Molecular characterisation of two mumps virus genotypes circulating during an epidemic in Lithuania from 1998 to 2000

Summary.  An epidemic of mumps in Lithuania started in December 1998 and continued until May 2000. The total registered number of cases was about 11.000 of a total of 3,7 million inhabitants in Lithuania (29,7 cases/10000). Virus- containing samples were collected from 80 patients treated at the hospital of Kaunas from October 1999 until the end of the epidemic. Out of the 80 patients with parotitis, meningitis was observed in 11 patients and orchitis in 22 of 69 male patients. Twenty-seven virus strains were genotyped by nucleotide sequencing of the small hydrophobic (SH) protein gene, and the 57 amino acid sequences of the gene were deduced. Twenty-five virus strains belonged to the C genotype and two were of the D genotype. By phylogenetic analysis the virus strains causing meningitis grouped in a separate cluster, designated C1, within the C genotype. Another group of ten of the 25 genotype C strains exhibited an amino acid triplet at amino acid positions 28 to 30 of the protein, consisting of valine, alanine and serine, instead of the previously recognised valine, valine and serine combination of genotype C. The amino acid alanine at position 29 was found in combination with the amino acid serine at position 48. This variant was designated C2 and it was associated with parotitis. The amino acid alanine at position 29 and serine in position 48 of the C2 genotype may constitute a marker of low neurovirulence compared to other genotype C strains. Received July 9, 2001 Accepted October 23, 2001     

Genetic and antigenic characterization of measles viruses that circulated in Korea during the 2000-2001 epidemic

Despite the marked reduction in the incidence of measles in Korea by the introduction of measles vaccine, a large measles epidemic occurred during 2000-2001. During the epidemic, more than 55,000 measles cases were reported and at least 7 children were dead. In this study, we analyzed the genetic and antigenic properties of 15 measles viruses that isolated during the epidemic. Sequence analyses of entire hemagglutinin (H) and nucleoprotein (N) genes of the viruses indicated that all Korean isolates had a high degree of homology (>99.8%) when compared with each other. They differed from other wild-type viruses by as much as 6.8% in the H gene and 6.5% in the N gene at the nucleotide level. The deduced amino acid variability was up to 6.4% for the H protein and up to 6.5% for the N protein. Phylogenetic analysis of nucleotide sequences and deduced amino acid sequences of the H and N genes revealed that all Korean viruses were grouped into the genotype H1. This strongly demonstrated that single genotype of measles virus has been circulated in Korea during the 2000-2001 epidemic. Plaque reduction neutralizing antibody titers against vaccine strains, Edmonston and Schwarz, and recently isolated Korean strains were measured using sera from vaccinees and recently infected children. Although sera of recently infected children demonstrated higher neutralizing antibody titers against wild-type strains than against vaccine strains, both sera neutralized both strains and the reciprocal geometric mean titers (GMTs) were not significantly different against both strains.     

Molecular epidemiology of mumps virus in Japan and proposal of two new genotypes

We isolated 872 strains of mumps virus from naso-pharyngeal secretions in seven different districts of Japan from January 2000 to July 2001. Among them, 57 strains were geno-typed by nucleotide sequencing in part of the hemagglutinin-neuraminidase (HN) and small hydrophobic (SH) protein regions. Four different genotypes (B, G, K, and L) of mumps virus were co-circulating in Japan and the distribution of genotypes varied in geographically different districts. Two new clusters designated as genotypes K and L had more than 7% nucleotide variation in the SH gene. Among the 57 strains, 11 were classified as B, 35 as G, three as K, and eight as L, which was mainly isolated in Tokyo. We also examined 104 stains isolated in a clinic in Mie prefecture from 1993 to 2003. Genotype B was the indigenous strain and genotype K was introduced in 1994. Genotypes B and K co-circulated in the 1990s and were replaced by genotype G in 2000. There was no significant change in neutralizing test antibody titers against genotypes B, G, K, and L using seven post-vaccination sera with Hoshino strain (genotype B) and these four genotypes had a different antigenicity from genotype A. We should continue to watch on mumps virus molecular epidemiology.     

Molecular identification of two genotypes of mumps virus causing two regional outbreaks in Asturias, Spain

BACKGROUND: In spite of universal vaccination, several sporadic cases of mumps infection, which could produce outbreaks, are detected every year in different countries. OBJECTIVE: Mumps virus strains causing two regional outbreaks in Asturias (Spain) were phylogenetically characterized. STUDY DESIGN: Mumps virus strains, which were detected in samples from patients belonging to two regional outbreaks in Asturias, were characterized by sequencing of the SH gene and further alignment to homologous sequences of representative strains of the different mumps genotypes. RESULTS: Two different strains (Ast/SP02 and Ast/SP07) were isolated. Sequence analysis revealed that while Ast/SP02 belonged to genotype H, Ast/SP07 was phylogenetically close to UK02-19, a reference strain for a new genotype. Both strains belonged to different genotypes from those used in the vaccination (Jeryl-Lynn strain is genotype A). CONCLUSION: Mumps virus strains different from those used in vaccination program can cause mumps outbreaks even in vaccinated patients.     

