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Evolutionary dynamics analysis of human metapneumovirus subtype A2: genetic evidence for its dominant epidemic.

Li J, Ren L, Guo L, Xiang Z, Paranhos-Baccalà G, Vernet G, Wang J - PLoS ONE (2012)

Bottom Line: Sequences of hMPV_A2b retrieved from GenBank boosted simultaneously with the two fusions respectively, indicating that fusion of genetic transmission routes from different regions improved survival of hMPV_A2.Epidemic and evolutionary dynamics of hMPV_A2b were similar to those of hMPV_A2.Overall, our findings provide important molecular insights into hMPV epidemics and viral variation, and explain the occurrence of an atypical epidemic of hMPV_A2, particularly hMPV_A2b.

View Article: PubMed Central - PubMed

Affiliation: MOH Key Laboratory of Systems Biology of Pathogens, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences (CAMS), Beijing, People's Republic of China.

ABSTRACT
Human metapneumovirus (hMPV) is a respiratory viral pathogen in children worldwide. hMPV is divided into four subtypes: hMPV_A1, hMPV_A2, hMPV_B1, and hMPV_B2. hMPV_A2 can be further divided into hMPV_A2a and A2b based on phylogenetic analysis. The typical prevalence pattern of hMPV involves a shift of the predominant subtype within one or two years. However, hMPV_A2, in particular hMPV_A2b, has circulated worldwide with a several years long term high epidemic. To study this distinct epidemic behavior of hMPV_A2, we analyzed 294 sequences of partial G genes of the virus from different countries. Molecular evolutionary data indicates that hMPV_A2 evolved toward heterogeneity faster than the other subtypes. Specifically, a bayesian skyline plot analysis revealed that hMPV_A2 has undergone a generally upward fluctuation since 1997, whereas the other subtypes experienced only one upward fluctuation. Although hMPV_A2 showed a lower value of mean dN/dS than the other subtypes, it had the largest number of positive selection sites. Meanwhile, various styles of mutation were observed in the mutation hotspots of hMPV_A2b. Bayesian phylogeography analysis also revealed two fusions of diffusion routes of hMPV_A2b in India (June 2006) and Beijing, China (June 2008). Sequences of hMPV_A2b retrieved from GenBank boosted simultaneously with the two fusions respectively, indicating that fusion of genetic transmission routes from different regions improved survival of hMPV_A2. Epidemic and evolutionary dynamics of hMPV_A2b were similar to those of hMPV_A2. Overall, our findings provide important molecular insights into hMPV epidemics and viral variation, and explain the occurrence of an atypical epidemic of hMPV_A2, particularly hMPV_A2b.

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Number of hMPV_A2b sequences deposited to GenBank from India and Beijing, China between 2004 and 2009.G and F gene sequences of hMPV_A2b collected from India and Beijing, China between 2004 and 2009 were retrieved from GenBank. All the G and F sequences were obtained from different isolates to avoid repetitive statistics. Genotyping of these sequences was based on the relative reports and confirmed by Neighbor-joining based phylogeny reconstruction as described previously (55).
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pone-0034544-g006: Number of hMPV_A2b sequences deposited to GenBank from India and Beijing, China between 2004 and 2009.G and F gene sequences of hMPV_A2b collected from India and Beijing, China between 2004 and 2009 were retrieved from GenBank. All the G and F sequences were obtained from different isolates to avoid repetitive statistics. Genotyping of these sequences was based on the relative reports and confirmed by Neighbor-joining based phylogeny reconstruction as described previously (55).

Mentions: To determine the mechanism behind the rise of hMPV_A2b in recent years, the spatial diffusion of the time-scaled genealogy of hMPV_A2b was traced using a recently developed BSSVS approach (Figure 5). By June 2002, hMPV_A2b had emerged in the Netherlands and spread to Canada, Japan, and Beijing, China. By June 2006, the spread routes from the Netherlands and Japan had joined in India, and another route from Canada to USA had emerged. By June 2008, hMPV_A2b had spread from USA to Beijing, China and joined the route from the Netherlands. Coincidently, hMPV_A2b sequences retrieved from GenBank boosted from India in 2006 and Beijing, China in 2008 (Figure 6, Table S3). The consistency between the phylogeographic data and the atypical epidemic of hMPV_A2 show that viral transmission plays an important role in the growth of the virus-infected population, which further explains the atypical epidemic of hMPV_A2b in recent years.


Evolutionary dynamics analysis of human metapneumovirus subtype A2: genetic evidence for its dominant epidemic.

