Molecular characterization of two genotypes of mumps virus circulated in Korea during 1998-2001

Sequence analyses of the entire small hydrophobic (SH) and hemagglutinin-neuraminidase (HN) genes of mumps viruses circulated in Korea from 1998 to 2001 showed that these isolates were grouped into two genotypes, H and I. While genotype I was predominant throughout the country during this period, genotype H was found in the restricted region, 1999. The nucleotide and deduced amino acid sequences of Korean isolates showed the type-specific changes including the signature motif at positions 28-30 in the SH gene and the neutralizing epitopes in the HN gene. Particularly, Asian strains including Korean isolates and European strains differed from 2.3 to 3.8% at the nucleotide sequence level in the SH gene although they belonged to the same genotype H. Furthermore, none of Korean isolates were genetically related to the vaccine strains used in Korea. The results provide important information to understand the epidemiology of mumps infection and to facilitate the development of more efficient vaccine program in Korea.     

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.     

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.     

Co‐circulation of multiple measles virus genotypes during an epidemic in France in 2008

In 2008, measles reappeared in France in a series of outbreaks. During this period, 604 measles cases were reported to a routine surveillance system and 305 (50%) of these cases were then confirmed in the laboratory. To understand better the current epidemiological situation and the circulation of different measles strains, a phylogenetic characterization of 113 (19%) of the measles cases from these outbreaks was performed. All measles cases met the WHO clinical criteria and were confirmed either by laboratory detection of measles‐specific IgM and/or by detection of the virus genome by polymerase chain reaction (PCR) and viral isolation. PCR products generated from blood, oral fluid, urine, or nasopharyngeal‐swab samples were sequenced for molecular epidemiology studies. Phylogenetic analysis showed a co‐circulation of genotypes D4 and D5 during the first measles outbreak in the city of Reims in early 2008. Over the course of the year, the A, B3.2, D8, and D9 genotypes also appeared. The data from this study show the simultaneous circulation of several measles genotypes in France and describe genotypes D8 and D9 for the first time in this country. The data also suggest that there are still many pockets of unvaccinated individuals helping to maintain the circulation of measles virus in the population. Phylogenetic studies allowed the corroboration of epidemiologic links and showed that nosocomial transmission can create significant risk for measles dissemination. Finally, the pattern of changes in viral genotypes during 2008 suggests a regular introduction of measles strains from abroad. J. Med. Virol. 82:1033–1043, 2010. © 2010 Wiley‐Liss, Inc.     

Rapid diversification of measles virus genotypes circulating in Morocco during 2004-2005 epidemics

Measles virus strains circulating in six different regions in Morocco during 2004-2005 were analysed. They were genotyped using two different methods: the recently developed method based on real-time PCR amplification and melting curve analyses, and the conventional method based on nucleic acid sequencing and phylogenetic analysis of 456 nucleotides of the 3'-region of the nucleoprotein (N) gene sequence. Five genotypes (A, B3.2, C2, D7 and D8) were shown to be circulating during this period. Previous studies on measles virus genotypes in Morocco (1998-2003) showed that only the genotype C2 was present and was considered to be endemic. Sequence comparison of the 2004-2005 viruses with other measles strains suggests that measles strains belonging to genotype B3.2 were probably imported from West Africa, whereas those belonging to genotypes D7 and D8 were imported from Europe. These studies which identify the route of importation of measles are important for developing strategies for measles elimination in Morocco.     

Molecular characterisation of HCV genotype 4 isolates circulating in Italy

The characteristics of genotype 4 subtype variability of HCV isolates circulating in Italy were studied. The viral isolates were identified from 736 HCV-RNA positive sera originated from seroepidemiological studies undertaken in 4 different regions of North, South Italy and Sardinia. 24 out of 28 genotype 4 isolates (86%) were classified by phylogenetic analysis of E1 genome region (915-1128) as belonging to subtype 4d (Neighbour Joining Method). Three isolates classified as subtype 4a were detected in haemophilic patients, possibly related to infections from blood products. One isolate classified as a new subtype derived from an Eritrean patient subjected to haemodialysis. Very high genome homogeneity (mean 4.3%) was shown by genetic comparisons (DNA dist programs Phylip Package) for all the 4d isolates relative to the studies performed in Veneto, Calabria and Sardinia and originated from subjects from the general population and outpatients (19 subtype 4d isolates out of 24). In the 3 studies different prevalence rates of HCV genotype 4 (3.1%, 1. 3%, 14% respectively) were found. In contrast a considerable degree of heterogeneity, both intragroup and with the other groups (mean 8. 2% and 8.7%, respectively) was observed among subtype 4d isolates identified in the patients of a haemodialysis centre in Apulia region. In conclusion the subtype 4d of genotype 4 was highly prevalent and endemic in Italy. An elevated level of viral heterogeneity was observed in one study carried out in a region of Southern Italy. This can be related to a longer period of past endemicity of this genotype and to a high level of exposure to reinfections in particular categories of patients such as haemodialysis patients.     

Molecular characterisation of two divergent variants of grapevine leafroll-associated virus 3 in New Zealand

Partial genomic sequences of two divergent grapevine leafroll-associated virus 3 (GLRaV-3) variants, NZ1-B and NZ2, from New Zealand were determined and analysed (11,827 nt and 7,612 nt, respectively). At the nucleotide level, both variants are more than 20 % different from the previously published GLRaV-3 sequences, from phylogenetic groups 1 to 5. Phylogenetic analysis indicated that NZ1-B is a variant of the previously identified divergent NZ-1, while NZ2 is a novel sequence with only 76 % nucleotide sequence identity to GLRaV-3 variants NZ-1, GH11, and GH30. Therefore, NZ2 is a new variant of GLRaV-3. Amino acid sequence analysis of the NZ1-B and NZ2 coat proteins indicated significant substitutions that are predicted to alter the coat protein structure, which potentially leads to the observed reduced immunological reactivity of both variants to the Bioreba anti-GLRaV-3 conjugated monoclonal antibody.     