Molecular analysis of S gene of spike glycoprotein of winter dysentery bovine coronavirus circulated in Korea during 2002-2003

Since the molecular analysis of spike (S) glycoprotein gene of bovine coronavirus (BCoV) has been conducted and compared mainly among American and Canadian isolates and/or strains, it is unclear whether BCoV circulated in the other countries are distinctive in genetic characteristics. In the present study, we analyzed the S glycoprotein gene to characterize 10 winter dysentery (WD) coronavirus strains circulated in Korea during 2002-2003 and compared the nucleotide (nt) and deduced amino acid (aa) sequences with the other known BCoV. The phylogenetic analysis of the entire S glycoprotein gene revealed that the aa sequences of all Korean WD strains were more homologous to each other and were very closely related to respiratory bovine coronavirus (RBCV) strain OK and enteric bovine coronavirus (EBCV) strain LY-138, but were distinct from the other known BCoVs. Based on the phylogenetic analysis of the hypervariable region of the S1 subunit, all Korean WD strains clustered with the respiratory strain OK, BCQ3994 and the enteric strain LY-138, while the Canadian BCQ calf diarrhea and WD strains, and the American RBCV LSU, French EBCV F15 and avirulent VACC, L9, and Mebus strains clustered on a separate major branch. These data suggest that the WD strains circulated in Korea had a genetic property of both RBCV and EBCV and were significantly distinct from the ancestral enteric strain.     

Molecular characterization of mumps virus strains circulating during an epidemic in Eastern Switzerland 1992/93

Summary Ten mumps virus isolates recovered during an epidemic in Switzerland between Autumn 1992 and Spring 1993 were compared by nucleotide sequence analysis of the SH gene. The isolates were found to belong to two distinct yet closely related wild type strains in a newly identified European mumps virus lineage.     

Phylogenetic analysis of clinical mumps virus isolates from vaccinated and non-vaccinated patients with mumps during an outbreak, Switzerland 1998-2000

During the past decade mumps outbreaks have occurred in several European countries with universal vaccination programs probably due to poor efficacy of the Rubini vaccine strain. However, the evolution of vaccine escape mutants has also been considered. A phylogenetic analysis was undertaken on 69 clinical mumps isolates obtained from 39 vaccinated and 22 non-vaccinated mumps cases (and six cases with unknown vaccination status) during an outbreak in 1998-2000. Two major strain clusters (SWI-H, SWI-C) with two subgroups each (SWI-H1/2, SWI-C1/2) were identified, which belonged to genotypes C and H. No association between viral clusters and vaccination status or a specific vaccine strain (Jeryl-Lynn or Rubini) was found. Cluster SWI-C1 occurred more frequently in the Western part of Switzerland (P < 0.001). Isolates causing complicated disease tended to cluster more frequently with SWI-H1 (P = 0.11). Wild-type strains homologous or similar to the Rubini vaccine strain (isolated in Switzerland in 1974) were no longer circulating. Therefore, there was no evidence for vaccine escape mutants. Strain redistribution may have occurred during the past decades. Continuous monitoring of circulating mumps virus populations is needed.     

Genetic characterization of measles viruses that circulated in Thailand from 1998 to 2008

During the period between 1998 and 2008, 48 representative measles viruses (MeVs) circulating in Thailand were subjected to genetic characterization. Three genotypes, G2, D5, and D9 were detected. The results suggested that measles genotype D5, which has been circulating since at least 1998, is the endemic genotype in Thailand. Genotype G2 was detected between 1998 and 2001. In addition, almost all of the MeVs detected throughout the country in 2008 were genotype D9. This is the first report of genotype D9 in Thailand. This report provides important baseline data about measles genotypes in Thailand and this information will be needed to help verify measles elimination in Thailand.     

Molecular characterization of two genotypes of a new polerovirus infecting brassicas in China

The genomic RNA sequences of two genotypes of a brassica-infecting polerovirus from China were determined. Sequence analysis revealed that the virus was closely related to but significantly different from turnip yellows virus (TuYV). This virus and other poleroviruses, including TuYV, had less than 90% amino acid sequence identity in all gene products except the coat protein. Based on the molecular criterion (>10% amino acid sequence difference) for species demarcation in the genus Polerovirus, the virus represents a distinct species for which the name Brassica yellows virus (BrYV) is proposed. Interestingly, there were two genotypes of BrYV, which mainly differed in the 5′-terminal half of the genome.     

Genomic characterization of two predominant genotypes of herpes simplex virus type 1

Summary Genomic profiles of 66 strains of herpes simplex virus type 1 (HSV-1) isolated in Japan were investigated with regard to restriction fragment length polymorphism (RFLP) and length variation of fragments containing reiterations. There were two predominant genotypes of F1 and F35, and the genomic characteristics of each were studied. The nucleotide change between F1 and F35 was estimated to be 1.5%. An RFLP marker (VR23) peculiar to genotype F35 was identified as the first case of genomic marker specific to a predominant genotype of HSV-1, and is the diagnostic marker of F35. Thea sequences (repeating in an HSV-1 genome and containing reiterations) of F35 were cleaved by Sac II on the DR4 (direct repeat 4) stretch, whilea sequences of F1 had a rearranged DR4 and were resistant to Sac II digestion. Thus, analyses of fragments containing reiterations, such asa sequences, can serve to classify HSV-1 strains as well as for purpose of differentiation. The proportion of strains derived from primary infection to those from recurrent infection was higher in strains of F35 than in those of F1, and this genotypic difference within HSV-1 may possibly influence clinical manifestations.     

Molecular characterization of two strains of Shope fibroma virus

An isolate of Shope fibroma virus (SFV), designated Indiana (SFV-I), was previously described to be tumorigenic in vivo as SFV, cytocidal in vitro as the orthopoxviruses (vaccinia, rabbitpox, etc.), and to share antigenic determinants with SFV and vaccinia. The genetic relatedness of SFV-I to SFV and vaccinia was studied by means of Southern blotting and hybridization. The results indicated that SFV-I shares extensive DNA homology with vaccinia, but few common sequences with SFV. By contrast, SFV and vaccinia show no sequence homology. These findings suggest that SFV-I is an orthopoxvirus which carries some genetic information from the leporipoxviruses. Recombinants between two genera of poxviruses have not been reported before.     

Molecular characterization of influenza B viruses circulating in northern Italy during the 2001-2002 epidemic season

During the 2001-2002 influenza season, virological surveillance highlighted the predominant circulation of B viruses (86% of isolates) in Italy, in contrast to many other countries in Europe and North America where AH3N2 viruses were isolated most frequently, and in contrast to the infrequent isolation of B viruses in Italy during the previous two years. Associated with this predominance of influenza B was the re-emergence of B/Victoria/2/87-lineage viruses, closely related to B viruses prevalent during the 1980s, which are distinct antigenically and genetically from circulating B/Sichuan/379/99-like viruses of the B/Yamagata/16/88 lineage, which predominated in most parts of the world during the last 10 years. Ninety-four viruses isolated in two regions of northern Italy were characterized, 50 by direct sequencing of haemagglutinin (HA). Viruses of both Victoria and Yamagata lineages co-circulated throughout the 12 weeks of the influenza season. The HAs of the Yamagata-lineage viruses were heterogeneous and comprised two sublineages, represented by B/Sichuan/379/99 and B/Harbin/7/94, whereas the Victoria-lineage viruses were more homogeneous and closely related to B/Hong Kong/330/01, the current prototype vaccine strain. The antigenic and genetic characteristics of the viruses correlated with certain epidemiological features. In particular, the low age (<14 years) of individuals infected with B/Hong Kong/330/01-like viruses is likely to reflect the greater susceptibility of the youngest cohort, due to lack of previous exposure to Victoria-lineage viruses, and is consistent with the conclusion that vaccination with a B/Sichuan/379/99-like virus would give poor protection against infection with B/Hong Kong/330/01-like (Victoria-lineage) viruses.     

Pneumocystis jirovecii dihydropteroate synthase genotypes in French patients with pneumocystosis: a 1998-2001 prospective study.

Dihydropteroate synthase gene (DHPS) mutations at codons 55 and 57 have been associated with sulfa/sulfone resistance in Pneumocystis jirovecii strains from patients who previously received prophylaxis. To evaluate the prevalence of these mutations, a portion of P. jirovecii DHPS gene was analysed using PCR combined with restriction fragment length polymorphism (RFLP) analysis in 92 bronchoalveolar fluid samples collected between January 1998 and September 2001 from French patients with pulmonary pneumocystosis (PCP). Seventy-six samples contained the wild-type DHPS genotype (82.6%) and 16 contained a mutant genotype (17.4%). Twelve out of the 16 isolates with a mutant DHPS genotype corresponded to patients who had never received sulfa or sulfone prophylaxis, suggesting that DHPS mutants may be acquired de novo. There was no significant difference in favourable or adverse outcome in PCP caused by the wild or mutant DHPS genotypes (P = 0.34).     

