Small Hydrophobic Protein Gene Research Articles

Mumps resurgence in a highly vaccinated population: Insights gained from surveillance in Canada, 2002–2020

Although mumps vaccination has been routine in Canada for decades, mumps cases and outbreaks continue to occur periodically. Mumps surveillance, including monitoring of the mumps virus genotype associated with disease activity, is important to document baseline activity and to advance further research into vaccine effectiveness. Here we describe a detailed analysis of mumps cases that have been detected in Canada from 2002 to 2020, with a focus on the mumps molecular epidemiology. In total, 7395 cases of mumps were reported to the surveillance system, with outbreaks occurring in the years 2007, 2010 and 2016 to 2018. Adolescents and young adults aged 15 to 29 years had the highest risk of being a case (rate ratios ranging from 1.50 to 2.29), compared to adults aged 30 to 39. Genotypes of mumps viruses were determined in 3225 specimens. Genotype G was predominantly detected (96% of genotyped specimens) and was first reported in 2005. Other genotypes were more likely to be detected in cases that also reported travel (or were linked to imported cases) than the cases with genotype G detected (p < 0.0001). The genotype G viruses had little sequence diversity in the 316 nucleotide window used for genotyping (the small hydrophobic protein gene) and mainly belonged to a single phylogenetic lineage that included the MuVi/Sheffield.GBR/1.05 reference sequence. The analysis of over ten years of data has demonstrated that mumps genotype G, specifically belonging to a single lineage, the Sheffield lineage, is the endemically circulating virus in Canada. This lineage is seen also in other countries using the genotype A vaccine. Mumps remains endemic despite high MMR vaccination coverage which has been sufficient to eliminate circulation of measles and rubella in Canada, raising the hypothesis of the evolution towards a vaccine escape mumps virus.

Genomic non-coding regions reveal hidden patterns of mumps virus circulation in Spain, 2005 to 2015.

BackgroundSince mumps vaccination was introduced in 1981 in Spain, the incidence of the disease has dropped significantly. However, cyclic epidemic waves and outbreaks still occur, despite high vaccination coverage. The World Health Organization (WHO) recommends genotyping to trace the pattern of mumps virus (MuV) circulation. Genotype H was predominant in Spain, but was replaced in 2005 by genotype G which has subsequently remained dominant. Of the small hydrophobic protein gene sequences, 78% are identical and belong to the MuVi/ Sheffield.GBR.1.05/[G]-variant. Aim: Our study aimed to investigate whether the circulation of MuV strains in Spain was continuous after the emergence of genotype G in 2005. Method: We obtained 46 samples from Spanish patients infected with MuVi/Sheffield.GBR.1.05/[G] during two epidemic waves and analysed them using new molecular markers based on genomic non-coding regions (NCRs) that discriminate subvariants of this virus strain. Results: Phylogenetic analyses of the nucleoprotein–phosphoprotein and matrix protein–fusion protein NCR indicated strain replacement after a drop in incidence in 2009, which had not been detectable by SH sequencing. Clustering of sequences from patients epidemiologically linked in the same outbreak suggests a potential use for these NCRs in outbreak characterisation. Conclusion: We suggest to consider their use in conjunction with the SH gene in the future WHO recommendations for MuV epidemiological surveillance.

A Recombinant Respiratory Syncytial Virus Vaccine Candidate Attenuated by a Low-Fusion F Protein Is Immunogenic and Protective against Challenge in Cotton Rats.

Although respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in infants, a safe and effective vaccine is not yet available. Live-attenuated vaccines (LAVs) are the most advanced vaccine candidates in RSV-naive infants. However, designing an LAV with appropriate attenuation yet sufficient immunogenicity has proven challenging. In this study, we implemented reverse genetics to address these obstacles with a multifaceted LAV design that combined the codon deoptimization of genes for nonstructural proteins NS1 and NS2 (dNS), deletion of the small hydrophobic protein (ΔSH) gene, and replacement of the wild-type fusion (F) protein gene with a low-fusion RSV subgroup B F consensus sequence of the Buenos Aires clade (BAF). This vaccine candidate, RSV-A2-dNS-ΔSH-BAF (DB1), was attenuated in two models of primary human airway epithelial cells and in the upper and lower airways of cotton rats. DB1 was also highly immunogenic in cotton rats and elicited broadly neutralizing antibodies against a diverse panel of recombinant RSV strains. When vaccinated cotton rats were challenged with wild-type RSV A, DB1 reduced viral titers in the upper and lower airways by 3.8 log10 total PFU and 2.7 log10 PFU/g of tissue, respectively, compared to those in unvaccinated animals (P < 0.0001). DB1 was thus attenuated, highly immunogenic, and protective against RSV challenge in cotton rats. DB1 is the first RSV LAV to incorporate a low-fusion F protein as a strategy to attenuate viral replication and preserve immunogenicity. RSV is a leading cause of infant hospitalizations and deaths. The development of an effective vaccine for this high-risk population is therefore a public health priority. Although live-attenuated vaccines have been safely administered to RSV-naive infants, strategies to balance vaccine attenuation with immunogenicity have been elusive. In this study, we introduced a novel strategy to attenuate a recombinant RSV vaccine by incorporating a low-fusion, subgroup B F protein in the genetic background of codon-deoptimized nonstructural protein genes and a deleted small hydrophobic protein gene. The resultant vaccine candidate, DB1, was attenuated, highly immunogenic, and protective against RSV challenge in cotton rats.

