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Reassortment and distinct evolutionary dynamics of Rift Valley Fever virus genomic segments.

Freire CC, Iamarino A, Soumaré PO, Faye O, Sall AA, Zanotto PM - Sci Rep (2015)

Bottom Line: Moreover, we also found that despite similar selection regimens, the three segments have distinct evolutionary dynamics; the longer segment L evolves at a significant lower rate.Episodes of discordance between population size estimates per segment also coincided with reassortment dating.Our results show that RVFV segments are decoupled enough to have distinct demographic histories and to evolve under different molecular rates.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil.

ABSTRACT
Rift Valley Fever virus (RVFV) is a member of Bunyaviridae family that causes a febrile disease affecting mainly ruminants and occasionally humans in Africa, with symptoms that range from mid to severe. RVFV has a tri-segmented ssRNA genome that permits reassortment and could generate more virulent strains. In this study, we reveal the importance of reassortment for RVFV evolution using viral gene genealogy inference and phylodynamics. We uncovered seven events of reassortment that originated RVFV lineages with discordant origins among segments. Moreover, we also found that despite similar selection regimens, the three segments have distinct evolutionary dynamics; the longer segment L evolves at a significant lower rate. Episodes of discordance between population size estimates per segment also coincided with reassortment dating. Our results show that RVFV segments are decoupled enough to have distinct demographic histories and to evolve under different molecular rates.

No MeSH data available.


Related in: MedlinePlus

Reassortments revealed by the incongruities among phylogenies for RVFV segments.a) Reassortments between L and M segments. b) Reassortments between M and S segments. Pairs of reassortant taxa are show in colors specific to the reassortant pair. The order of taxa is the same between each pair of trees. Parental strains can be observed in Figure S1. Only reassortant taxon names are shown for clarity. Reconciled, parallel trees, showing reassortants, including all taxon names are shown in Figure S1.
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f1: Reassortments revealed by the incongruities among phylogenies for RVFV segments.a) Reassortments between L and M segments. b) Reassortments between M and S segments. Pairs of reassortant taxa are show in colors specific to the reassortant pair. The order of taxa is the same between each pair of trees. Parental strains can be observed in Figure S1. Only reassortant taxon names are shown for clarity. Reconciled, parallel trees, showing reassortants, including all taxon names are shown in Figure S1.

Mentions: We analyzed the posterior set of trees (PST) generated during independent phylodynamic Monte Carlo Markov Chain (MCMC) runs for all segments and identified two RVFV lineages with discordant phylogenetic histories for M and for L and S segments. Our results confirmed previous findings that the Kenyan bovine isolate 2007000608 was formed via reassortment of M segments22 (Table 1 and green taxon labels in Fig. 1). Furthermore, we observed a new reassortment event in the Tanzanian lineage TANTan00107 (Table 1 and red taxon labels in Fig. 1), sampled from a human source. Since TANTan00107 was used in concatenated datasets19, this finding demonstrates the importance of checking genome sequences with recombination and reassortment detection programs such as RDP423 and GiRaF20, respectively, to prevent systematic errors during phylogenetic inferences. Moreover, we investigated the occurrence of reassortment between pairs of segments (L and M, L and S, M and S), using the largest datasets (Fig. 1 and Table 1). We found no additional reassortants between the L and the other two segments. However, we were able to detect five additional new reassortants between M and S segments (Fig. 1B and Table 1). Three of these reassortant lineages (76370, SA75 and 3574), isolated in Zimbabwe and South Africa in human, cattle and sheep (Table 1), form a highly supported reassortant cluster that reappears in independent phylogenies for both the M and S segments (orange, purple and blue taxon labels in Fig. 1B). The other two reassortants were from Mauritania (211HMMRRO1987 and 11ANMMRHG1998, pink and cyan taxon labels in Fig. 1B), and were isolated from human and sheep, respectively (Table 1). The parental relationships can be accessed in Figure S1.


