In Table 2, the sequence information for the Nichols and Mexico A strains at nucleotide position 2,388 of the tp92 gene was inadvertently switched. The correct sequence at this position is as follows: a deletion in Mexico A and an A in Nichols. Please see the corrected Table 2 here.
Table 2. Table of polymorphisms included in phylogenetic analysis.
| T. pallidum subspecies | Straina | deoD | gpd | tp92 | tprI | cfpA | tpF-1 | |||||||||||||||||||
| endemicum | Bosnia | T | T | A | G | C | C | T | T | G | T | A | C | C | C | G | T | C | G | T | G | A | C | A | G | G |
| Iraq | T | T | A | G | C | C | T | T | G | T | A | C | C | C | G | T | C | G | T | G | A | C | A | G | G | |
| pertenue | Brazzaville | T | T | A | G | C | C | C | T | G | T | A | C | - | C | G | T | C | A | T | G | A | C | A | G | G |
| CDC1 | T | T | A | G | C | C | T | T | G | T | A | C | - | C | A | T | C | A | T | A | A | C | A | G | G | |
| CDC2 | T | T | A | G | C | C | T | T | G | T | A | C | - | C | G | T | C | A | T | G | A | C | A | G | G | |
| CDC2575 | T | T | A | G | C | C | T | T | G | T | A | C | - | C | A | T | C | A | T | A | A | C | A | G | G | |
| Gauthier | T | T | A | G | C | C | C | T | G | T | A | C | - | C | G | T | C | A | T | G | A | C | A | G | G | |
| Ghana | T | T | A | G | C | C | T | T | G | T | A | C | - | C | A | T | C | A | T | A | A | C | A | G | G | |
| Pariaman | T | T | A | G | C | A | T | T | G | T | A | C | - | C | G | T | C | A | T | G | A | C | A | G | G | |
| Samoa D | T | T | A | G | C | C | T | T | G | T | A | C | - | C | G | T | C | A | T | G | A | C | A | G | G | |
| Samoa F | T | T | A | G | C | C | T | T | G | T | A | C | - | C | G | T | C | A | T | G | A | C | A | G | G | |
| pallidum | Chicago B | T | C | A | A | C | C | T | T | G | T | A | C | A | C | G | T | C | G | G | A | A | C | G | G | A |
| Dallas | T | C | A | A | C | C | T | T | G | T | A | C | A | C | G | T | C | G | G | A | G | C | G | G | A | |
| Grady | T | C | A | A | C | C | T | G | G | T | A | C | C | C | G | T | C | G | G | A | A | C | G | G | A | |
| Haiti B | T | C | A | A | T | C | T | T | G | T | A | C | C | C | G | T | C | G | G | A | A | C | G | G | A | |
| Madras | T | C | A | A | C | C | T | T | G | T | A | C | A | C | G | T | C | G | G | A | G | C | G | G | A | |
| Mexico A | T | C | A | A | C | C | T | G | G | T | A | C | - | C | G | T | C | G | G | A | A | C | G | G | A | |
| Nichols | T | C | A | A | C | C | T | T | G | T | A | C | A | C | G | T | C | G | G | A | G | C | G | G | A | |
| Philadelphia 1 | T | C | A | A | C | C | T | G | G | T | A | C | C | C | G | T | C | G | G | A | A | C | G | G | A | |
| South Africa | T | C | A | A | C | C | T | G | G | T | A | C | - | C | G | T | C | G | G | A | A | C | G | G | A | |
| N/A | TPC A | C | T | G | G | C | C | T | T | A | T | A | C | - | - | G | C | T | - | - | - | A | T | A | A | G |
| N/A | TPC H | C | T | G | G | C | C | T | T | A | C | A | G | - | - | G | C | T | - | - | - | A | T | A | A | G |
| N/A | TPC M | C | T | G | G | C | C | T | T | A | T | A | G | - | - | G | C | T | - | - | - | A | T | A | A | G |
| N/A | Baboon: SNP | C | T | A | G | C | C | T | T | G | T | A | C | - | C | G | T | C | A | T | G | A | C | A | A | G |
| N/A | Baboon: LMNP | T | T | A | G | C | C | T | T | G | T | G | C | - | C | G | T | C | A | T | A | A | C | A | G | G |
| N/A | Baboon: Guinea | T | T | A | G | C | C | T | T | G | T | A | C | - | C | G | T | C | A | T | G | A | C | A | A | G |
| Synonymous or Nonsynonymous Substitution | S | S | S | S | N | N | N | N | S | N | N | N | N/D b | D | N | N | S | N | N | N | N | S | S | S | N | |
| Nucleotide Residue | 744 | 759 | 459 | 579 | 1592 | 1964 | 1966 | 1967 | 2010 | 2101 | 2209 | 2326 | 2388 | 2382-2399 | 2405 | 2408 | 2421 | 137 | 143 | 151 | 92 | 121 | 303 | 117 | 122 |
TPC = Treponema paraluiscuniculi (agent that causes rabbit syphilis); SNP = Serengeti National Park; LMNP = Lake Manyara National Park
Deletion from nucleotide residues 2384-2
The incorrect information in Table 2 was used to create the phylogenetic tree in Figure 2. Please see the corrected Figure 2 here.
Figure 2: A phylogeny demonstrates that T. pallidum strains infecting baboons in Serengeti National Park and Lake Manyara National Park are genetically distinct from one another.
Phylogenies were constructed using both Maximum Parsimony and Maximum Likelihood methods to analyze 25 polymorphisms in six concatenated regions of the Treponema genome. The phylogenies were congruent and a Maximum Parsimony tree was chosen for display, with bootstrap support displayed at all nodes that received greater than 50% using both methods.
The authors' explanation of the changes can be viewed on the Comments tab of the article page.
Reference
- 1. Harper KN, Fyumagwa RD, Hoare R, Wambura PN, Coppenhaver DH, et al. (2012) Treponema pallidum Infection in the Wild Baboons of East Africa: Distribution and Genetic Characterization of the Strains Responsible. PLoS ONE 7(12): e50882 doi:10.1371/journal.pone.0050882 [DOI] [PMC free article] [PubMed] [Google Scholar]