Antigenic relationships between six genotypes of the small hydrophobic protein gene of mumps virus.

Six different genotypes of mumps virus, A, C, D, G, H and I, genotyped on the basis of the small hydrophobic protein gene sequence, were subjected to antigenic comparison. Monoclonal antibodies directed against the haemagglutinin-neuraminidase protein of the SBL-1 strain of genotype A were used in immunofluorescence tests with different mumps virus strains. In addition, the six virus genotypes were compared by cross-neutralization tests with human post-vaccination sera after vaccination with the Jeryl Lynn (JL) strain of mumps virus and with rabbit hyperimmune sera directed against the A or D genotypes of mumps virus. Genotypes C, D, G, H and I could not be antigenically separated. In contrast, three different virus strains of genotype A, SBL-1, JL and Kilham, were distinct and were found to represent three different serotypes within the A genotype of mumps virus. Vaccination of Swedish children with the JL strain of mumps virus resulted in clearly lower neutralization titres against the SBL-1 strain, which is endemic in Sweden, compared to the homologous vaccine titres.

Antigenic and genetic characterization of the fusion (F) protein of mumps virus strains.

Twelve strains of mumps virus, belonging to the A, C and D genotypes of the small hydrophobic (SH) protein gene, were investigated by nucleotide sequencing of the fusion protein gene. The nucleotide sequences and deduced amino acid sequences were aligned and compared with previously reported sequences of the gene. In addition an antigenic comparison between the F protein of different strains of the A, C and D genotypes was performed with ten monoclonal antibodies directed against the F protein of genotype A. Phylogenetic analysis of the coding region of the F gene showed the expected clustering of the different genotypes, as previously determined from the SH protein gene. Comparison of the 538 long amino acid sequence of the protein showed that only a small number of amino acids differed between the viral strains. The A genotype differed from B, C and D whereas the latter showed fewer consistent amino acid differences between themselves. Nine of the ten monoclonal antibodies reacted with the C and D genotypes and one failed to react with these genotypes. It is concluded that the structure and antigenicity of the F protein is well conserved both intra- and intergenotypically over long periods of time.

Characterization of three co-circulating genotypes of the small hydrophobic protein gene of mumps virus.

Eighteen virus isolates and 22 serum samples collected between 1971 and 1997 from patients with mumps were genotyped by PCR with specific primer pairs for the A, C and D genotypes of the small hydrophobic (SH) protein gene. All serum samples were subjected to nucleotide sequence analysis of the gene, and the deduced 57-amino-acid sequences were aligned with previously published sequences from the USA, Canada, Portugal, the UK, France, Germany, Switzerland, Denmark, Sweden, Russia, China and Japan. The existence of six genotypes of the SH protein gene, named A to F, was confirmed. In the Stockholm area, co-circulation of genotypes A, C and D at different times was found. There was a striking difference in genotype between the virus isolates and the serum samples. The 18 virus isolates represented genotypes C and D, whereas the 22 serum samples contained genotype A. In most cases, the amino acid sequences of the 22 genotype A specimens were identical to the previously described SBL-1 strain of genotype A. Genotypes C and D were always associated with meningitis, and in some cases parotitis, whereas infection with genotype A most often resulted in parotitis and seldom in meningitis.

Characterization of genotype-specific epitopes of the HN protein of mumps virus.

The SBL-1 strain of mumps virus, grouping with genotype A on the basis of the small hydrophobic protein gene sequence, was grown in the presence of three different monoclonal antibodies. The monoclonal antibodies were directed against the haemagglutinin-neuraminidase (HN) protein and they inhibited haemagglutinating activity and infectivity of the virus. The HN genes of the nine neutralization-escape virus mutants were sequenced and the predicted amino acid sequences were compared with that of the parental virus. Amino acid substitutions were found at positions 269, 352 and 354, respectively, of the 582 amino acid long protein. The three monoclonal antibodies did not react with 35 virus strains isolated in Stockholm during the years 1970 to 1985. Thirteen and four of the strains were found to belong to the D and C genotypes, respectively. A type-specific neutralization antibody response was also found in sera of rabbits hyperimmunized with purified virions of genotype A and D. The genotype-specific difference in neutralizing activity in mice and rabbits was not corroborated by an overall difference in the amino acid sequence of the HN protein of the different genotypes. Further studies are needed to explore the efficacy of mumps virus vaccines for protection against homologous and heterologous genotypes of mumps virus.

Nucleotide and predicted amino acid sequence analysis of the ovine respiratory syncytial virus non-structural 1C and 1B genes and the small hydrophobic protein gene.