Detection and characterization of mumps virus V protein

By cDNA cloning, DNA sequencing, and RNAse mapping analyses two distinct mRNA species were shown to be transcribed from the mumps virus P gene; one faithful and the other edited copies. The former was found to direct the synthesis of the V protein (25K), while the latter, after the addition of two nontemplated G residues, was found to direct the synthesis of the P protein (40K-42K). The carboxy terminal of the V protein contained a cysteine-rich region which was similar but not identical to the metal binding domain motif found in several nucleic acid binding proteins. The V protein was detected not only in mumps virus-infected cells but also in the virions by antiserum raised against a synthetic peptide.     

Genomic diversity of mumps virus and global distribution of the 12 genotypes

The WHO recently proposed an updated nomenclature for mumps virus (MuV). WHO currently recognizes 12 genotypes of MuV, assigned letters from A to N (excluding E and M), which are based on the nucleotide sequences of small hydrophobic (SH) and haemagglutinin‐neuraminidase (HN) genes. A total of 66 MuV genomes are available in GenBank, representing eight of the 12 genotypes. To complete this dataset, whole genomes of seven isolates representing six genotypes (D, H, I, J, K and L) and one unclassified strain were sequenced. SH and HN genes of other representative strains were also sequenced. The degree of genetic divergence, predicted amino acid substitutions in the HN and fusion (F) proteins and geographic distributions of MuV strains were analysed based on the updated dataset. Nucleotide heterogeneity between genotypes reached 20% within the SH gene, with a maximum of 9% within the HN gene. The geographic and chronologic distributions of the 12 genotypes were summarised. This review contributes to our understanding of strain diversity for wild type MuV, and the results support the current WHO nomenclature. © 2014 Crown copyright. Reviews in Medical Virology © 2014 John Wiley & Sons, Ltd.     

Molecular characterization of KGH, the first human isolate of rabies virus in Korea

The complete genome sequence of the KGH strain of the first human rabies virus, which was isolated from a skin biopsy of a patient with rabies, whose symptoms developed due to bites from a raccoon dog in 2001. The size of the KGH strain genome was determined to be 11,928 nucleotides (nt) with a leader sequence of 58 nt, nucleoprotein gene of 1,353 nt, phosphoprotein gene of 894 nt, matrix protein gene of 609 nt, glycoprotein gene of 1,575 nt, RNA-dependent RNA polymerase gene of 6,384 nt, and trailer region of 69 nt. Sequence similarity was compared with 39 fully sequenced rabies virus genomes currently available, and the result showed 70.6–91.6 % at the nucleotide level, and 82.8–97.9 % at the amino acid level. The deduced amino acids in the viral protein were compared with those of other rabies viruses, and various functional regions were investigated. As a result, we found that the KGH strain only had a unique amino acid substitution that was identified to be associated either with host immune response and pathogenicity in the N protein, or with a related region regulating STAT1 in the P protein, and related to pathogenicity in G protein. Based on phylogenetic analyses using the complete genome of 39 rabies viruses, the KGH strain was determined to be closely related with the NNV-RAB-H strain and transplant rabies virus serotype 1, which are Indian isolates, and was confirmed to belong to the Arctic-like 2 clade. The KGH strain was most closely related to the SKRRD0204HC and SKRRD0205HC strain when compared with Korean animal isolates, which was separated around the same time and place, and belonged to the Gangwon III subgroup.     

Single genotype of measles virus is dominant whereas several genotypes of mumps virus are co-circulating

We have reported that in Japan measles virus strains have been classified into three distinct different genotypes (C1, D3 and D5) under the new international genotype classification since 1984. Similarly, mumps virus strains have been divided into two genotypes with three subtypes (B1, B2, B3, and D) under the proposed international classification since 1976. To differentiate these genotypes we developed a restriction fragment length polymorphism assay in the hemagglutinin (H) region for measles virus and in the hemagglutinin-neuraminidase (HN) region for mumps virus to facilitate the expanded molecular epidemiology. In the Sapporo 1995/1996 measles outbreak, all 26 strains were classified as D5. Among 32 samples from patients with measles from 1994 to 1997 in Tokyo, 28 were identified as D5 and four were D3; these D3 strains were ascertained as a same hospital acquired infection. Among 45 strains obtained in the Tokyo 1999 outbreak, 38 were D3 and the remaining seven were D5. The dominant genotype of measles in Tokyo has replaced from D5 to D3 similar to the Chicago1/89 strain. We obtained 220 samples from patients with mumps from 1993 to 1997 and they were classified into one strain of B1, 14 strains of B2, 151 strains of B3, and 54 strains of D. Therefore, we suggest that two or three subtypes of mumps virus are co-circulating with a different geographic pattern in genotype distribution, whereas a single measles virus genotype is dominantly observed, showing different epidemiological patterns.