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Title Molecular evolution of respiratory syncytial virus subgroup A genotypeNA1 and ON1 attachment glycoprotein (G) gene in central Vietnam
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Highlights:
Shifting patterns of RSV-A NA1 linages were observed in 2010 - 2012 seasons.
RSV-A ON1 lineage 1 with E262K appeared as the major genetic cluster in 2012.
Vietnamese RSV-A ON1 and NA1 were evolving with the faster substitution rates.
N-glycosylation patterns within G gene of Vietnamese NA1 shifted every year.
N-glycosylation pattern of Vietnamese NA1 and ON1 strains were distinct.
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Figures 1
Figure legend 2
Figure 1 (a) and (b). Phylogenetic trees of RSV-A ON1 / 2 (a) and NA1 (b) G gene 3
hypervariable region with Maximum Likelihood (ML) method 4
RSV-A strains from central Vietnam are indicated as the RED-colored line. Bootstrap values higher 5
than 70 were considered to be statistically significant and shown at each branch node. Scale bar 6
indicates nucleotide substitutions per site. 7
Figure 2. Time-scaled phylogenetic tree of RSV-A G gene hypervariable region with Bayesian 8
Markov Chain Monte Carlo (MCMC) 9
RSV-A strains from central Vietnams are indicated as the BLACK-filled objects. Uncertainties for 10
the year of divergences are indicated as 95% highest probability density (95%HPD) in the horizontal 11
light BLUE boxes at each branch point. Scale bar represents the unit of time (in year). 12
Figure 3. Time-scaled phylogenetic tree of RSV-A ON1 / 2 G gene hypervariable region with 13
Bayesian Markov Chain Monte Carlo (MCMC) 14
RSV-A strains from central Vietnam are indicated as “●” with the 4-digit strain specific ID numbers. 15
Uncertainties for the year of divergences are indicated as 95% highest probability density (95%HPD) 16
in the horizontal light BLUE boxes at each branch point. Scale bar represents the unit of time (in 17
year). 18
Figure 4. Phylodynamics of central Vietnam RSV-A strains G gene hypervariable region with 19
Bayesian Skyline Plot (BSP) 20
The Y-axis represents the effective population size, and the X-axis represents the generation time (in 21
year). The BLACK-solid line indicates the median effective population size, and the two light purple 22
lines present the range for 95% highest probability density (HPD). 23
24
2
Figure 1 (a) and (b). Phylogenetic trees of RSV-A ON1 / 2 (a) and NA1 (b) G gene hypervariable region with Maximum Likelihood (ML) 25
method 26
27
28
3
Figure 2. Time-scaled phylogenetic tree of RSV-A G gene hypervariable region with Bayesian 29
Markov Chain Monte Carlo (MCMC) 30
31
32 33
4
Figure 3. Time-scaled phylogenetic tree of RSV-A ON1 / 2 G gene hypervariable region with 34
Bayesian Markov Chain Monte Carlo (MCMC) 35
36
37
5
Figure 4. Phylodynamics of central Vietnam RSV-A strains G gene hypervariable region with 38
Bayesian Skyline Plot (BSP) 39
40
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Tables 1
Table 1. Summary demographic and clinical information of RSV-A paediatric ARI 2
hospitalization cases in central Vietnam 3
4
Year of sample collection (January 2010 - December 2012)
(Jan - Dec 2010) (Jan - Dec 2011) (Jan - Dec 2012)
Paediatric ARI cases (n) 542 513 797
RSV-A ARI cases (%) 66 (12.2%) 34 (6.6%) 169 (21.2%)
Genotype NA1 (n) 66 34 38
Genotype ON1 (n) 0 0 123
Demographic information Sex
Male (%) 310 (57.2%) 294 (57.3%) 448 (56.2%)
Female (%) 232 (42.8%) 219 (42.7%) 349 (43.8%)
Age (in month)a 17 (IQR: 8 - 27) 18 (IQR: 8 - 31) 15 (IQR: 7 - 25)
LRTI (%)c 99 (18.3%) 53 (10.3%) 246 (30.9%) a Data are presented in median (IQR (Interquartile Range): 1st - 3rd). b URTI: upper respiratory tract infection c LRTI: lower respiratory tract infection
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Table 2. Prevalence of RSV-A genotypes NA1 and ON1 lineages in central Vietnam during 2010 6
a Lineage proportion comparisons between years were performed with two-tailed Fisher's exact test. Values of p-value less than 0.05 were considered to be statistically significant and indicated as bold style. b NA1 lineage proportion comparison between (Jan - Dec 2010) and (Jan - Dec 2011). c NA1 lineage proportion comparison between (Jan - Dec 2011) and (Jan - Dec 2012).
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Table 3. RSV-A molecular evolutionary rate comparison between central Vietnam and global strains 10
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Study site / reference study RSV-A categorization (subgroup / genotype) Molecular evolution rate (substitutions/site/year) (95%HPD)a Year of divergence (95%HPD)a
Central Vietnam paediatric ARI surveillance Overall RSV-A (with global reference strains) 5.99 × 10-3 (5.00 × 10-3 - 7.03 × 10-3) 1954 (1951 - 1956)
(Yoshihara et al., 2016) Overall RSV-A (only from central Vietnam) (Jan 2010 - Dec 2012) 8.67 × 10-3 (6.27 × 10-3 - 1.16 × 10-2)b N/A
a 95%HPD stands for 95% highest probability density. b Mean molecular evolution rates comparison between overall RSV-A (only from central Vietnam) and RSV-A global reference strains. c Mean molecular evolution rates comparison between central Vietnam genotypes ON1 and ON1 global reference strains. d Mean molecular evolution rates comparison between central Vietnam genotypes NA1 and NA1 global reference strains.
Statistically significant values were indicated in bold style.
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Table 4. N-glycosylation pattern of central Vietnam RSV-A NA1 and ON1 G gene 13
hypervariable regions 14
15
RSV-A genotype(s) Genotype NA1 Genotype ON1
Year of sample collection (Overall) (Jan - Dec 2010) (Jan - Dec 2011) (Jan - Dec 2012) (Jan - Dec 2012)
Number of strains (n) (n=138) (n=66) (n=34) (n=36) (n=122)
p-valuea < 0.001b < 0.001c < 0.001d a Statistical analyses for the proportion comparison of N-glycosylation pattern between two independent groups were performed with two-tailed Fisher's exact test. Values of p-value less than 0.05 were considered to be statistically significant and indicated as bold style. b N-glycosylation pattern comparison between NA1 (Jan - Dec 2010) and NA1 (Jan - Dec 2011). c N-glycosylation pattern comparison between NA1 (Jan - Dec 2011) and NA1 (Jan - Dec 2012). d N-glycosylation pattern comparison between overall NA1 (Jan 2010 - Dec 2012) and ON1 (Jan 2012 - Dec 2012).
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Table 5. Positively selected amino acid substitution sites of central Vietnam RSV-A NA1 and 17
Genotype NA1 (Jan - Dec 2011) (No positive selection site detected)
(n=34) Genotype NA1 F250S * *
(Jan - Dec 2012) N273Y * * *
(n=38) I320T * * * *
Values of p-value less than 0.05 were considered to be statistically significant and indicated as the asterisk (*) a SLAC: Single Likelihood Ancestor Counting b FEL: Fixed Effects Likelihood
c IFEL: Internal Fixed Effects Likelihood
d MEME: Mixed Effects Model for Episodic Diversifying Selection