The spatial and temporal dynamics of rabies in China

Abstract

Background and objectives: Recent years have seen a rapid increase in the number of rabies cases in China and an expansion in the geographic distribution of the virus. In spite of the seriousness of the outbreak and increasing number of fatalities, little is known about the phylogeography of the disease in China. In this study, we report an analysis of a set of Nucleocapsid sequences consisting of samples collected through the trial Chinese National Surveillance System as well as publicly available sequences. This sequence set represents the most comprehensive dataset from China to date, comprising 210 sequences (including 57 new samples) from 15 provinces and covering all epidemic regions. Using this dataset we investigated genetic diversity, patterns of distribution, and evolutionary history.

Results: Our analysis indicates that the rabies virus in China is primarily defined by two clades that exhibit distinct population subdivision and translocation patterns and that contributed to the epidemic in different ways. The younger clade originated around 1992 and has properties that closely match the observed spread of the recent epidemic. The older clade originated around 1960 and has a dispersion pattern that suggests it represents a strain associated with a previous outbreak that remained at low levels throughout the country and reemerged in the current epidemic.

Conclusions: Our findings provide new insight into factors associated with the recent epidemic and are relevant to determining an effective policy for controlling the virus.

Figure 1. Maximum likelihood tree of 211 RABV from China partial N gene sequences generated by PHYML.

Bootstrap values are indicated at the main nodes. Most sequences are contained in clade I and clade II. Underlined provinces are from the southwest, provinces with a line above the name are from the east. New isolates are marked with a blue diamond, human isolates are marked with a green cross. Clade I shows statistically significant geographic subdivision (see Table S4) according to east and southwest China with older sequences generally isolated from the southwest and sequences from the east only appearing in the younger subgroups. No such division appears in clade II. Subgroup II-A and II-C correspond to ferret badger samples (marked in red). A full list of sequences in each clade with background information is given in Table S1.

Figure 2. Distribution of human rabies cases in China from 2000–2007.

Points represent counties where human cases were reported.

Figure 3. Predicted translocation events for clade I and clade II.

Statistically significant (p<0.05) predicted translocation events for (a) clade I and (b) clade II. The left hand side of the figure shows the estimated BEAST tree for each clade. The branches are colored coded by location (see legend on right). For clarity, Shanghai, Zhejiang, Fujian, Anhui and Shandong are grouped together as they are bordering provinces and there are no migration events amongst them. The arrows at the bottom of the tree show the location of sequences with an ancestral sequence predicted to originate in Jiangsu (JS) province. The map on the right shows the translocation events predicted to originate from Jiangsu. These translocation events can also be seen in the marked region on the tree which, in contrast to other parts of the tree, contain multiple branches with two different colors. (b) map shows no clear centers for translocation, but a statistically significant translocation event is predicted for wildlife (ferret badger) from Jiangsu to Zhejiang province (dashed arrow on right of map).

Figure 4. UniFrac analysis of shared evolutionary history according to location.

First two principal components for UniFrac metric for (a) clade I and (b) clade II. Clade I shows a strong division between east and southwest provinces in China. The eastern provinces are closely grouped together, with the exception of Jiangsu province which is a source of multiple translocation events to southwestern provinces. Clade II shows no apparent geographical division.

Figure 5. Evolutionary and transmission history of clade I and clade II.

Bayesian skyline plots showing the evolutionary and transmission histories of a) clade I and b) clade II and their corresponding trees. (a) also shows the number of human rabies cases recorded by year (bottom) and (b) shows the skyline plot for clade I on the same time scale (insert bottom right). Clade I shows greater variation in genetic diversity compared to clade II. Although both clades show a drop in genetic diversity around 2003 ((a) blue arrow on left), this is not correlated to number of human cases as they were still increasing rapidly and didn't peak until 2007 (red arrow on right of (a)). However, the drop appears to coincide with the introduction of translocation events, (a) and (b) top, as at this time multiple events appear in the trees.