Sónia Gonçalves

A genomic toolkit for surveillance and elimination of the principal malaria vectors in Southeast Asia.

The paper provides genomic resources for malaria vector surveillance in Southeast Asia, revealing population structure and resistance regions in Anopheles dirus.

Characterising recent antimalarial resistance in West Africa: Insights from amplicon sequencing of 17,384 Plasmodium falciparum infection samples

The paper analyzes amplicon sequencing data from 17,384 Plasmodium falciparum samples in West Africa to characterize antimalarial resistance patterns and their geographic distribution.

Targeted genomic surveillance of insecticide resistance in African malaria vectors

This paper develops a targeted genomic surveillance approach for insecticide resistance in malaria vectors, identifying resistance variants and demonstrating predictive modeling with high accuracy.

A complex Plasmodium falciparum cryptotype circulating at low frequency across the African continent

The paper identifies a cryptotype in Plasmodium falciparum genomes across Africa, characterized by a complex genetic background that is geographically widespread but genetically distinct.

A molecular barcode and online tool to identify and map imported infection with Plasmodium vivax

The paper develops a molecular barcode and online tool to identify and map imported Plasmodium vivax infections using SNP analysis and machine learning.

Nanopore sequencing for real-time genomic surveillance of Plasmodium falciparum

This study implements a Nanopore sequencing workflow for P. falciparum genomic surveillance in Ghana, identifying drug resistance patterns and vaccine antigen variations.

The protective effect of sickle cell haemoglobin against severe malaria depends on parasite genotype

The paper investigates the association between host sickle cell haemoglobin and parasite genetic variation in malaria severity, finding that parasite alleles linked to HbS show strong linkage disequilibrium and frequency covariation with HbS.

Population genomics reveal distinct and diverging populations of An. minimus in Cambodia - a widespread malaria vector in Southeast Asia

The paper uses whole-genome sequencing to analyze genetic diversity and population structure of An. minimus in Cambodia, identifying four distinct populations with unique selection signals.

Patterns of within-host genetic diversity in SARS-CoV-2

This study analyzes within-host genetic diversity in 1,181 SARS-CoV-2 samples, finding high mutation rates, strand asymmetries, and purifying selection, with implications for transmission chain reconstruction.

MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

MAJORA enables decentralized sequencing and integration of SARS-CoV-2 genomic data and metadata across the COG-UK network, supporting rapid genomic surveillance.