Respiratory syncytial virus (RSV) infects humans and cattle causing serious respiratory tract disease in both. The genome of the human and bovine RSV (HRSV and BRSV) codes for two non-structural and eight structural proteins. RSV has also been isolated from naturally infected sheep, but the genome of the ovine RSV (ORSV) has not been characterized and nor has the virus host range been identified. Here we report on the cloning and sequencing of the two non-structural 1C and 1B genes and of the small hydrophobic (SH) protein gene of the ORSV. The nucleotide identity of the ORSV 1C gene to those of subgroups A and B of HRSV was 70% and 65% respectively whereas the predicted amino acid identity was 68% and 69% respectively. The ORSV 1B gene had a 70% and 72% nucleotide identity with that of subgroups A and B of the HRSV respectively, and 79% predicted amino acid identity with both HRSV subgroups. The identity level of these two ORSV 1C and 1B genes to those of the BRSV could not be determined since these two BRSV genes have not been sequenced. The SH protein of RSV is a structural protein expressed on the surface of infected cells. In common with HRSV and BRSV subgroups, the ORSV SH had the three proposed domains with the C-terminal domain least conserved among the viruses. In the latter domain, the ORSV SH gene had a nucleotide identity of 68 to 69% and 47 to 51% with those of the BRSV and HRSV, respectively, and a predicted amino acid identity of 56% and 33 to 47% with those of BRSV and HRSV, respectively. Defining the genes and their products should help determine which genes and gene products are most suitable for use as diagnostic tools or as vaccine candidates.

Analysis of respiratory syncytial virus strain variation in successive epidemics in one city.

The variability of respiratory syncytial virus isolates from five successive epidemics in an urban population was determined. A total of 187 isolates of respiratory syncytial virus from the southern part of Birmingham, United Kingdom, were classified into subgroups A and B and were then further assigned to genetic lineages. Allocation of isolates into lineages was achieved by reverse transcription of infected cell RNA and then PCR amplification of selected regions of the genome; PCR products were examined by restriction mapping or nucleotide sequencing of parts of the nucleoprotein gene, the small hydrophobic protein gene, and the attachment protein gene. Previous work has shown that estimations of genetic diversity by analysis of genes coding for proteins likely (attachment protein) and unlikely (nucleoprotein and small hydrophobic protein) to be under immune pressure gave concordant results. Six genetic lineages of subgroup A isolates have been defined by this procedure; these isolates differ by up to 20% in the amino acid sequences of their attachment proteins; likewise, subgroup B isolates can be divided into two categories by restriction mapping of parts of their nucleoprotein and attachment protein genes. The same genetic lineages appeared to be present worldwide during the same period. The analysis of isolates from successive epidemics showed that different lineages predominated in each epidemic and that not all lineages were present in every epidemic. Some lineages appeared to increase in numbers over several years and then decline, possibly indicating a buildup of resistance in the community to a particular genotype.

The Jeryl Lynn vaccine strain of mumps virus is a mixture of two distinct isolates.

Sequence analysis of the region of the mumps virus genome encoding the putative small hydrophobic protein gene confirms that it is a highly variable region. Jeryl Lynn, the mumps vaccine strain used in the U.K., is shown to be a mixture of two closely related viruses, both probably of American origin.

Identification of variable domains of the attachment (G) protein of subgroup A respiratory syncytial viruses

We have previously classified isolates from a respiratory syncytial (RS) virus epidemic into distinct lineages by restriction mapping and nucleotide sequencing of parts of the nucleocapsid protein and small hydrophobic protein genes, which are areas of the genome not considered to be under immunological pressure. This study has now been extended by the determination of the nucleotide sequences of the attachment (G) protein genes of isolates from each subgroup A lineage. Deduced amino acid identities of the G proteins ranged between 80% and 99%, corresponding closely to the previously determined relatedness of the lineages. The amino acid variability was not evenly distributed; in the extracellular part of the protein there was a sharply defined hypervariable domain which was separated from a more extended variable domain by a highly conserved region. Most nucleotide changes in the variable domains were in the first and second positions of the codon triplets. These results suggest that there may be considerable immunological pressure for change in certain areas of the G protein and this may account for the ability of this virus to reinfect individuals repeatedly. The results presented here reflect the pattern of published data comparing prototype strains of the A and B subgroups.

MRNA sequence and deduced amino acid sequence of the mumps virus small hydrophobic protein gene.

The mRNA of a putative small hydrophobic protein (SH) of mumps virus was identified in mumps virus-infected Vero cells, and its complete nucleotide sequence was determined by sequencing the genomic RNA and cDNA clones and partial sequencing of mRNA. The SH mRNA is 310 nucleotides long excluding the poly(A) and contains a single open reading frame encoding a protein of 57 amino acids with a calculated molecular weight of 6,719. The predicted protein is highly hydrophobic and contains a stretch of 25 hydrophobic amino acids near the amino terminus which could act as a membrane anchor region. There is no homology between the putative SH protein of mumps virus and the SH protein of simian virus 5, even though the SH genes are located in the same locus in the corresponding genome. One interesting observation is that the hydrophobic domain of simian virus 5 SH protein is at the carboxyl terminus, whereas that of mumps virus putative SH protein is near the amino terminus.