Genomic S segment of Crimean-Congo hemorrhagic fever virus circulating in Russia and Bulgaria

S-segment nucleotide sequences for two Crimean-Congo hemorrhagic fever (CCHF) virus strains isolated in the Rostov Region of Russia and in Bulgaria have been determined. Analysis of complete S-segment nucleotide sequences in the viral strains from different regions of the world has established that the CCHF virus strains isolated from ticks and human beings in different southern Russian regions in 1967 and 2000 are very closely genetically and they form an individual subgroup in the basic European genetic group. By the S-segment structure, the CCHF virus strain isolated in Bulgaria in 1978 belongs to the same genetic group as a representative of its second subgroup. Analysis of the S-segment 3'-noncoding region suggests that the CCHF virus circulating in Europe, Central Asia, and China may have originated from one global focus of infection, including several CCHF virus genovariants. During evolution, fragmental exchange apparently occurred in the S-segment 3'-noncoding region as a result of homological recombination.     

Genetic analysis of the M RNA segment of Crimean-Congo hemorrhagic fever virus strains involved in the recent outbreaks in Russia

Summary. Crimean-Congo hemorrhagic fever (CCHF) is a severe zoonosis with a high fatality rate. In Russia, local CCHF outbreaks have occurred in the Stavropol Territory, and the Volgograd and Astrakhan Regions during 2000 and 2001. Seven strains of CCHF virus (CCHFV) were isolated from infected patients and collected ticks. Two fragments of the CCHF virus M genome segment were PCR amplified and their nucleotide sequences were determined. All these virus strains appear to be closely related (up to 5.8% nucleotide sequence differences) and form a distinct clade on the CCHFV phylogenetic tree. Within this clade, CCHFV strains from Stavropol and Astrakhan cluster together, whereas those from Volgograd form a separate subgroup.     

Genetic characterization of the M RNA segment of a Balkan Crimean-Congo hemorrhagic fever virus strain

Crimean-Congo hemorrhagic fever (CCHF) virus causes one of the most severe diseases in humans, with a mortality rate of up to 30%. It is transmitted to humans by the bite of hard ticks or by contact with blood or tissues from human patients or infected livestock. Balkan Peninsula is an endemic region of the disease, and sporadic cases or even outbreaks are observed every year. The M RNA segment encodes for the glycoprotein precursor of two surface glycoproteins Gn and Gc. Up to now complete M RNA CCHF virus sequences have been published from strains isolated in Nigeria, China, Pakistan, Tajikistan, and Russia. In the present study, the genetic characterization of the complete nucleotide sequence of the M RNA segment of a Balkan CCHF virus strain, Kosovo/9553/2001, isolated in summer of 2001 from a human fatal case in Kosovo is reported. This is the first published complete M nucleotide sequence of a CCHF virus strain isolated in Balkans. It was found that the Balkan strain is similar to the Russian strain, both strains differing from all other completely sequenced CCHF virus strains by approximately 22% at the nucleotide level forming an independent clade in the phylogenetic tree.     

Genetic variants of the Crimean-Congo hemorrhagic fever virus circulating in endemic areas of Southern Tajikistan in 2009

Five-hundred-and-six Hyalomma anatolicum ticks were collected and studied in two Crimean-Congo hemorrhagic fever (CCHF) endemic regions of Tajikistan. Antigen and RNA of the CCHF virus were detected in 3.4% of tick pools from the Rudaki district using ELISA and RT-PCR tests. As for the Tursunzade district, viral antigen was identified in 9.0% of the samples and viral RNA was identified in 8.1% of the samples. Multiple alignment of the obtained nucleotide sequences of a region of the S-segment of the genome of the CCHF virus 287 nucleotides in length (996–1282) and the multiple alignment of the deduced amino-acid sequences of the samples carried out to compare with CCHF virus strains from the GenBank database, as well as their phylogenetic analysis, enabled us to conclude that the Asia 1 and Asia 2 genotypes of the CCHF virus are circulating in Tajikistan. It is important to note that the genotype Asia 1 virus was detected in Tajikistan for the first time.     