Molecular characterisation of Hepatitis E virus isolates from north India

PurposeHepatitis E virus (HEV) is responsible for >50% of acute viral hepatitis (AVH) in developing countries. It has 4 major genotypes and various subtypes which vary in geographical distribution, clinical manifestations and epidemiological patterns. This study was conducted to characterise HEV isolates from north India to study the effect of host and viral factors on HEV infection.MethodsSerum samples collected from 536 AVH patients admitted to Department of Medicine, King George's Medical University, Lucknow from July 2016 to June 2017 were screened for anti HEV IgM, anti HAV IgM, HBsAg and anti HCV antibodies using commercial ELISA kits. Samples either positive for anti HEV IgM antibodies (n ?= ?204) or negative for all 4 hepatotropic viruses (n ?= ?37) were enrolled and tested by real time PCR for HEV RNA. HEV RNA positive samples with high viral load were further subjected to nested PCR for amplification of capsid gene. Sequencing and phylogenetic analysis were performed. HEV strains isolated from this study were deposited to GenBank under accession numbers MG571274 to MG571283.ResultsAnti HEV IgM positivity was observed among 38% clinically suspected AVH cases. HEV RNA was detected in 31.8% seropositive HEV cases and additional 3 seronegative cases. Males outnumbered females and the most affected age group was of young adults. Maximum number of cases were seen during the months of June to September. Phylogenetic analysis showed that HEV strains in our study belonged to genotype 1a. Mortality in HEV infected pregnant females was 23.5% as compared to 2.4% in non-pregnant females. Adverse fetal outcome was recorded in 51% of HEV infected pregnancies.ConclusionsHEV genotype 1a is prevalent in our setting. HEV during pregnancy is associated with adverse maternal and fetal outcome.     

Influenza virus circulation in wild aquatic birds in Italy during H5N2 and H7N1 poultry epidemic periods (1998 to 2000).

Two epidemics of avian influenza due to H5 and H7 highly pathogenic viruses occurred in poultry in Italy in 1997/98 and 1999/2000, respectively. The circulation of these serotypes in wild aquatic birds was investigated examining 638 cloacal swabs and 621 sera collected from 150 gulls, 162 coots, and 326 ducks trapped in Italian wetlands from 1998 to 2000. Seroprevalences against influenza A viruses, detected by a double-antibody sandwich-blocking enzyme-linked immunosorbent assay (ELISA), were 11% in gulls, 16% in coots, and 45% in ducks. Among the Anatidae group, duck species wintering in Mediterranean areas showed significantly higher values than ducks wintering in South-Saharan areas of Africa. In order to detect H5 and H7 antibodies, the haemagglutination-inhibition assay and two competitive ELISA tests (H5-ELISA and H7-ELISA) using monoclonal antibodies specific for H5 and H7 subtypes were performed. None of the aquatic bird species were found seropositive for H7 subtype, whereas H5-positive sera were found by both the haemagglutination-inhibition and ELISA assays in ducks only. The highest H5 seroprevalences were detected by H5-ELISA; overall, 5% (10/201) of duck species wintering in Mediterranean areas tested positive by this assay, with annual seroprevalences ranging from 2% (2/123) to 12% (6/51). In the present study, only five viruses belonging to H1N1, H11N6, and H2N3 subtypes were isolated from ducks. However, the H5 seroconversion observed in one mallard duck at the beginning of 1998 indicates that H5 virus circulation also occurred in the study area.     

RT-PCR based diagnosis and molecular characterisation of mumps viruses derived from clinical specimens collected during the 1996 mumps outbreak in Portugal

Clinical specimens collected during an outbreak of mumps were characterised by RT-PCR, nested PCR, and nucleotide sequencing. Mumps virus was positively identified in 12/21(57%) saliva, 9/21(43%), throat and 1/33(3%) urine specimens and further sequence comparison revealed that at least six strains of viruses, which differed from 0–9.43% at the nucleotide levels, were co-circulating during the epidemic. However, phylogenetic analysis showed that these viruses grouped with two previously identified lineages which were mostly composed of other European mumps virus isolates. J. Med. Virol. 52:349–353, 1997. © 1997 Wiley-Liss, Inc.     

Measles virus strains circulating in Central and West Africa: Geographical distribution of two B3 genotypes

Africa remains one of the major reservoirs of measles infection. Molecular epidemiological studies have permitted different measles virus isolates to be grouped into clades and genotypes; the major group, which has been identified as indigenous to Africa, is clade B. The viruses from epidemics in the Gambia (1993) and in the Cameroon (2001) were examined. In both studies, the homogeneity of the virus isolates within the epidemic as shown by sequence analysis revealed less than 0.2% variation of nucleotides between isolates. The measles viruses isolated in 1983 in Yaoundé, Cameroon, were designated as the B1 genotype. However, in 2001 only viruses belonging to the B3 genotype were found in this city. The viruses in the Gambia (1993) were also of the B3 genotype. However, these viruses could be distinguished from each other at the antigenic level and by comparative sequence analysis. The B3 Cameroon (2001) viruses were related to the proposed B3.1 subgroup, whereas the Gambian (1993) isolates corresponded to the B3.2 subgroup. The geographical distribution for the period 1993-2001 of these two viruses shows that B3.1 is found from the Sudan to Nigeria and Ghana extending south to the Cameroon, whereas the B3.2 genotype is found in West Africa. In Nigeria and Ghana, the viruses co-circulate. The identification of these viruses will permit more meaningful epidemiological studies after the proposed increase in measles vaccination coverage.