Whole Genome Sequencing and Evolutionary Analysis of Human Respiratory Syncytial Virus A and B from Milwaukee, WI 1998-2010

Rebuffo-Scheer, Cecilia; Bose, Michael E.; He, Jun; Khaja, Shamim; Ulatowski, Michael; Beck, Eric T.; Fan, Jun; Kumar, Swati; Nelson, Martha I.; Henrickson, Kelly J.

doi:10.1371/journal.pone.0025468

Cited by 60 publications

(81 citation statements)

References 49 publications

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“…Analysis of RSV complete genome evolutionary dynamics was conducted on a data set containing a combination of newly obtained RSV-B isolates and strains from a recent study by Rebuffo-Scheer et al (47). The latter five full-genome sequences (JN032115 to JN032117 and JN032119 and JN032120) were derived from nasopharyngeal and nasal swabs collected from patients in the Milwaukee metropolitan area.…”

Section: Methodsmentioning

confidence: 99%

“…Importantly, as has recently been demonstrated in many other virus groups, full-genome analyses can provide valuable insights into the processes that shape viral epidemiology and evolution (45). Complete genome sequences from RSV clinical isolates have, however, been generated in sufficiently large numbers to facilitate such analyses only recently (46)(47)(48), and that work is further extended with this study.…”

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confidence: 93%

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The Comparative Genomics of Human Respiratory Syncytial Virus Subgroups A and B: Genetic Variability and Molecular Evolutionary Dynamics

Tan

Coenjaerts

Houspie

et al. 2013

J Virol

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Genomic variation and related evolutionary dynamics of human respiratory syncytial virus (RSV), a common causative agent of severe lower respiratory tract infections, may affect its transmission behavior. RSV evolutionary patterns are likely to be influenced by a precarious interplay between selection favoring variants with higher replicative fitness and variants that evade host immune responses. Studying RSV genetic variation can reveal both the genes and the individual codons within these genes that are most crucial for RSV survival. In this study, we conducted genetic diversity and evolutionary rate analyses on 36 RSV subgroup B (RSV-B) whole-genome sequences. The attachment protein, G, was the most variable protein; accordingly, the G gene had a higher substitution rate than other RSV-B genes. Overall, less genetic variability was found among the available RSV-B genome sequences than among RSV-A genome sequences in a comparable sample. The mean substitution rates of the two subgroups were, however, similar (

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 93%

The Comparative Genomics of Human Respiratory Syncytial Virus Subgroups A and B: Genetic Variability and Molecular Evolutionary Dynamics

Tan

Coenjaerts

Houspie

et al. 2013

J Virol

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“…The strains of subgroup A can be subclassified into eight genotypes (GA1-GA7 and SAA1), as can those of subgroup B (BA, GB1-GB4 and SAB1-3) (Parveen et al, 2006). A recent study showed that subgroup A genotypes GA1, GA2, GA5 and GA7, and subgroup B genotype BA have been detected in the USA (Rebuffo-Scheer et al, 2011). In addition, our recent studies suggest that GA2, GA5 and BA are detected in most Japanese infants with ARI (Fujitsuka et al, 2011;Goto-Sugai et al, 2010;Nakamura et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Molecular epidemiology of the attachment glycoprotein (G) gene in respiratory syncytial virus in children with acute respiratory infection in Japan in 2009/2010

Yoshida

Kiyota²,

Kobayashi

et al. 2012

Journal of Medical Microbiology

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This study performed a detailed genetic analysis of the glycoprotein (G) gene of respiratory syncytial virus (RSV) detected in 50 Japanese children with acute respiratory infection (ARI) in the 2009/2010 season. A phylogenetic tree constructed by the neighbour-joining method showed that 34 and 16 of the RSV strains could be classified into subgroups A and B, respectively. Strains belonging to subgroups A and B were further subdivided into GA2 and BA, respectively. The nucleotide and deduced amino acid sequence identities were relatively high among these strains (.90 %). The deduced amino acid sequences implied that a relatively high frequency of amino acid substitutions occurred in the C-terminal 3rd hypervariable region of the G protein in these strains. In addition, some positively selected sites were estimated. The results suggest that RSV with genotypes GA2 and BA was associated with ARI in Japanese children in 2009/2010. Abbreviations: AdV, Adenovirus; ARI, acute respiratory infection; CI, confidence interval; EV, enterovirus; FEL, fixed effects likelihood; HBoV, human bocavirus; HMPV, human metapneumovirus; HPIV, human parainfluenza virus; HRV, human rhinovirus; IFEL, internal fixed effects likelihood; NJ, neighbour-joining; REL, random effects likelihood; RSV, respiratory syncytial virus; SLAC, single likelihood ancestor counting.The GenBank/EMBL/DDBJ accession numbers for the nucleotide sequences determined in this study are AB683188-AB683237. et al., 1999). RSV infection may cause major problems in infants ,1 year of age and can lead to life-threatening ARIs such as bronchiolitis and bronchopneumonia (Leung et al., 2005; Shay et al., 1999;Yorita et al., 2007). In addition, recent studies have shown that RSV infections may be associated with the initiation or exacerbation of asthma (Pérez-Yarza et al., 2007;Sigurs et al., 2000).The RSV genome encodes ten proteins (Peter & James, 2006). Among these, the attachment glycoprotein (G) is a major structural protein and may be associated with both infectivity and antigenicity (Anderson et al., 1985;Johnson et al., 1987;Rueda et al., 1991). Previous reports suggest that the amino acid sequences of the G protein show both conservative and hypervariable regions (Cane et al., 1991). The highly conserved region is mainly a receptor-binding region between aa 164 and 176, whilst the C-terminal 3rd hypervariable region is situated around positions 210-290 (Botosso et al., 2009). This region contains multiple epitopes for neutralizing antibodies (Palomo et al., 1991). Indeed, there may be a mass of sites under positive selection in this region. In addition, the G protein partially mimics a chemokine (CX3C) as well as fractalkine (a chemokine, CX3CL1) (Tripp et al., 2001). Thus, it is important to analyse the G protein to obtain a better understanding of the properties of RSV.Molecular epidemiological studies have shown that RSV can be classified into two phylogenetic subgroups, RSV-A and RSV-B (Mufson et al., 1985). The strains of subgroup A can be subclassified int...

