(updated March 2022)
Sequence types T2 and T6 are the most closely related pair of sequence types within Acanthamoeba. We have previously argued that together the two sequence types should be considered a supergroup (Fuerst, Booton & Crary. 2014; Fuerst. 2014). This is because many isolates fall intermediate between the two types to form a total of five subtypes: T2, T2/6A, T2/6B, T2/6C and T6. More than 420 isolates in the DNA databases are assigned to one of the subtypes.
Alleles within the T2/6 supergroup were first described at the 2019 FLAM meeting (Fuerst and Booton, 2020). They occur in the same portion of the 18S rRNA gene sequence that was used to define alleles in T3, T4, T11 and T15. Only 198 isolates have sequences that completely overlap the DF3 region containing the allele segment, while 201 sequence do not overlap the complete allele region. Examination of sequences from all the isolates with completely overlapping allele sequences resulted in an interesting finding. Alleles that occur a specific subtype are not observed in any of the remaining subbtypes. This is similar to the finding of alleles restricted to subtype within sequence type T4.
The frequencies of isolates assigned to the various subgroups based on complete or partial sequences of the 18S rRNA genes is given on the following table. Isolates that fall into the two original sequence types, T2 and T6, represent 59% of the isolates assigned into the supergroup.
The allele sequences and their frequencies within the five subtypes are:
Among T2 isolates, 59 of 136 isolates can be classified to one of 9 alleles that are shared between at least two isolates. An additional 4 isolates have alleles that are unique within the databases. Three of the alleles account for more than 55% of T2 isolates that could be assigned to alleles, as shown below. There are 16 isolates assigned to type T2 that have “almost complete” 18S rRNA gene sequences. Each of these 16 isolates contained an allele that is classified as shared, with 12 sequences assigned to allele T2/01, one assigned to allele T2/02, four assigned to T2/03, and a single isolate carrying allele T2/05. The sequences of the nine T2 alleles shared by at least two isolates are:
The frequency of isolates within the nine T2 alleles in July 2021 was:
The sequences of only 13 of the 41 isolates assigned to subgroup T2/6A completely overlap the allele region. Of these only 9 isolates contain alleles that are shared with another isolate. Four isolates in this subgroup contain “almost complete” sequences. One of these carried allele T26a/01, while two long isolates carried allele T25a/04, and the fourth carried an unique allele. The sequences and the frequencies of the alleles are given below:
In contrast to the isolates assigned to subgroup T2/6A, most isolates (26 of 30) assigned into subgroup T2/6B contained sequences that completely overlap the allele region. 17 isolates contained one of the four shared alleles. Among the isolates carried a shared allele were all 11 of the isolates with “almost complete” sequences. Alleles T26B/01 and T26B/03 each were found in two of these long isolates, while allele T26B/02 occurred in 7 longisolates. No long isolate had a unique allele.
This subtype showed a similar pattern to T2/6A, in that a large proportion of the isolates (78 of 107) assigned to this subgroup did not have sequences that completely overlapped the allele region. Four shared alleles were found among 24 of the remaining 29 isolates with sequences and frequencies shown below. Four isolates placed into subtype T2/6C contained “almost complete” sequences. One of these carried a unique allele, while one carried allele T26c/01 and two others carried allele T26c/02.
More than two-thirds of T6 isolates (71 of 109) contain sequences that overlap the allele region and 60% of these contain one of the seven shared alleles. One allele (T6/02) is shared by appreciably more isolates than other alleles. It should be noted that allele T6/02 has been found in studies of isolates from Taiwan, Iran and Brazil. Another interesting observation concerning alleles within the T6 subtype is that none of the seven isolates for which “almost complete” 18S rRNA gene sequences have been obtained contains any of the shared alleles, and all have unambiguous “unique” allele sequences. sequences and frequencies of alleles within the T6 subtype are: