in the antigenic properties TAHV and its potential genetic variability, we analyzed complete nucleotide sequences of the small (S) and medium (M) genomic segments of field TAHV strains with different combinations of phenotypic markers. S segment was highly conservative in all analyzed TAHV strains. Within the M segment, the highest variability was observed in the G(C) gene encoding viral envelope protein and to a less extent also in the NSm gene. However, 5' and 3' non-coding regions of M segment, as well as in G(N) gene exhibited highly conservative pattern, indicating its functional importance, but minor or no role in the determination of biological properties of TAHV field strains.

Integration of a tick-borne encephalitis virus and Borrelia burgdorferi sensu lato into mountain ecosystems, following a shift in the altitudinal limit of distribution of their vector, Ixodes ricinus (Krkonose mountains, Czech Republic).

The altitudinal shift in the limit of Ixodes ricinus occurrence above the previously established altitude of 750 m above sea level has been monitored over the long-term (2002-2008) in the Krkonose Mts. (Giant Mts.), the highest in the Czech Republic, along two vertical transects in their eastern and central parts (600-1020 and 600-1270 m). Ticks were collected by flagging three times annually, and examined individually by PCR or RT-PCR for the presence of Borrelia burgdorferi sensu lato or tick-borne encephalitis virus (TBEV). A total of 5999 I. ricinus ticks were tested. TBEV RNA was detected in 26 ticks at up to 1140 m. Demonstration of TBEV in two larvae of I. ricinus indicates transovarial transmission. Similar infection rates in larvae and nymphs show vertical transmission in TBEV circulation to be very important under these mountain conditions. B. burgdorferi sensu stricto was found at up to 1040-1065 m, Borrelia garinii and Borrelia afzelii up to 1080-1140 m, and Borrelia valaisiana up to 1270 m. The total infection rates of nymphs and larvae were 7.3% and 2%, respectively. B. garinii was the most prevalent (37%), followed by B. afzelii (29%), B. burgdorferi s.s. (11%), and B. valaisiana (9%). Double to quadruple coinfections were detected in 32% of the infected ticks, most frequently B. garinii/B. afzelii. Predominance of B. garinii and B. valaisiana over B. afzelii suggests that small passerine birds moving on the ground are responsible for permanent local populations of I. ricinus in mountain localities with low numbers of small terrestrial mammals. The detection of B. burgdorferi sensu lato and TBEV in host-seeking larvae indicates an autochthonic infection. Upon analysis of the local climate we consider climate warming to be responsible for the spreading of ticks and tick-transmitted pathogens to higher altitudes.