Genetic analysis of human parainfluenza virus type 3 obtained in Croatia, 2011–2015

Košutić-Gulija, Tanja; Slović, Anamarija; Ljubin‐Sternak, Sunčanica; Mlinarić‐Galinović, Gordana; Forčić, Dubravko

doi:10.1099/jmm.0.000459

Cited by 15 publications

(36 citation statements)

References 33 publications

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“…However, distribution of the distances in our study was similar to those in previous reports of the HRV3 F gene (Tsutsui et al, 2017), and also the HRV3 HN gene (Mao et al, 2012). This implied that the F and HN genes may be categorized into the same cluster and subcluster (Godoy et al, 2016;Košutić-Gulija et al, 2017). In addition, the genetic distances of the HRSV-A and HRSV-B F gene based on globally collected strains were also smaller than the present study, reported as 0.025 and 0.017, respectively (Kimura et al, 2016(Kimura et al, , 2017.…”

Section: Discussionsupporting

confidence: 90%

“…These findings may contribute to a better understanding of HRV3 infection in humans. Some molecular epidemiological studies of the HRV3 F gene have been reported (Godoy et al, 2016;Košutić-Gulija et al, 2017;Tsutsui et al, 2017). Godoy et al (2016) created a phylogenetic tree based on the partial sequence of the F gene (390 nt) by the neighbor-joining method.…”

Section: Discussionmentioning

confidence: 99%

“…Godoy et al (2016) created a phylogenetic tree based on the partial sequence of the F gene (390 nt) by the neighbor-joining method. Moreover, Košutić-Gulija et al (2017) and Tsutsui et al (2017) performed a molecular epidemiologic study by the ML method using the full-length nucleotide sequences of the F gene from domestic HRV3 strains (Japanese and Croatian strains, respectively). Assessment of viral gene evolutionary rates may help to predict the emergence of new mutants adept at evading host immunity (Motoya et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

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Molecular Evolution of the Fusion Protein (F) Gene in Human Respirovirus 3

et al. 2020

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To elucidate the evolution of human respirovirus 3 (HRV3), we performed detailed genetic analyses of the F gene (full-length) detected from hundreds of HRV3 strains obtained from various geographic regions. First, we performed time-scaled evolutionary analyses using the Bayesian Markov chain Monte Carlo method. Then, we performed analyses of phylodynamics, similarity, phylogenetic distance, selective pressure, and conformational B-cell epitope with the F-protein structural analyses. Time-scaled phylogenetic tree showed that the common ancestor of HRV3 and bovine respirovirus 3 diverged over 300 years ago and subdivided it into three major clusters and four subclusters during the most recent 100 years. The overall evolutionary rate was approximately 10 −3 substitutions/site/year. Indigenous similarity was seen in the present strains, and the mean phylogenetic distance were 0.033. Many negative selection sites were seen in the ectodomain. The conformational epitopes did not correspond to the neutralizing antibody binding sites. These results suggest that the HRV3 F gene is relatively conserved and restricted in this diversity to preserve the protein function, although these strains form many branches on the phylogenetic tree. Furthermore, HRV3 reinfection may be responsible for discordances between the conformational epitopes and the neutralizing antibody binding sites of the F protein. These findings contribute to a better understanding of HRV3 virology.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Molecular Evolution of the Fusion Protein (F) Gene in Human Respirovirus 3

et al. 2020

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“…This is especially interesting as no changes that could distinguish different phylogenetic subgroups were present when we analyzed HPIV3 F and HN proteins [40], which are more diverse, and therefore used for phylogenetic classification [41, 42]. Also, in the case of HPIV3, most of the amino acid changes in glycoproteins were restricted to cytoplasmic and transmembrane regions [40], which are regions thought to be important for interaction with the M proteins [43]. The fact that we could not observe any connection between substitutions and genetic clusters for HPIV1 samples might indicate that these groups contain viruses that are less divergent.…”

Section: Discussionmentioning

confidence: 99%

Genetic Variability and Sequence Relatedness of Matrix Protein in Viruses of the Families Paramyxoviridae and Pneumoviridae

