Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have caused successive global waves of infection. These variants, with multiple mutations in the spike protein, are thought to facilitate escape from natural and vaccine-induced immunity and often increase in affinity for ACE2. The latest variant to cause concern is BA.2.75, identified in India where it is now the dominant strain, with evidence of wider dissemination. BA.2.75 is derived from BA.2 and contains four additional mutations in the receptor-binding domain (RBD). Here, we perform an antigenic and biophysical characterization of BA.2.75, revealing an interesting balance between humoral evasion and ACE2 receptor affinity. ACE2 affinity for BA.2.75 is increased 9-fold compared with BA.2; there is also evidence of escape of BA.2.75 from immune serum, particularly that induced by Delta infection, which may explain the rapid spread in India, where where there is a high background of Delta infection. ACE2 affinity appears to be prioritized over greater escape.
\n \n\n \n \nBackground: Gestational diabetes mellitus (GDM) contributes to maternal and neonatal morbidity. As data from marginalized populations remains scarce, this study compares risk-factor-based to universal GDM screening in a low resource setting. Methods: This is a secondary analysis of data from a prospective preterm birth cohort. Pregnant women were enrolled in the first trimester and completed a 75g oral glucose tolerance test (OGTT) at 24-32 weeks' gestation. To define GDM cases, Hyperglycaemia and Adverse Pregnancy Outcomes (HAPO trial) criteria were used. All GDM positive cases were treated. Sensitivity and specificity of risk-factor-based selection for screening (criteria: age \u226530y, obesity (Body mass index (BMI) \u226527.5kg/m2), previous GDM, 1st degree relative with diabetes, previous macrosomia (\u22654kg), previous stillbirth, or symphysis-fundal height \u226590th percentile) was compared to universal screening using the OGTT as the gold standard. Adverse maternal and neonatal outcomes were compared by GDM status. Results: GDM prevalence was 13.4% (50/374) (95% CI: 10.3-17.2). Three quarters of women had at least one risk factor (n=271 women), with 37/50 OGTT positive cases correctly identified: sensitivity 74.0% (59.7-85.4) and specificity 27.8% (3.0-33.0). Burman women (self-identified) accounted for 29.1% of the cohort population, but 38.0% of GDM cases. Percentiles for birthweight (p=0.004), head circumference (p=0.002), and weight-length ratio (p=0.030) were higher in newborns of GDM positive compared with non-GDM mothers. 21.7% (75/346) of newborns in the cohort were small-for-gestational age (\u226410th percentile). In Burman women, overweight/obese BMI was associated with a significantly increased adjusted odds ratio 5.03 (95% CI: 1.43-17.64) for GDM compared with normal weight, whereas in Karen women, the trend in association was similar but not significant (OR 2.36; 95% CI 0.95-5.89). Conclusions: Risk-factor-based screening missed one in four GDM positive women. Considering the benefits of early detection of GDM and the limited additional cost of universal screening, a two-step screening program was implemented.
\n \n\n \n \nWe describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network.\u00a0 It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented.\u00a0 For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations.\u00a0 We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent.\u00a0 We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines.\u00a0 Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.
\n \n\n \n \nBackgroundHepatitis B causes significant disease and death globally, despite the availability of effective vaccination. Migration likewise affects hundreds of millions of people annually, many of whom are women and children, and increases risks for poor vaccine completion and mother to child transmission of hepatitis B. In the neighbouring countries of Thailand and Myanmar, vaccine campaigns have made progress but little is known about the reach of these programs into migrant worker communities from Myanmar living in Thailand.MethodsA cohort of 253 postpartum women (53 urban migrants in Chiang Mai and 200 rural migrants in Tak Province) were surveyed about their Hepatitis B knowledge and willingness to vaccinate their children between September 10, 2019 and March 30, 2019. They were subsequently followed to determine vaccine completion. When records of vaccination were unavailable at the birth facility, or visits were late, families were contacted and interviewed about vaccination elsewhere, and reasons for late or missed vaccines.ResultsThough women in Tak province displayed better knowledge of Hepatitis B and equal intention to vaccinate, they were 14 times less likely to complete Hepatitis B vaccination for their children compared to migrants in Chiang Mai. Tak women were largely undocumented, had private (non-profit) insurance and had more transient residence. In Chiang Mai migrant women were mostly documented and had full access to the Thai national health services. Though minor individual and facility-level differences may have contributed, the major driver of the disparity seems to be the place of migrants within local socio-political-economic systems. The COVID-19 pandemic further disproportionately affected Tak province migrants who faced severe travel restrictions hampering vaccination. Sixty percent of families who were lost to vaccine follow-up in Tak province could not be contacted by phone or home visit. Chiang Mai migrants, with 86.8% vaccine completion, nearly reached the target of 90%.ConclusionsAchievement of high levels of hepatitis B vaccination in migrant communities is important and feasible, and requires inclusive policies that integrate migrants into national health and social services. This is more urgent than ever during the COVID-19 era.
