Octomitus genotypes

Seabolt, Matthew H., Alderisio, Kerri A., Xiao, Lihua & Roellig, Dawn M., 2021, Prevalence and molecular characterization of novel species of the Diplomonad genus Octomitus (Diplomonadida: Giardiinae) from wildlife in a New York watershed, International Journal for Parasitology: Parasites and Wildlife 14, pp. 267-272 : 268-269

3.2. Octomitus genotypes in wildlife

Sequences of 74 PCR-positive specimens were aligned against the available reference sequence of Octomitus intestinalis ( Keeling and Brugerolle, 2006) for species and genotype determination. None of the sequences matched this reference with 100% nucleotide identity, thus they were designated as novel genotypes and named in sequential order by the host in which the genotype was first identified (e.g. opossum genotype I, II, etc.). Within Octomitus , the average nucleotide identity between non-redundant pairs of sequences was 97.00%, ranging from 95.74% to 99.86%, which equated to an average of 15 SNPs. Octomitus sequences shared an average identity of 80.8% (=35 SNPs) with the homologous region of Giardia . In total, 13 novel genotypes were identified and summarized in Table 2. Five genotypes (deer mouse genotypes I, II, and III; opossum genotypes I and II) were identified in at least two host species each, with the house mouse ( Mus musculus ), deer mice ( Peromyscus spp. ), opossum ( Didelphicus virginiana ), and eastern chipmunk ( Tamias striatus ) identified most commonly. The remaining genotypes were observed in a single host species. Some host species were found to host multiple unique genotypes of Octomitus , namely the house mouse (5 genotypes); deer mice (4 genotypes); opossum, eastern chipmunk, meadow voles (3 genotypes each); Norway rat and boreal red-backed vole (2 genotypes each). No samples were found to have

268

Host Total no. No. of Prevalence Genotypes (no.

of positive (%) positive)

samples samples

Rodents 200 63 31.5 Sciuridae 46 5 10.9

Sciurus 31 1 3.2 Opossum carolinensis genotype I (1) (eastern grey squirrel)

Sciurus vulgaris 2 0 0.0 (red squirrel)

Glaucomys 1 0 0.0 volans (southern flying squirrel)

Tamias striatus 7 3 42.9 Deer mouse (eastern genotype I (1), chipmunk) deer mouse genotype II (1),

deer mouse genotype III (1)

Marmota monax 5 1 20.0 Woodchuck (woodchuck) genotype (1) Castoridae 15 0 0.0

Castor 15 0 0.0 canadensis (beaver) Erethizontidae 4 0 0.0

Erethizon 4 0 0.0 dorsatum (North American porcupine) Muridae 33 13 39.4

Rattus 7 2 28.6 Rat genotype (1), norvegicus deer mouse ( Norway rat) genotype V (1)

Mus musculus 26 11 42.3 Mouse genotype I (house mouse) (1), mouse genotype II (6),

opossum genotype I (1),

deer mouse genotype I (1),

deer mouse genotype II (2) Zapodidae 1 0 0.0

Napaeozapus 1 0 0.0 insignis (woodland jumping mouse) Cricetidae 101 45 44.6

Peromyscus sp. 85 39 45.9 Deer mouse (deer and wood genotype I (22), mice) deer mouse genotype II (15),

deer mouse genotype III (1),

deer mouse genotype IV (1)

Myodes gapperi 5 2 40.0 Vole genotype I (boreal red- (1), Vole backed vole) genotype III (1)

Microtus 10 4 40.0 Vole genotype II pennsylvanicus (2), deer mouse (meadow vole) genotype I (1),

opossum genotype II (1)

Ondatrini 1 0 0.0 zibethicus (muskrat)

Carnivores 61 0 0.0

Mustela vison 6 0 0.0

(mink)

Mustela erminea 1 0 0.0

(ermine)

30 0 0.0

Table 1 (continued)

mixed genotypes, which would have appeared as double peaks or background signals in the sequence chromatograms.