Temporal evolution of sulfadoxine-pyrimethamine resistance genotypes and genetic diversity in response to a decade of increased interventions against Plasmodium falciparum in northern Ghana

Background Anti-malarial drug resistance remains a key concern for the global fight against malaria. In Ghana sulfadoxine-pyrimethamine (SP) is used for intermittent preventive treatment of malaria in pregnancy and combined with amodiaquine for Seasonal Malaria Chemoprevention (SMC) during the high malaria season. Thus, surveillance of molecular markers of SP resistance is important to guide decision-making for these interventions in Ghana. Methods A total of 4469 samples from uncomplicated malaria patients collected from 2009 to 2018 was submitted to the Wellcome Trust Sanger Institute, UK for DNA sequencing using MiSeq. Genotypes were successfully translated into haplotypes in 2694 and 846 mono infections respectively for pfdhfr and pfdhps genes and the combined pfhdfr/pfdhps genes across all years. Results At the pfdhfr locus, a consistently high (> 60%) prevalence of parasites carrying triple mutants (IRNI) were detected from 2009 to 2018. Two double mutant haplotypes (NRNI and ICNI) were found, with haplotype NRNI having a much higher prevalence (average 13.8%) than ICNI (average 3.2%) across all years. Six pfdhps haplotypes were detected. Of these, prevalence of five fluctuated in a downward trend over time from 2009 to 2018, except a pfdhps double mutant (AGKAA), which increased consistently from 2.5% in 2009 to 78.2% in 2018. Across both genes, pfdhfr/pfdhps combined triple (NRNI + AAKAA) mutants were only detected in 2009, 2014, 2015 and 2018, prevalence of which fluctuated between 3.5 and 5.5%. The combined quadruple (IRNI + AAKAA) genotype increased in prevalence from 19.3% in 2009 to 87.5% in 2011 before fluctuating downwards to 19.6% in 2018 with an average prevalence of 37.4% within the nine years. Prevalence of parasites carrying the quintuple (IRNI + AGKAA or SGEAA) mutant haplotypes, which are highly refractory to SP increased over time from 14.0% in 2009 to 89.0% in 2016 before decreasing to 78.9 and 76.6% in 2017 and 2018 respectively. Though quintuple mutants are rising in prevalence in both malaria seasons, together these combined genotypes vary significantly within season but not between seasons. Conclusions Despite high prevalence of pfdhfr triple mutants and combined pfdhfr/pfdhps quadruple and quintuple mutants in this setting SP may still be efficacious. These findings are significant as they highlight the need to continuously monitor SP resistance, particularly using deep targeted sequencing to ascertain changing resistance patterns.

Sir John Edward Sulston CH. 27 March 1942—6 March 2018

In 2002 Sir John Sulston shared the Nobel Prize for Physiology or Medicine for his contribution to understanding the genetic control of cell fate during the development of the roundworm Caenorhabditis elegans . However, it was his position as one of the leaders of the international and publicly funded Human Genome Project that brought him to public prominence. Both his work on the worm cell lineage and his later commitment to genome sequencing as founding director of the Wellcome Trust Sanger Institute stemmed from his conviction that investing in large-scale data collection would have long-term benefits for future scientific discovery. He was a key figure in promoting the principle, now widely accepted, that genomic data should be universally and freely shared. After retiring from his post at the Sanger Institute he engaged with organizations with interests in biomedical ethics and global equality. He was a loyal and supportive colleague to many, delighting in the international collegiality of the ‘worm community’, of which he was a founding member.

A High HIV-1 Strain Variability in London, UK, Revealed by Full-Genome Analysis: Results from the ICONIC Project

Background & MethodsThe ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. fromgagtonef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospital and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker.ResultsThe pipeline generated sequences of at least 1Kb of length (median=7.4Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n=149, 40.8%) and C (n=77, 21.1%) and the circulating recombinant form CRF02_AG (n=32, 8.8%). We found 14 different CRFs (n=66, 18.1%) and multiple URFs (n=32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RTpolregion, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similarpolsequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset.ConclusionsThe initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.

