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

Abstract

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.

Antibody recognition of Plasmodium falciparum infected red blood cells by symptomatic and asymptomatic individuals in the Brazilian Amazon

“…Very little is known about the adhesion binding properties and antigenic variation related to the var genes and PfEMP-1 proteins in Amazonian isolates. Previous reports by our group based on the analysis of PfEMP1-DBLα encoding tags showed that the var gene repertoires seem much smaller in Amazonian P. falciparum isolates compared to other endemic settings (Albrecht et al 2006, 2010). It is also known that the absolute number of malaria-infected people in the Amazon may be underestimated due to a high incidence of asymptomatic infections in riverside settlements (Alves et al.…”

“…Perhaps as a consequence of low transmission and quick treatment, the overall diversity of variant protein encoding genes, such as the var genes, in the Amazon seems much smaller than in any other endemic area so far tested (Albrecht et al 2006); development to severe malaria is also likely prevented by quick treatment. The herein used isolates possess var genes, which represent part of the repertoire of circulating strains in the Amazon (Albrecht et al 2010). In order to elucidate the differential presence of antibodies against the IRBC surface in asymptomatic (“protected”) and symptomatic (“susceptible”) individuals, we tested the recognition of P. falciparum isolates from the western Brazilian Amazon and compared them to four lineages of 3D7 that expressed different var genes/PfEMP1.…”

Evolutionary structure of Plasmodium falciparum major variant surface antigen genes in South America: Implications for epidemic transmission and surveillance

“…Specifically, the major P. falciparum variant surface antigen of the blood stages, Pf EMP1, is a key marker as it is a virulence factor and immunity to this antigen determines the dynamics of infection within and between hosts (e.g., (Artzy‐Randrup et al., 2012)). To date few malaria surveillance studies have used var genes encoding Pf EMP1 due to the extreme diversity and the complexity of undertaking population genetics with this multigene family (Albrecht et al., 2010; Artzy‐Randrup et al., 2012; Chen et al., 2011; Day et al., 2017; Tessema et al., 2015). Here, using the 454 high throughput sequencing approach to obtain well‐sampled populations, we show that the conserved DBLα domain of var genes constitutes a promising biomarker to infer population structure, and more generally for epidemiological disease surveillance.…”

“…In contrast to P. falciparum in Africa, we observed “limited” var DBLα type diversity within the local South American populations, which was consistent with previous surveys (Albrecht et al., 2010; Chen et al., 2011). One hypothesis to explain this “limited” var DBLα type diversity could be linked to relatively lower transmission and hence fewer co‐infections/superinfections (i.e., multiple genotypes within an isolate) existing in the South American human population.…”

Recombination and Diversification of the Variant Antigen Encoding Genes in the Malaria Parasite Plasmodium falciparum

“…While such studies detected extreme var gene diversity on a global scale, within a given location, especially one with lower transmission rates, the variability can be more limited (37,38). By comparing the degree of var gene diversity with that found within the rest of the genome, it is possible to gain insights into how the large multicopy gene families are maintained differently.…”