CCHF virus variants in Pakistan and Afghanistan: Emerging diversity and epidemiology

BackgroundCrimean Congo hemorrhagic fever (CCHF) has been reported from more than 30 countries in Africa, Asia, Eastern Europe and Middle East. The disease is considered endemic in Pakistan and neighboring countries like Iran and Afghanistan.ObjectivesThis study aimed to explore the genetic diversity of CCHF virus (CCHFV) detected in Pakistan and Afghanistan based on analysis of partial S-segment sequences.Study designDuring 2011, one hundred samples satisfying the CCHF case definition were tested by (ELISA) and RT-PCR for detection of IgM antibodies and viral RNA, respectively. Phylogenetic analysis was carried out on partial S-segment nucleotide sequences using MEGA 5.0.ResultsOut of one hundred collected during 2011, 49 (49%) were positive for CCHF either by ELISA/RT-PCR or both. The mean age of the CCHFV positive cases was 30.32 years (range 18–56 years) and overall mortality rate was 20.4%. All CCHF virus isolates from this study clustered with strains previously reported from Pakistan, Iran and Afghanistan within the Asia-1 genogroup. Four distinct sub-clades were found circulating within Asia-1 genogroup. Six CCHFV strains found in Pakistan and Afghanistan grouped into a new sub-clade-D.ConclusionsData from this study shows that endemic foci of CCHFV span the international border between Pakistan and Afghanistan with genetically diverse variants circulating in this region. Our findings emphasize to establish a laboratory based surveillance program and devise health policy measures to control CCHF infection especially in Baluchistan.     

Genetic analysis of Crimean-congo hemorrhagic fever virus in Iran

Crimean-Congo hemorrhagic fever (CCHF) is a potentially fatal disease caused by a tick-borne virus in the family Bunyavridae. The disease occurs in parts of Africa, Asia, Middle East, and Eastern Europe. During recent years, an increasing number of human CCHF cases have been diagnosed in Iran, but very little information is available on the prevalence and genetic diversity of CCHFV in Iran. In the present study, CCHF virus (CCHFV) isolates from nine Iranian patients infected during 2002 were examined genetically. Nucleotide sequencing of the S- and M-segments, encoding the nucleocapsid protein (NP) and the glycoproteins, respectively, revealed that the different isolates were related closely to each other with nucleotide sequence identities exceeding 98% for both S- and M-segments. Phylogenetic analysis of partial S-segment nucleotide sequences showed that the viruses clustered along with strains from Pakistan and Madagascar in one distinct lineage. Phylogenetic analysis also demonstrated that the Iranian isolates examined in this study and the previously published CCHFV strain ArTeh193-3 clustered into different genetic groups, indicating that at least two genetic lineages of CCHFV could be co-circulating in Iran.     

Genetic Characterization of the M RNA Segment of Crimean-Congo Hemorrhagic Fever Virus Strains Isolated in Russia and Tajikistan

The data on the structure of the M genome segment of CCHF virus strains from Russia and Central Asia (Tajikistan) are presented. Data obtained have been compared with other available published sequences of the middle segment of strains from China, Nigeria, and Pakistan. It has been found that all the known strains can be divided into four genetic groups, based on the nucleotide sequence of the M genome segment and an amino acid sequence of the glycoprotein precursor it encodes, whereas VLG/TI29414 and STV/HU29223 strains from Russia form a separate group. The CCHF virus strain from Tajikistan, TADJ/HU8966, was genetically related to strains 7803 and 75024 from China, and together with these and the Nigerian IbAr 10200 strain, it forms another group.     

Characteristic of the new Khatanga virus genotype

Complete nucleotide sequence of the S-segment and partial sequences of M- and L-segments (981 and 1005 nucleotide respectively) have been determined in 20 strains of California encephalitis serocomplex, isolated in Yakitiya, Sakhalin, and Kamchatka. The phylogenetic analysis ofgenomic S-, M-, and L-segments showed that all 20 strains are related to Khatanga virus (La Cross subtype of California encephalitis serotype). Eight strains belong to group 2 of Khatanga virus while the remaining 12 make up a new (third) genetic group of this virus having original S- and M-segments and L-segment similar to that of the second group.     

