Extense variant gene family repertoire overlap in Western Amazon Plasmodium falciparum isolates

Albrecht, Letusa; Merino, Emilio F.; Hoffmann, Érika Hellena Esther; Ferreira, Marcelo Urbano; Ferreira, Ricardo Rodrigues; Osakabe, Ana Lúcia; Martha, Rosimeire Cristina Dalla; Ramharter, Michael; Durham, Alan Mitchell; Ferreira, João Eduardo; Portillo, Hernando A. del; Wunderlich, Gerd

doi:10.1016/j.molbiopara.2006.07.007

Cited by 37 publications

(51 citation statements)

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“…Accordingly, previous reports showed that the var repertoire is virtually unlimited in Southeast Asian or Kenyan isolates (Barry et al, 2007). In contrast, we (Albrecht et al, 2006) and others (Barry et al, 2007) have shown that in distinct geographic areas and/or times of sample collection the var repertoire may be limited to a certain extent. In order to expand the previous finding of a limited var gene repertoire in Brazilian isolates independently from the year of collection or geographic origin, we analyzed exhaustively the genomic var gene repertoires in isolates from all over Brazil and included the public sequence data from the HB3 strain from Honduras, the Brazilian strain 7G8, collected in the early 1980s, three Venezuelan strains and compared the data against var DBLα sequences available in GenBank.…”

Section: Introductionmentioning

confidence: 60%

“…For the amplification of the 360-420 bp var DBLα tags the previously published degenerated var oligonucleotides (Taylor et al, 2000a;Peters et al, 2002) were used. These oligonucleotides were previously tested on genomic P. falciparum DNA from Brazilian isolates and did not result in significantly biased amplification of determined var tags (Albrecht et al, 2006). Amplified products were separated in TAE agarose gels, excised and purified by the modified glassmilk method (Boyle and Lew, 1995) and ligated in pTZ57-T (Fermentas).…”

Section: Nucleic Acid Extraction Pcr and Sequencingmentioning

confidence: 99%

“…The remaining sequences were either published by us (Albrecht et al, 2006) or sequenced herein (Supplemental Table S1). The complete list of GenBank entries can be found in Supplemental Table 2 and the dataset of different tags sequenced in this work and the previous work of Albrecht et al (2006) is in Supplemental File 1.…”

Section: Origin Of Published Sequencesmentioning

confidence: 99%

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The South American Plasmodium falciparum var gene repertoire is limited, highly shared and possibly lacks several antigenic types

Albrecht

Castiñeiras

Carvalho

et al. 2010

Gene

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The Plasmodium falciparum var gene family encodes large variant antigens, which are important virulence factors, and also targets of the humoral host response. The frequently observed mild outcomes of falciparum malaria in many places of the Amazon area prompted us to ask whether a globally restricted variant (var) gene repertoire is present in currently circulating and older isolates of this area. By exhaustive analysis of var gene tags from 89 isolates and clones taken during many years from all over the Brazilian Amazon, we estimate that there are probably no more than 350-430 distinct sequence types, less than for any similar sized area studied so far. Detailed analysis of the var tags from genetically distinct clones obtained from single isolates revealed restricted and redundant repertoires suggesting either a low incidence of infective bites or restricted variant gene diversity in inoculated parasites. Additionally, we found a structuring of var gene repertoires observed as a higher pairwise typing sharing in isolates from the same microregion compared to isolates from different regions. Fine analysis of translated var tags revealed that certain Distinct Sequence Identifiers (DSIDs) were differently represented in Brazilian/South American isolates when compared to datasets from other continents. By global alignment of worldwide var DBLalpha sequences and sorting in groups with more than 76% identity, 125 clusters were formed and more than half of all genes were found in nine clusters with 50 or more sequences. While Brazilian/South American sequences were represented only in 64 groups, African sequences were found in the majority of clusters. DSID type 1 related sequences accumulated almost completely in one single cluster, indicating that limited recombination occurs in these specific var gene types. These data demonstrate the so far highest pairwise type sharing values for the var gene family in isolates from all over an entire subcontinent. The apparent lack of specific sequences types suggests that the P. falciparum transmission dynamics in the whole Amazon are probably different from any other endemic region studied and possibly interfere with the parasite's ability to efficiently diversify its variant gene repertoires.

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Section: Introductionmentioning

confidence: 60%

Section: Nucleic Acid Extraction Pcr and Sequencingmentioning

confidence: 99%

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The South American Plasmodium falciparum var gene repertoire is limited, highly shared and possibly lacks several antigenic types

Albrecht

Castiñeiras

Carvalho

et al. 2010

Gene

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“…In a recent study, the global repertoire of variant genes, namely var genes, was estimated significantly smaller in Western Amazon parasites than from other areas (Albrecht et al 2006). This turns the massive sequencing of symptomatic-and asymptomatic infection associated repertoires a feasible and not an never-ending task, as would be expected from African settings (see a study by Bull and colleagues (Bull et al 2005).…”

Section: Discussionmentioning

confidence: 99%

“…In the Western Amazon, circulating P. falciparum genotypes seem to share a high number of variant antigens suggesting a low frequency of truly recombinatory events and favoring inbreeding of circulating strains (Albrecht et al 2006). Taking into account the relatively low transmission (Gil et al 2003) in the study area, we asked if distinct P. falciparum strains could be identified in the observed symptomatic or non-symptomatic infections in the same population.…”

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confidence: 99%