DNA samples from 74 patients with non-malarial acute febrile illness (AFI), 282 rodents, 100 cattle, 56 dogs and 160 Rhipicephalus sanguineus ticks were screened for the presence of Anaplasma phagocytophilum DNA using a quantitative PCR (qPCR) assay targeting the msp2 gene. The test detected both A. phagocytophilum and Anaplasma sp. SA/ZAM dog DNA. Microbiome sequencing confirmed the presence of low levels of A. phagocytophilum DNA in the blood of rodents, dogs and cattle, while high levels of A. platys and Anaplasma sp. SA/ZAM dog were detected in dogs. Directed sequencing of the 16S rRNA and gltA genes in selected samples revealed the presence of A. phagocytophilum DNA in humans, dogs and rodents and highlighted its importance as a possible contributing cause of AFI in South Africa. A number of recently described Anaplasma species and A. platys were also detected in the study. Phylogenetic analyses grouped Anaplasma sp. SA/ZAM dog into a distinct clade, with sufficient divergence from other Anaplasma species to warrant classification as a separate species. Until appropriate type-material can be deposited and the species is formally described, we will refer to this novel organism as Anaplasma sp. SA dog.
Supplementary Materials: Table S1: List of rodent species captured from the three habitat areas, Table S2: Origin and list of samples on
which circular consensus sequencing (CCS) and multilocus gene sequencing were performed, Table S3: GenBank
accession numbers of sequences used in the phylogenetic analysis of the Anaplasma species, Table S4: Sample
information for the 16S rRNA, gltA, msp4 and ankA sequences generated in this study, Figure S1: Alignment of
msp2 sequences from A. platys and A. phagocytophilum, Figure S2: Representative rarefaction curves from samples
tested, Figure S3: Alignment of msp4 sequences from several species of Anaplasma, Figure S4: Alignment of ankA
sequences from a few Anaplasma species showing the region that was amplified in this study.