Abstract
Rift Valley fever virus (RVFV) is a vector-borne pathogen and is the most widely known virus in the genus Phlebovirus. Since it was first reported, RVFV has spread to western Africa, Egypt and Madagascar from its traditional endemic region, and infections continue to occur in new areas. In this study, we analyzed genomic patterns according to the infection properties of RVFV. Among the four segments of RVFV, the nucleotide composition, overall GC content and the difference of GC composition in the third position of the codons (%GC3) between groups were the largest in the S (NP) segment, showing that more diverse codons were used than in other segments. Furthermore, the results of CAI analysis of the S (NP) segment showed that viruses isolated from regions where no previous infections had been reported had the highest values, indicating greater adaptability to human hosts compared with other viruses. This result suggests that mutations in the S (NP) segment co-evolve with the infected hosts and may lead to expansion of the geographic range. The distinctive codon usage patterns observed in specific genomic regions of a group with similar infection properties may be related to the increasing likelihood of RVFV infections in new areas.
Highlights
Infection with Rift Valley fever virus (RVFV) was reported for the first time in China (Liu et al, 2017)
The RVFV sequences from Kenya and Sudan in 2007–2008 that were subjected to analysis were found to form a single group, and RVFV infection caused a considerable number of deaths in Kenya (155 deaths; case fatality rate 23%) and Sudan (230 deaths; case fatality rate 30.8%) (World Health Organiza-Figure 1 - Phylogenetic analysis of RVFV; (a) L segment, (b) M segment, (c) S segment, (d) S segment RVFVs were classified into five groups (Group 1: [pink triangle]; Group 2: [sky blue circle]; Group 3: [dark blue circle]; Group 4: [red circle]; Group 5: [light green triangle])
The genetic lineages (A~G) of RVFV have been classified by previous studies (Bird et al, 2007; Ikegami, 2012), the groups of RVFV in this study were re-classified based on the phylogenetic analysis for the collected sequences
Summary
Infection with Rift Valley fever virus (RVFV) was reported for the first time in China (Liu et al, 2017). RVFV infections were found mostly in parts of Africa such as Kenya, but infections are increasing outside the traditional endemic region, such as in the Middle East and Europe (Madani et al, 2003; Chevalier et al, 2010; Grobbelaar et al, 2011). This trend indicates that RVFV is highly likely to cause infections in new areas. We analyzed the infection properties of RVFV based on previously reported sequence information
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