Malaria genotyping for epidemiologic surveillance

Greenhouse, Bryan; Smith, David L.

doi:10.1073/pnas.1507727112

Cited by 21 publications

(18 citation statements)

References 15 publications

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“…There may be social reasons why respondents might be reluctant to provide accurate information, including recreational travel. Even with reliable travel histories of those who have been locally mobile there is no guarantee that an infection can be linked to the travel location or the usual residence, even with current genotype barcodes of the parasite [26, 27]. Where genotyping parasites will become valuable is in the mapping of onward transmission.…”

Section: Discussionmentioning

confidence: 99%

The changing malaria landscape in Aseer region, Kingdom of Saudi Arabia: 2000–2015

Al-Shahrani

Abdelgader

Saeed

et al. 2016

Malar J

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BackgroundIn 2004, a revised action plan was developed, supported by the World Health Organization, to eliminate malaria from Saudi Arabia by preventing re-introduction of malaria into regions since declared malaria free, eliminating foci of transmission in the Mecca and Medina areas and a concerted effort of foci surveillance and control, to eliminate malaria from the regions of Jazan and Aseer. This paper provides the context, activities, progress, and possible contributions toward malaria elimination in the Aseer region since 2000, with a more detailed analysis of the spatial location of locally acquired case incidence since 2012.MethodsThis is a descriptive study of all available Ministry of Health surveillance data and process reports since 2000, with higher spatial resolution analysis of data between 2012 and 2015.ResultsIn 2000, there were 511 cases of Plasmodium falciparum locally acquired infection. The following 4 years witnessed a dramatic decline in cases to only 18 locally acquired infections reported in 2005. A resurgence in local infections was reported in 2006 (93) and 2007 (165), thereafter (2008–2014) local cases continued to decline to fewer than 40 per year across the region. However, in 2015, a small rise was noted (51). All locally acquired infections were P. falciparum. There has been a constant flow of imported infections into Aseer since 2000, mostly among immigrant labour from Pakistan, India, Sudan, and Yemen. Imported infections have included both Plasmodium vivax and P. falciparum. The spatial extent of malaria appears to be changing, but there remain two intractable areas Sarat Abeda and Dhran Aljanub, where risks per reporting centre have changed little since 2001, remaining above 0.5 per 10,000 population. Only seven villages contributed 55% of all locally acquired infection since 2012.DiscussionAseer has reached a state of very low incidence of locally acquired infections, despite a constant source of imported infections from outside the country. How many of the local infections are F2 generations from imported infections or how many are a result of residual active transmission between asymptomatic carriers of infections transmitted by pockets of existing Anopheles arabiensis populations remains unknown. A more detailed investigation of the spatial and temporal patterns of infected hosts, parasites and vectors would help define whether this region has managed to effectively prevent local transmission of new infections.

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Section: Discussionmentioning

confidence: 99%

The changing malaria landscape in Aseer region, Kingdom of Saudi Arabia: 2000–2015

Al-Shahrani

Abdelgader

Saeed

et al. 2016

Malar J

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“…It is widely accepted that relationships exist between the regional epidemiology of malaria and the genetic diversity of local parasite populations. For example, the evolution of antimalarial drug resistance, patterns of parasite migration and variation in transmission intensity may all have relationships with population genetic diversity (reviewed in [1][2][3][4][5][6][7]). In most cases, however, the precise nature of these relationships remains unclear.…”

Section: Introductionmentioning

confidence: 99%

Elucidating relationships betweenP.falciparumprevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria

Hendry¹,

Kwiatkowski²,

McVean

2020

Preprint

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There is an abundance of malaria genetic data being collected from the field, yet using this data to understand features of regional epidemiology remains a challenge. A key issue is the lack of models that relate parasite genetic diversity to epidemiological parameters. Classical models in population genetics characterize changes in genetic diversity in relation to demographic parameters, but fail to account for the unique features of the malaria life cycle. In contrast, epidemiological models, such as the Ross-Macdonald model, capture malaria transmission dynamics but do not consider genetics. Here, we have developed an integrated model encompassing both parasite evolution and regional epidemiology. We achieve this by combining the Ross-Macdonald model with an intra-host continuous-time Moran model, thus explicitly representing the evolution of individual parasite genomes in a traditional epidemiological framework. Implemented as a stochastic simulation, we use the model to explore relationships between measures of parasite genetic diversity and parasite prevalence, a widely-used metric of transmission intensity. First, we explore how varying parasite prevalence influences genetic diversity at equilibrium. We find that multiple genetic diversity statistics are correlated with prevalence, but the strength of the relationships depends on whether variation in prevalence is driven by host- or vector-related factors. Next, we assess the responsiveness of a variety of statistics to malaria control interventions, finding that those related to mixed infections respond quickly (~months) whereas other statistics, such as nucleotide diversity, may take decades to respond. These findings provide insights into the opportunities and challenges associated with using genetic data to monitor malaria epidemiology.

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“…More complex genotype infections, de ned as the presence of more than one parasite genome in a single patient, are found in higher transmission settings as a consequence of outcrossing between genetically distinct parasite types [17]. Thus, detection of more complex parasite genotypes among travellers in low transmission settings is consistent with these infections originating from higher transmission areas [18][19][20][21][22][23]. Genetic data can provide more precise information about infection origin and connectivity (i.e., the degree of genetic relatedness) between infections [8], information that can be used to determine if a malaria infection is local or imported.…”

Section: Introductionmentioning

confidence: 84%

Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal

Volkman¹,

Sarr

Steketee³

et al. 2020

Preprint

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Background Malaria elimination efforts can be undermined by imported malaria infections. Imported infections are classified based on travel history. Methods A genetic strategy was applied to better understand the contribution of imported infections and to test for local transmission in the very low prevalence region of Richard Toll, Senegal. Results Genetic relatedness analysis, based upon molecular barcode genotyping data derived from diagnostic material, provided evidence for both imported infections and ongoing local transmission in Richard Toll. Evidence for imported malaria included finding that a large proportion of Richard Toll parasites were genetically related to parasites from Thiès, Senegal, a region of moderate transmission with extensive available genotyping data. Evidence for ongoing local transmission included finding parasites of identical genotype that persisted across multiple transmission seasons as well as enrichment of highly related infections within the households of non-travellers compared to travellers. Conclusions These data indicate that, while a large number of infections may have been imported, there remains ongoing local malaria transmission in Richard Toll. These proof-of-concept findings underscore the value of genetic data to identify parasite relatedness and patterns of transmission to inform optimal intervention selection and placement.

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Malaria genotyping for epidemiologic surveillance

Cited by 21 publications

References 15 publications

The changing malaria landscape in Aseer region, Kingdom of Saudi Arabia: 2000–2015

The changing malaria landscape in Aseer region, Kingdom of Saudi Arabia: 2000–2015

Elucidating relationships betweenP.falciparumprevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria

Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal

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