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“…Analysis of differences in genomic sequences between virus strains has also confirmed both the existence of two distinct subtypes and the widest variation in the G gene (187)(188)(189)(190)(191)(192). For this reason genotyping of RSV strains has been based on partial or complete sequencing of G (190).…”

Section: Genetic Diversitymentioning

confidence: 94%

“…The second C-terminal hypervariable region (HVR2) is sufficient for distinguishing between subtypes and has thus been used by the majority of studies investigating RSV genetic diversity (190,(193)(194)(195)(196)(197)(198)(199)(200)(201)(202)(203)(204). More recently, whole genome sequencing has also been applied to RSV strains from various clinical settings (188,189,191,192), adding valuable information to our understanding of RSV evolution.…”

Section: Genetic Diversitymentioning

confidence: 99%

Viral/bacterial respiratory tract co-infections in children

Brealey¹

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Respiratory syncytial virus (RSV) is the most significant cause of paediatric acute respiratory infection (ARI). RSV and other respiratory viruses are commonly co-detected with potentially pathogenic bacteria, such as Streptococcus pneumoniae, in the upper airways of young children.While these bacteria are known to be carried asymptomatically, they are also capable of opportunistic infections. Interactions between RSV and S. pneumoniae have been demonstrated in both clinical and molecular studies. However, the clinical significance of these interactions remains debated, and the effect of clinically relevant strain variation in both virus and bacteria on these interactions is also unknown. This work aimed to better understand the role of S. pneumoniae colonisation during RSV infections.To determine the effect of RSV and S. pneumoniae co-detection on disease severity during ARI, molecular pathogen screening of nasopharyngeal samples was conducted in a cohort of young children under the age of two years presenting with ARI at the emergency department of the Royal Brisbane Children's Hospital, Australia. S. pneumoniae was co-detected in approximately 52% of RSV infections, and co-detection was associated with increased disease severity, suggesting that S. pneumoniae plays a pathogenic role in severe paediatric RSV infections.Having established a clinical role for S. pneumoniae during RSV infection, the dynamics of pneumococcal colonisation of the nasal cavity was investigated in the four weeks prior and subsequent to an RSV infection in a longitudinal birth cohort of Brisbane-based children.Approximately 33% of infants and young children with RSV infections were colonised by S. pneumoniae prior to the RSV detection, and strain characterisation of S. pneumoniae in the weeks immediately surrounding the viral infection suggested that any observed growth of S. pneumoniae during RSV infection arose from the pre-existing strain colonising the URT. In another 14% of RSV infections, S. pneumoniae was first detected during the virus infection, suggesting simultaneous acquisition of RSV and S. pneumoniae and possible co-transmission of the two pathogens.The results from the two paediatric cohorts suggested an interaction between RSV and S.pneumoniae that was advantageous to the bacteria. It was therefore hypothesised that the molecular mechanisms governing RSV and S. pneumoniae interactions might be pneumococcal strain-specific and stronger in strains frequently co-detected with RSV. Studies have shown that RSV can increase S. pneumoniae colonisation by enhancing pneumococcal adherence to airway epithelia, and virions iii can bind directly to the bacterium to form co-pathogen complexes. These interactions are in part mediated through the binding interactions between S. pneumoniae surface receptors and the RSV G surface glycoprotein. RSV G is highly variable, both antigenically and genetically, and is the main protein used to type RSV into subtypes A and B. The genetic variation of RSV G was characterised from nasophar...

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Whole Genome Sequencing and Evolutionary Analysis of Human Respiratory Syncytial Virus A and B from Milwaukee, WI 1998-2010

Cited by 60 publications

References 49 publications

The Comparative Genomics of Human Respiratory Syncytial Virus Subgroups A and B: Genetic Variability and Molecular Evolutionary Dynamics

The Comparative Genomics of Human Respiratory Syncytial Virus Subgroups A and B: Genetic Variability and Molecular Evolutionary Dynamics

Molecular epidemiology of the attachment glycoprotein (G) gene in respiratory syncytial virus in children with acute respiratory infection in Japan in 2009/2010

Viral/bacterial respiratory tract co-infections in children

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