| Summary: | A novel <i>Borrelia</i> species, <i>Candidatus Borrelia javanense</i>, was found in ectoparasite ticks, <i>Amblyomma javanense</i>, from <i>Manis javanica</i> pangolins seized in anti-smuggling operations in southern China. Overall, 12 tick samples in 227 (overall prevalence 5.3%) were positive for <i>Candidatus B. javanense</i>, 9 (5.1%) in 176 males, and 3 (5.9%) in 51 females. The phylogenetic analysis, based on the 16S rRNA gene and the flagellin gene sequences of the <i>Borrelia</i> sp., exhibited strong evidence that <i>Candidatus B. javanense</i> did not belong to the Lyme disease <i>Borrelia</i> group and the relapsing fever <i>Borrelia</i> group but another lineage of <i>Borrelia</i>. The discovery of the novel <i>Borrelia</i> species suggests that <i>A. javanense</i> may be the transmit vector, and the <i>M. javanica</i> pangolins should be considered a possible origin reservoir in the natural circulation of these new pathogens. To our knowledge, this is the first identification of a novel <i>Borrelia</i> species agent in <i>A. javanense</i> from pangolins. Whether the novel agent is pathogenic to humans is unknown and needs further research.
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