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Volume 12, Number 3—March 2006

Identifying and Quantifying Genotypes in Polyclonal Infections due to Single Species

James M. Colborn*, Ousmane Koita†, Ousmane Cissé†, Mamadou W. Bagayoko†, Edward J. Guthrie‡, and Donald J. Krogstad*Comments to Author 
Author affiliations: *Tulane University Health Sciences Center, New Orleans, Louisiana, USA; †University of Bamako, Bamako, Mali; ‡Agilent Technologies, Wilmington, Delaware, USA

Main Article

Table 4

Evidence for insertions, deletions, and repeats in human pathogens*

Pathogen Genomic site of variation Observed size variations Reference
Plasmodium falciparum Block 2 variable region of merozoite surface protein 1 (msp1), PCR 150–200 bp with multiple 9-bp insertions and deletions based on number of tripeptide repeats (14)
Dengue 3´ NCR after the NS5 stop codon 2–14 and 75-nt deletions, 4 copies of 8-nt imperfect repeat (16)
Yellow fever virus 3´ NCR 216-nt duplication, 40-nt deletion (repeat hairpin motif) (17)
HIV env gene 35- and 48-nt insertions, 21- and 36-nt deletions (18)
gp120 V3 and V4 loops 9- and 12-nt deletions (19)
Mycobacterium tuberculosis Novel IS6110 insertions† 36-bp DRs interspersed with variable spacers for DVRs (20)
VNTRs Repeating units of 53–79 bp with 16–17 copies (21)
Genomic deletions Based on genomic microarrays (21)
Bacillus anthracis MLVA† Variations of 12, 9, 18, 72, and 5 bp for MLVA markers vrrA, vrrB1, vrrB2, vrrC2, and CG3 (23)
Subtyping of 2001 bioterrorism organism All isolates were genotype 62 (24)
Yersinia pestis MLVA† with 25 markers for tandem repeat loci with 9–60 bp repeats of 3–36 units Amplicon sizes for complete alleles ranging from 119 to 786 bp (25)
Smallpox virus Coding regions of the viral genome Variable numbers of 9- and 21-bp repeats (n = 5–31 and 15–38, respectively), insertions of 32 and 464 bp and a 251-bp deletion (26)
Inverted terminal repeats between nonrepetitive elements 1 and 2 (NR1, NR2) 0–4 copies of a 69-bp sequence
Potential virulence proteins Smallpox inhibitor of complement enzymes, chemokine-binding protein II, and Z-DNA binding protein (27)

*PCR, polymerase chain reaction; NCR, noncoding region; DRs, direct repeats; DVRs, direct variant repeats; VNTRs, variable numbers tandem repeats; MLVA, multiple locus VNTR analysis; msp1, merozoite surface protein 1.
†Exists at multiple sites within the pathogen genome.

Main Article

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