Li J, Ren L, Guo L, Xiang Z, Paranhos-Baccalà G, Vernet G, Wang J - PLoS ONE (2012)

Number of hMPV_A2b sequences deposited to GenBank from India and Beijing, China between 2004 and 2009.G and F gene sequences of hMPV_A2b collected from India and Beijing, China between 2004 and 2009 were retrieved from GenBank. All the G and F sequences were obtained from different isolates to avoid repetitive statistics. Genotyping of these sequences was based on the relative reports and confirmed by Neighbor-joining based phylogeny reconstruction as described previously (55).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3316673&req=5

pone-0034544-g006: Number of hMPV_A2b sequences deposited to GenBank from India and Beijing, China between 2004 and 2009.G and F gene sequences of hMPV_A2b collected from India and Beijing, China between 2004 and 2009 were retrieved from GenBank. All the G and F sequences were obtained from different isolates to avoid repetitive statistics. Genotyping of these sequences was based on the relative reports and confirmed by Neighbor-joining based phylogeny reconstruction as described previously (55).
Mentions: To determine the mechanism behind the rise of hMPV_A2b in recent years, the spatial diffusion of the time-scaled genealogy of hMPV_A2b was traced using a recently developed BSSVS approach (Figure 5). By June 2002, hMPV_A2b had emerged in the Netherlands and spread to Canada, Japan, and Beijing, China. By June 2006, the spread routes from the Netherlands and Japan had joined in India, and another route from Canada to USA had emerged. By June 2008, hMPV_A2b had spread from USA to Beijing, China and joined the route from the Netherlands. Coincidently, hMPV_A2b sequences retrieved from GenBank boosted from India in 2006 and Beijing, China in 2008 (Figure 6, Table S3). The consistency between the phylogeographic data and the atypical epidemic of hMPV_A2 show that viral transmission plays an important role in the growth of the virus-infected population, which further explains the atypical epidemic of hMPV_A2b in recent years.

Bottom Line: Sequences of hMPV_A2b retrieved from GenBank boosted simultaneously with the two fusions respectively, indicating that fusion of genetic transmission routes from different regions improved survival of hMPV_A2.Epidemic and evolutionary dynamics of hMPV_A2b were similar to those of hMPV_A2.Overall, our findings provide important molecular insights into hMPV epidemics and viral variation, and explain the occurrence of an atypical epidemic of hMPV_A2, particularly hMPV_A2b.

View Article: PubMed Central - PubMed

Affiliation: MOH Key Laboratory of Systems Biology of Pathogens, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Peking Union Medical College (PUMC) & Chinese Academy of Medical Sciences (CAMS), Beijing, People's Republic of China.

ABSTRACT
Human metapneumovirus (hMPV) is a respiratory viral pathogen in children worldwide. hMPV is divided into four subtypes: hMPV_A1, hMPV_A2, hMPV_B1, and hMPV_B2. hMPV_A2 can be further divided into hMPV_A2a and A2b based on phylogenetic analysis. The typical prevalence pattern of hMPV involves a shift of the predominant subtype within one or two years. However, hMPV_A2, in particular hMPV_A2b, has circulated worldwide with a several years long term high epidemic. To study this distinct epidemic behavior of hMPV_A2, we analyzed 294 sequences of partial G genes of the virus from different countries. Molecular evolutionary data indicates that hMPV_A2 evolved toward heterogeneity faster than the other subtypes. Specifically, a bayesian skyline plot analysis revealed that hMPV_A2 has undergone a generally upward fluctuation since 1997, whereas the other subtypes experienced only one upward fluctuation. Although hMPV_A2 showed a lower value of mean dN/dS than the other subtypes, it had the largest number of positive selection sites. Meanwhile, various styles of mutation were observed in the mutation hotspots of hMPV_A2b. Bayesian phylogeography analysis also revealed two fusions of diffusion routes of hMPV_A2b in India (June 2006) and Beijing, China (June 2008). Sequences of hMPV_A2b retrieved from GenBank boosted simultaneously with the two fusions respectively, indicating that fusion of genetic transmission routes from different regions improved survival of hMPV_A2. Epidemic and evolutionary dynamics of hMPV_A2b were similar to those of hMPV_A2. Overall, our findings provide important molecular insights into hMPV epidemics and viral variation, and explain the occurrence of an atypical epidemic of hMPV_A2, particularly hMPV_A2b.

Show MeSH
Related in: MedlinePlus