Reassortment and distinct evolutionary dynamics of Rift Valley Fever virus genomic segments.

Freire CC, Iamarino A, Soumaré PO, Faye O, Sall AA, Zanotto PM - Sci Rep (2015)

Reassortments revealed by the incongruities among phylogenies for RVFV segments.a) Reassortments between L and M segments. b) Reassortments between M and S segments. Pairs of reassortant taxa are show in colors specific to the reassortant pair. The order of taxa is the same between each pair of trees. Parental strains can be observed in Figure S1. Only reassortant taxon names are shown for clarity. Reconciled, parallel trees, showing reassortants, including all taxon names are shown in Figure S1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4477411&req=5

f1: Reassortments revealed by the incongruities among phylogenies for RVFV segments.a) Reassortments between L and M segments. b) Reassortments between M and S segments. Pairs of reassortant taxa are show in colors specific to the reassortant pair. The order of taxa is the same between each pair of trees. Parental strains can be observed in Figure S1. Only reassortant taxon names are shown for clarity. Reconciled, parallel trees, showing reassortants, including all taxon names are shown in Figure S1.
Mentions: We analyzed the posterior set of trees (PST) generated during independent phylodynamic Monte Carlo Markov Chain (MCMC) runs for all segments and identified two RVFV lineages with discordant phylogenetic histories for M and for L and S segments. Our results confirmed previous findings that the Kenyan bovine isolate 2007000608 was formed via reassortment of M segments22 (Table 1 and green taxon labels in Fig. 1). Furthermore, we observed a new reassortment event in the Tanzanian lineage TANTan00107 (Table 1 and red taxon labels in Fig. 1), sampled from a human source. Since TANTan00107 was used in concatenated datasets19, this finding demonstrates the importance of checking genome sequences with recombination and reassortment detection programs such as RDP423 and GiRaF20, respectively, to prevent systematic errors during phylogenetic inferences. Moreover, we investigated the occurrence of reassortment between pairs of segments (L and M, L and S, M and S), using the largest datasets (Fig. 1 and Table 1). We found no additional reassortants between the L and the other two segments. However, we were able to detect five additional new reassortants between M and S segments (Fig. 1B and Table 1). Three of these reassortant lineages (76370, SA75 and 3574), isolated in Zimbabwe and South Africa in human, cattle and sheep (Table 1), form a highly supported reassortant cluster that reappears in independent phylogenies for both the M and S segments (orange, purple and blue taxon labels in Fig. 1B). The other two reassortants were from Mauritania (211HMMRRO1987 and 11ANMMRHG1998, pink and cyan taxon labels in Fig. 1B), and were isolated from human and sheep, respectively (Table 1). The parental relationships can be accessed in Figure S1.

Bottom Line: Moreover, we also found that despite similar selection regimens, the three segments have distinct evolutionary dynamics; the longer segment L evolves at a significant lower rate.Episodes of discordance between population size estimates per segment also coincided with reassortment dating.Our results show that RVFV segments are decoupled enough to have distinct demographic histories and to evolve under different molecular rates.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil.

ABSTRACT
Rift Valley Fever virus (RVFV) is a member of Bunyaviridae family that causes a febrile disease affecting mainly ruminants and occasionally humans in Africa, with symptoms that range from mid to severe. RVFV has a tri-segmented ssRNA genome that permits reassortment and could generate more virulent strains. In this study, we reveal the importance of reassortment for RVFV evolution using viral gene genealogy inference and phylodynamics. We uncovered seven events of reassortment that originated RVFV lineages with discordant origins among segments. Moreover, we also found that despite similar selection regimens, the three segments have distinct evolutionary dynamics; the longer segment L evolves at a significant lower rate. Episodes of discordance between population size estimates per segment also coincided with reassortment dating. Our results show that RVFV segments are decoupled enough to have distinct demographic histories and to evolve under different molecular rates.

No MeSH data available.


Related in: MedlinePlus