Slović

Košutić-Gulija²,

Šantak³

et al. 2017

Intervirology

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Background: The families Paramyxoviridae and Pneumoviridae comprise a broad spectrum of viral pathogens that affect human health. The matrix (M) protein of these viruses has a central role in their life cycle. In line with this, molecular characteristics of the M proteins from variable viruses that circulated in Croatia were investigated. Methods: Sequences of the M proteins of human parainfluenza virus (HPIV) 1–3 within the family Paramyxoviridae, human metapneumovirus (HMPV), and human respiratory syncytial virus from the family Pneumoviridae were obtained and analyzed. Results: M proteins were very diverse among HPIVs, but highly conserved within each virus. More variability was seen in nucleotide sequences of M proteins from the Pneumoviridae family. An insertion of 8 nucleotides in the 3′ untranslated region in 1 HMPV M gene sequence was discovered (HR347-12). As there are no samples with such an insertion in the database, this insertion is of interest and requires further research. Conclusion: While we have confirmed that M proteins were conserved among individual viruses, any changes that are observed should be given attention and further researched. Of special interest is inclusion of HPIV2 M proteins in this analysis, as these proteins have not been studied to the same extent as other paramyxoviruses.

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“…To date there appears to be no unified phylogenetic classification of HPIV3. Recently the HN gene has been used to characterize emerging strains as well as tracing outbreaks [10][11][12][13][14] . Automatic barcode gap discovery (ABGD) 15 was used to separate HPIV3 into 3 clusters with currently circulating strains confined to one of these.…”

Section: Introductionmentioning

confidence: 99%

UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis

Smielewska¹,

Emmott²,

Ranellou³

et al. 2018

Wellcome Open Res

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Background: Human parainfluenza viruses type 3 (HPIV3) are a prominent cause of respiratory infection with a significant impact in both pediatric and transplant patient cohorts. Currently there is a paucity of whole genome sequence data that would allow for detailed epidemiological and phylogenetic analysis of circulating strains in the UK. Although it is known that HPIV3 peaks annually in the UK, to date there are no whole genome sequences of HPIV3 UK strains available. Methods: Clinical strains were obtained from HPIV3 positive respiratory patient samples collected between 2011 and 2015. These were then amplified using an amplicon based method, sequenced on the Illumina platform and assembled using a new robust bioinformatics pipeline. Phylogenetic analysis was carried out in the context of other epidemiological studies and whole genome sequence data currently available with stringent exclusion of significantly culture-adapted strains of HPIV3. Results: In the current paper we have presented twenty full genome sequences of UK circulating strains of HPIV3 and a detailed phylogenetic analysis thereof. We have analysed the variability along the HPIV3 genome and identified a short hypervariable region in the non-coding segment between the M (matrix) and F (fusion) genes. The epidemiological classifications obtained by using this region and whole genome data were then compared and found to be identical. Conclusions: The majority of HPIV3 strains were observed at different geographical locations and with a wide temporal spread, reflecting the global distribution of HPIV3. Consistent with previous data, a particular subcluster or strain was not identified as specific to the UK, suggesting that a number of genetically diverse strains circulate at any one time. A small hypervariable region in the HPIV3 genome was identified and it was shown that, in the absence of full genome data, this region could be used for epidemiological surveillance of HPIV3.

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Genetic analysis of human parainfluenza virus type 3 obtained in Croatia, 2011–2015

Abstract: The HPIV3 subclaster C3 (genetic lineage C3a) became the most detected circulating HPIV3 strain in Croatia. The results indicated that the HN 582 nt and the entire F gene sequences were as good for phylogenetic analysis as the entire HN gene sequence.

Cited by 15 publications

References 33 publications

Molecular Evolution of the Fusion Protein (F) Gene in Human Respirovirus 3

Molecular Evolution of the Fusion Protein (F) Gene in Human Respirovirus 3

Genetic Variability and Sequence Relatedness of Matrix Protein in Viruses of the Families Paramyxoviridae and Pneumoviridae

UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis

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