ALLELES WITHIN SEQUENCE TYPE T15

(edited March 2022)

Sequence type T15 was first identified by Hewett et al., 2003, using partial sequences of the 18S rRNA gene. The sequence type was found to be associated with the species Acanthamoeba jacobsi, which had been first isolated and described by Sawyer, Nerad and Visvesvara in 1992.  Full sequences of the 18S rRNA gene were not reported until 2017 (Corsaro et al., 2017).   The reason why full sequences were difficult to obtain may be related to the fact that a number of isolates of A. jacobsi are found to possess an intron in the latter half of the 18S rRNA gene.  

As of March 2022, 162 isolates assigned to genotype T15 had been identified in various studies using 18S rRNA gene sequences, with results deposited in the DNA databases.  Variation in the hypervariable stem 29.1 of the 18S rRNA gene has been examined in these sequences.  This provides a tally of alleles equivalent to those identified in sequence type T3, T4 and T11.

By 2019, 12 sequences had been identified that occur in more than a single isolate.  The alleles ranged in size from 62 to 87 nucleotides.  The sequence of the 12 alleles is given as:

The T15 allele sequences are available as a pdf file.

As can be seen, the alleles appear to fall into two groups, one associated with allele 15.01, including 8 of the alleles, while a second group is associated with alleles 15.02 and includes only three alleles.  The second group is greater in length, and is distinguished by the presence of four multi-nucleotide insertions compared to the first group.

The frequency with which the alleles occur among T15 sequences in the DNA databases is shown in the following table.

Only two of the alleles, 15/01 and 15/02, occur more than 10 times in the data.  It should be noted that, among the 9 sequences that contain “almost complete” 18S rRNA gene sequences from T15 isolates, only a single isolate (A. jacobsi isolate Pool-4-37, acc # KY513796) contains the 15/02 allele.  This is also the only “almost complete” isolate that contains the intron found in some T15 isolates.  Seven “almost complete” isolates have the 15/01 allele, while a single “almost complete” isolate (A. jacobsi strain AFR13, acc #MN153026) contains the 15/07 allele.

The table includes 132 of the 162 T15 sequences present in the DNA databases.  The remaining 30 sequences represent several types of sequence.  For 14 sequences, the DNA sequence of the isolate does not completely overlap the region in which alleles are defined.  Two isolates show clear indication that they represent sequences from a mixed sample of distinct isolates.  The remaining 14 sequences show unique sequences which may be true alleles, or may represent sequencing artifacts, but which occur only a single time in the DNA databases.