Genetic diversity of the M RNA segment among Crimean-Congo hemorrhagic fever virus isolates in China

The complete nucleotide sequences of the medium (M) segment of seven Chinese isolates of Crimean-Congo hemorrhagic fever (CCHF) virus were determined. The M-segment RNA of CCHF virus comprises 5356-5377 nucleotides depending on the isolate and encodes a protein comprising 1689-1697 amino acids in a viral complementary sense. Phylogenetic analysis of the M segment showed that the Chinese CCHF virus isolates were clustered into three groups, one of which was more closely related to a Nigerian isolate. Pairwise comparison of a precursor protein showed that amino-terminal regions comprising 250 amino acids were extraordinary heterogeneous, with a 22.4% identity in amino acids being observed between the most distantly related isolates. Since all the viruses were isolated from 1966 to 1988 within a restricted area in the Xinjiang Autonomous Region in western China, the results indicate that a multisource virus population is endemic in this region.     

Complete Nucleotide Sequence of a Mumps Virus Genotype I Strain Isolated in Korea

The complete nucleotide sequence of mumps virus isolated in Korea, Dg1062/Korea/98 (Dg1062), was determined. As other mumps viruses, its genome was to be 15,384 nucleotides (nts) in length and encoded seven proteins. The both 5' and 3' ends were confirmed to be 55 and 24 nts by RACE method, respectively. The full-length nucleotide sequence of Dg1062 isolate differed from other strains by 2.9-6.8% in the nucleotide sequence level, resulting in 206 nucleotide and 54 amino acid substitutions which were observed in only Dg1062 isolate relative to the consensus sequences of other strains. Despite the variations of amino acids over the full genome including HN gene, it might be considered that this isolate have no significant variations in the antigenic sites. This result is the first report of full-length genome of genotype I strain and provides an overview on the diversity of genetic characteristics of circulating mumps virus.     

Characterization and analysis of the full-length genome of a strain of the European QX-like genotype of infectious bronchitis virus

In recent years, strains of infectious bronchitis virus belonging to the QX-like genotype have been causing huge economic losses in commercial chicken flocks in different countries in Europe. In order to expand the knowledge of the molecular features of these viruses, we have sequenced and characterized the complete genome of European QX-like IBV strain CK/SWE/0658946/10, which was isolated in 2010 in Sweden. The genome is 27664 nucleotides in length, comprising six genes and 5' and 3' untranslated regions. The ORF1a, spike and nucleocapsid genes were under strong positive selective pressure that resulted in genetic diversity in relation to classical IBV isolates. The full-length genome of the CK/SWE/0658946/10 strain has the highest nucleotide sequence identity (93.18%) to ITA/90254/2005 and the lowest nucleotide identity (89.10%) to strain CQ04-1. Phylogenetic analysis of partial S1 gene sequences of IBV strains showed that the European QX-like genotype comprises strains that have been predominantly circulating in this continent for the past decade.     

Nucleotide sequence of the Lassa virus (Josiah strain) S genome RNA and amino acid sequence comparison of the N and GPC proteins to other arenaviruses

The complete nucleotide sequence of the S genome RNA of the Josiah strain of Lassa virus was determined from cloned cDNA. The S RNA is 3402 nucleotides long with a calculated molecular weight of 1.09 x 10(6) Da. The nucleotide base composition is 26.84% adenine, 21.40% guanine, 22.75% cytosine, and 29.01% uridine. The 5' and 3' terminal nucleotide sequences are conserved and complimentary for 19 nucleotides, the nucleoprotein and glycoprotein genes are arranged in ambisense coding strategy, and the intergenic region contains an inverted complimentary sequence, as do all other arenavirus S RNAs characterized to date. Amino acid sequence comparisons between the nucleoproteins and glycoproteins of the Josiah and Nigerian (N sequences only) strains of Lassa virus, the WE and ARM strains of lymphocytic choriomeningitis virus (LCMV), Tacaribe, and Pichinde viruses are presented. These findings reveal that the G2 envelope glycoprotein is more conserved among different arenaviruses than the internal nucleoprotein.     

