Dispersal history of Miniopterus fuliginosus bats and their associated viruses in east Asia

Abstract

In this study, we examined the role of the eastern bent-winged bat (Miniopterus fuliginosus) in the dispersion of bat adenovirus and bat alphacoronavirus in east Asia, considering their gene flows and divergence times (based on deep-sequencing data), using bat fecal guano samples. Bats in China moved to Jeju Island and/or Taiwan in the last 20,000 years via the Korean Peninsula and/or Japan. The phylogenies of host mitochondrial D-loop DNA was not significantly congruent with those of bat adenovirus (m2XY = 0.07, p = 0.08), and bat alphacoronavirus (m2XY = 0.48, p = 0.20). We estimate that the first divergence time of bats carrying bat adenovirus in five caves studied (designated as K1, K2, JJ, N2, and F3) occurred approximately 3.17 million years ago. In contrast, the first divergence time of bat adenovirus among bats in the 5 caves was estimated to be approximately 224.32 years ago. The first divergence time of bats in caves CH, JJ, WY, N2, F1, F2, and F3 harboring bat alphacoronavirus was estimated to be 1.59 million years ago. The first divergence time of bat alphacoronavirus among the 7 caves was estimated to be approximately 2,596.92 years ago. The origin of bat adenovirus remains unclear, whereas our findings suggest that bat alphacoronavirus originated in Japan. Surprisingly, bat adenovirus and bat alphacoronavirus appeared to diverge substantially over the last 100 years, even though our gene-flow data indicate that the eastern bent-winged bat serves as an important natural reservoir of both viruses.

Fig 1. Sampling locations of 11 populations of M. fuliginosus in east Asia.

The abbreviations of each sampling location are referred to Table 1.

Fig 2. Gene flows among the populations of M. fuliginosus in east Asia.

The gene flows were estimated, based on the D-loop amplicon-sequencing results, determined by analysis with Migrate-n software. The arrowheads on the lines show the directions of gene flows and the numbers near the arrowheads are the relative values of the gene flows (×10³).

Fig 3. Gene flows among populations of M. fuliginosus bats in Japan (Wakayama, Nara, Fukui prefecture).

The gene flows were estimated based on the D-loop amplicon sequencing results and subsequent analysis with Migrate-n software. The arrowheads on the lines show the directions of gene flow and the numbers near the arrowheads are the relative values of the gene flows (×10³).

Fig 4. Congruence of phylogenetic patterns between M. fuliginosus and the related viruses.

Comparison of population phylogenetic trees of A) M. fuliginosus and bat alphaCoV, and B) M. fuliginosus and BtAdV. Procrustean superimposition plots of C) M. fuliginosus and bat alphaCoV, and D) M. fuliginosus and BtAdV produced using PACo. D-loop of M. fuliginosus in each population are represented in blue color. Bat alphaCoV and BtAdV populations are represented in red color and green color, respectively.

Fig 5. Divergence-time estimation of BtAdV based on the nucleotide-substitution rate per site per year of the hexon gene of HAdV-7.

The time-scaled phylogenetic tree summarizes all MCMC phylogenies of the hexon gene data set, analyzed under HKY+G and Coalescent constant size models in BEAST software, version 2.6.0. The number at each node indicates the divergence time (years ago).

Fig 6. Divergence-time estimation of bat alphaCoV based on the nucleotide-substitution rate per site per year of the RdRp gene of coronavirus.

The time-scaled phylogenetic tree summarizes all MCMC phylogenies of the RdRp gene data set, analyzed under HKY+G and Coalescent constant size models in BEAST software, version 2.6.0. The number at each node indicates the divergence time (years ago).