Καρδιομεταβολικοί δείκτες

Τα καρδιαγγειακά νοσήματα αποτελούν την κύρια αιτία θνησιμότητας παγκοσμίως με παράγοντες κινδύνου την υπέρταση, υπερλιπιδαιμία, παχυσαρκία, μη υγιεινή διατροφή, κάπνισμα, ηλικία, φύλο και γενετικό υπόβαθρο. Οι μελέτες σάρωσης του γονιδιώματος έχουν εντοπίσει περισσότερες από 100 περιοχές που συσχετίστηκαν με διάφορους καρδιομεταβολικούς δείκτες. Σκοπός της παρούσας μελέτης είναι η διερεύνηση της επίδρασης διατροφικών και γενετικών παραγόντων καθώς επίσης και των αλληλεπιδράσεών τους σε καρδιομεταβολικούς δείκτες σε δύο απομονωμένους πληθυσμούς. Συγχρονική μελέτη σε δύο Ελληνικούς πληθυσμούς: 1,553 άτομα από τα χωριά του Μυλοποτάμου, Κρήτη και 1,702 άτομα από τα Πομακοχώρια, Ξάνθη. Καταγράφηκαν ανθρωπομετρικά, βιοχημικά και κλινικά δεδομένα μαζί με δεδομένα του τρόπου ζωής. Τα διατροφικά πρότυπα προέκυψαν από ανάλυση σε κύριες συνιστώσες με βάση ένα ερωτηματολόγιο συχνότητας κατανάλωσης τροφίμων. Πραγματοποιήθηκε σάρωση του γονιδιώματος στο Wellcome Trust Sanger Institute, UK.Οι δύο πληθυσμοί ταυτοποιήθηκαν ως γενετικά απομονωμένοι. 82.5% του πληθυσμού των Κρητικών ήταν υπέρβαροι ή παχύσαρκοι. Μεγαλύτερη συμμόρφωση στο τοπικό πρότυπο σχετιζόταν με υψηλότερα επίπεδα γλυκόζης (β=4.026, p<0.001), ενώ μεγαλύτερη συμμόρφωση στο πρότυπο καφενείου σχετιζόταν με υψηλότερο λόγο περιφέρειας μέσης/περιφέρεια ισχίου (β=0.012, p<0.001), αρτηριακή πίεση (β=1.015, p=0.005) και ολική χοληστερόλη (β=5.398, p<0.001).67% του πληθυσμού των Πομάκων ήταν υπέρβαροι ή παχύσαρκοι. Μεγαλύτερη συμμόρφωση στο πρότυπο υψηλής περιεκτικότητας σε απλά σάκχαρα σχετιζόταν με αυξημένο κίνδυνο για χαμηλή HDL (ΣΛ1.84, p=0.003), συστολική και διαστολική υπέρταση (ΣΛ2.40, p=0.002 και ΣΛ2.61, p<0.001, αντίστοιχα) και υπεργλυκαιμία (ΣΛ1.85, p=0.018). Η αλληλεπίδραση 9 πολυμορφισμών με τα διατροφικά πρότυπα ήταν σημαντική στους εκάστοτε καρδιομεταβολικούς δείκτες και επαληθεύτηκε και στους δύο πληθυσμούς.Η διαλεύκανση της σχέσης του γενετικού υποβάθρου με τους διατροφικούς και άλλους περιβαλλοντικούς παράγοντες μέσω της συνδυαστικής μελέτης των αλληλεπιδράσεών τους στον καρδιαγγειακό κίνδυνο ίσως συμβάλει στην κατανόηση και πρόληψη των καρδιαγγειακών νοσημάτων.

Embedding gender equality into institutional strategy

The SiS (Sex in Science) Programme on the WGC (Wellcome Genome Campus) was established in 2011. Key participants include the Wellcome Trust Sanger Institute, EMB-EBI (EMBL-European Bioinformatics Institute), Open Targets and Elixir. The key objectives are to catalyse cultural change, develop partnerships, communicate activities and champion our women in science work at a national and international level (http://www.sanger.ac.uk/about/sex-science). In this paper, we highlight some of the many initiatives that have taken place since 2013, to address gender inequality at the highest levels; the challenges we have faced and how we have overcome these, and the future direction of travel.

Efficient analysis of mouse genome sequences reveal many nonsense variants

Genetic polymorphisms in coding genes play an important role when using mouse inbred strains as research models. They have been shown to influence research results, explain phenotypical differences between inbred strains, and increase the amount of interesting gene variants present in the many available inbred lines. SPRET/Ei is an inbred strain derived from Mus spretus that has ∼1% sequence difference with the C57BL/6J reference genome. We obtained a listing of all SNPs and insertions/deletions (indels) present in SPRET/Ei from the Mouse Genomes Project (Wellcome Trust Sanger Institute) and processed these data to obtain an overview of all transcripts having nonsynonymous coding sequence variants. We identified 8,883 unique variants affecting 10,096 different transcripts from 6,328 protein-coding genes, which is about 28% of all coding genes. Because only a subset of these variants results in drastic changes in proteins, we focused on variations that are nonsense mutations that ultimately resulted in a gain of a stop codon. These genes were identified by in silico changing the C57BL/6J coding sequences to the SPRET/Ei sequences, converting them to amino acid (AA) sequences, and comparing the AA sequences. All variants and transcripts affected were also stored in a database, which can be browsed using a SPRET/Ei M. spretus variants web tool (www.spretus.org), including a manual. We validated the tool by demonstrating the loss of function of three proteins predicted to be severely truncated, namely Fas, IRAK2, and IFNγR1.