Genetic analysis of the M RNA segment of Crimean-Congo hemorrhagic fever virus strains in Turkey

Summary Crimean-Congo hemorrhagic fever (CCHF) virus is member of the genus Nairovirus of the family Bunyaviridae. All members of the family Bunyaviridae are enveloped viruses containing tripartite, negative polarity, single-stranded RNA. CCHF is characterized by high case mortality, occurring in Asia, Africa, the Middle East and Europe. During recent years, outbreaks have been reported in Turkey. However, little information is available on the genetic diversity of CCHF virus in Turkey. In this study, a total of 1227 adult ticks were collected from domestic ruminants (796 specimens from cattle, 399 specimens from goats and 32 specimens from sheep). The presence of the M segment of CCHF virus was determined in 4 of 40 (10%) Hyalomma marginatum marginatum pools, in 2 of 38 (7.89%) Rhipicephalus bursa pools, and in 1 of 7 (7%) Boophylus annulatus pools. Hyalomma anatolicum anatolicum pools gave negative RT-PCR result against CCHF virus. Serum samples from seven patients infected with CCHF were selected and subjected to RT-PCR to amplify partial M segment of CCHF virus. This report introduces the first data on partial nucleotide sequences of M RNA segments of CCHF virus strains circulating in Turkey, isolated from ticks. Correspondence: Aykut Ozdarendeli, Department of Virology, Firat University College of Veterinary Medicine, 23119 Elazig, Turkey     

Newly isolated mink parvovirus strain

A new mink enteritis virus (MEV) strain, called Cherepanovo, was isolated in the Novosibirsk region (West Siberia). The level of this strain's accumulation in cell culture is lower than that of commercial MEV strains Rodniki or Beregovoi. Identification of Cherepanovo strain by hemagglutination inhibition test, protein electrophoresis in denaturing polyacrylamide gel, and PCR showed its similarity to the previously described MEV strains. Comparative analysis of this strain's 5' and 3' nucleotide sequences of VP2 gene showed its more than 98% homology with other feline parvoviruses. Nucleotide residues 2920, 2971, and 4245 in the Cherepanovo strain VP2 gene differed from those of all previously described MEV strains. It is noteworthy that transition at the position 4245 led to Phe-->Cys replacement in amino acid residue.     

Crimean-Congo Hemorrhagic Fever in Albania, 2001

During the spring and summer of 2001, an outbreak of eight cases of Crimean-Congo hemorrhagic fever (CCHF) occurred in Albania. The epidemiological investigation, the clinical presentation of the cases, and the course of the disease are described. Seven of the cases were laboratory confirmed. A nosocomial infection and a cluster of cases within a family were observed. Genetic analysis of the CCHF virus strain that caused the outbreak showed that it was clustered together with other European CCHF virus strains except the Greek one (strain AP92). The Greek strain, which forms an independent clade, differed from the causative strain by 25.3% at the nucleotide level. Electronic Publication     

Molecular comparison of echovirus 11 strains circulating in Europe during an epidemic of multisystem hemorrhagic disease of infants indicates that evolution generally occurs by recombination

We compared echovirus 11 (E11) strains implicated in a severe epidemic in Hungary in 1989 with the prototype E11 strain Gregory and with other E11 strains, most of which were isolated over the same period in Europe (Finland, The Netherlands, Romania, Russia) from sporadic cases or from environmental water. Partial sequencing indicated that the Hungarian strains were closely related to each other and to most European strains. They were particularly closely related to one Romanian strain associated with a sporadic case of hemiparesis and several Finnish strains isolated from environmental water. Sequencing of the complete genomes of one Hungarian strain, the Romanian strain, and one Finnish strain revealed differences of only a few nucleotides in the 5' half of the genome, including the 5' nontranslated region (5'-NTR) and the capsid coding region. However, significant differences were observed in the nucleotide sequences of the 3' half of the genome (nonstructural viral protein region and 3'-NTR), indicating that these strains evolved recently and independently by genetic recombination with other unknown E11 or enterovirus strains.