Alleles within sequence types T3 and T11

(updated March 2022)

Alleles within sequence type T3 had been described in only one publication (to our knowledge) until our recent review (Fuerst & Booton, 2020).   Alleles within sequence type T11 have never been described. 

We defined alleles within T3 during our study of isolates from water samples in Hong Kong (Booton et al. J. Clin. Micro. 2002).  As with alleles of sequence type T4, the alleles represent variability within the ASA.S1 subsequence of the 18S rRNA, specifically the primary nucleotide sequence of the variable region of segment DF3 (stem 29-1 of the Acanthamoeba 18S rRNA).

In our original study, we observed 5 alleles within sequence type T3.    As mentioned elsewhere in our discussion of alleles within T4, the results of our Hong Kong study were not an attempt to use the allele designations as a phylogenetic tool.  Rather, they are used simply as a means of categorizing the isolates observed in the study. 



There are (as of March 2022) 365 isolates whose 18S rRNA gene sequences have been categorized into sequence type T3.  The data set of T3 sequences has been examined to identify alleles that occurred more than once in this collection of sequences.  By January 2020, there were ten alleles that were identified in more than a single T3 isolate.  Since that time, 3 additional alleles have been seen in at least two isolates.  In addition, two of the alleles in our original study (alleles T3/02 and allele T3/05) have been observed only within the initial single isolates that we reported in the study of Hong Kong isolates of Acanthamoeba.  One additional allele (T3/06 ) occurred in the “almost complete” sequences from  isolates of A. pearcei  (Sawyer 205-1).  Two sequences of this isolate have been reported, representing the non-axenic (ATCC 50435) and axenic (ATCC 50436), versions of the isolate.

The 57 “almost complete” sequences identified as T3 (including the two duplicate sequences from A. pearcei strain 205-1), were examined to see if any of the allele sequence within the DF3 region of the gene used for allelic identification in any of these longer sequences had a unique variant sequence.  Only the almost complete sequences from A. pearcei  Sawyer 205-1  was unique.  Nine of the “almost complete sequences carried the T3/01 allele (including A. polyphaga Panola Mountain, ATCC 30487). Two of the “most complete isolates carried allele T3/03, while long sequences from 42 isolates carried allele T3/04. This latter group included A. griffini H37 (ATCC 50702).  Allele T3/11 was found in two “almost complete” sequences, including that from A. griffini S-7 (ATCC 30731).

The sequences of the 13 identified allele classes are given in the following:

Of the 18S rRNA sequences from 365 isolates of T3, 270 could be categorized into an allele class.  The remaining isolate sequences were not classified because they either: (1) did not completely overlap the region of the 18S rRNA sequence used to identify alleles, (2) had ambiguous nucleotides within the region, or (3) were partial 18S rRNA sequences that were classified as singletons in the allelic region. 

Four alleles (T3/01, T3/03, T3/04 and T3/12) are found frequently in the DNA databases.  The two isolates found carrying allele T3/11 were both “almost complete” sequences.  The frequency of the 13 allele classes (in July 2021) was:    




Isolates within sequence type T11 were not reported as part of studies described in previous reports.  This page was the first description of alleles of the DF3 region within the T11 sequence type, while we reported results through 2019 in our paper (Fuerst & Booton, 2020). 

As of March 2022, 197 isolates had been categorized into sequence type T11.   Examination of the dataset of T11 sequences identified 12 alleles that occurred more than once.  In addition, among the eleven “almost complete” sequences identified as T11, two isolates (A. stevensoni [AF019069, allele T11/05],  and A. sp. E13 [GU808311, allele T11/07]) each possessed a unique variant sequence that we have also designated as an allele.  Thus, 14 alleles are currently listed for T11.   The sequences of the alleles are given below:


Of the 197 isolates of T11, only 117 could be categorized into an allele class.  As previously noted, the sequences of the remaining isolates were not classified by allele because they either: (1) did not completely overlap the region of the 18S rRNA sequence used to identify alleles, (2) had ambiguous nucleotides in the region, or (3) were partial 18S rRNA sequences that were classified as singletons in the allelic region. 

Twelve T11 alleles occur more than once in the DNA databases.  However, unlike the distribution of alleles in sequence types T4 or T3, alleles in sequence type T11 show only slight evidence of a dominant allele or alleles, with six alleles occurring in 10-21 isolates, and only one allele exceeding 20 occurrences. 

Allele T11/01 occurs in two “almost complete” sequences, including A. hatchetti BH-2 (ATCC 30730,[AF019068] ), Allele T11/02 includes five of the “almost complete” sequences (including one “almost complete” sequences that was classified as belonging to the species A. hatchetii, isolate 4RE [AF251937].   Allele T11/06 occurs in three long sequences. Allele T11/11 occurs in 17 long sequences, while allele T11/12 occurs in 4 long sequences and allele T11/14 occur in 3 long isolates.  Single “almost complete” isolates are included in the counts for alleles T11/03, T11/05, T11/07, and T11/13. 

The frequency of isolates within the variouis allele classes (in March 2022) was:    



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