\n \n\n \n \nFalsified medicines are a major threat to global health. Antimalarial drugs have been particularly targeted by criminals. As DNA analysis has revolutionized forensic criminology, we hypothesized that these techniques could also be used to investigate the origins of falsified medicines. Medicines may contain diverse adventitious biological contamination, and the sealed nature of blister-packages may capture and preserve genetic signals from the manufacturing processes allowing identification of production source(s). We conducted a blinded pilot study to determine if such environmental DNA (eDNA) could be detected in eleven samples of falsified and genuine artesunate antimalarial tablets, collected in SE Asia, which could be indicative of origin. Massively Parallel Sequencing (MPS) was used to characterize microbial and eukaryote diversity. Two mitochondrial DNA analysis approaches were explored to detect the presence of human DNA. Trace eDNA from these low biomass samples demonstrated sample specific signals using two target markers. Significant differences in bacterial and eukaryote DNA community structures were observed between genuine and falsified tablets and between different packaging types of falsified artesunate. Human DNA, which was indicative of likely east Asian ancestry, was found in falsified tablets. This pilot study of the 'pharmabiome' shows the potential of environmental DNA as a powerful forensic tool to assist with the identification of the environments, and hence location and timing, of the source and manufacture of falsified medicines, establish links between seizures and complement existing tools to build a more complete picture of criminal trade routes. The finding of human DNA in tablets raises important ethical issues that need to be addressed.
\n \n\n \n \nTraditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799\u2009P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection's country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs\u2009>\u20090.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs.
\n \n\n \n \nPrimaquine prevents relapses of Plasmodium vivax malaria but can cause severe hemolysis in patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency. The clinical and laboratory features of this outcome are usually confounded by the clinical and hemolytic effects of concomitant malaria. We describe a case of severe hemolysis occurring after a total dose of 2.04 mg/kg of primaquine used for prophylaxis in a young, G6PD-deficient (Kaiping variant), Australian man without malaria. During acute hemolysis, he had markedly elevated urinary beta-2-microglobulin, suggestive of renal tubular injury (a well-recognized complication of primaquine-induced hemolysis). He also had albuminuria and significantly increased excretion of glycocalyx metabolites, suggestive of glomerular glycocalyx degradation and injury. We show that regularly dosed paracetamol given for its putative renoprotective effect is safe in the context of severe oxidative hemolysis. Acute drug-induced hemolysis transiently increases G6PD activity. Cases such as this improve our understanding of primaquine-induced hemolysis and ultimately will help facilitate widespread safe and effective use of this critically important drug.
\n \n\n \n \nAbstractSevere falciparum malaria is a major cause of death in tropical countries, particularly in African children. Rapid and accurate diagnosis and prognostic assessment are critical to clinical management. In 6027 prospectively studied patients diagnosed with severe malaria we assess the prognostic value of peripheral blood film counts of malaria pigment containing polymorphonuclear leukocytes (PMNs) and monocytes. We combine these results with previously published data and show, in an individual patient data meta-analysis (n\u2009=\u200932,035), that the proportion of pigment containing PMNs is predictive of in-hospital mortality. In African children the proportion of pigment containing PMNs helps distinguish severe malaria from other life-threatening febrile illnesses, and it adds to the prognostic assessment from simple bedside examination, and to the conventional malaria parasite count. Microscopy assessment of pigment containing PMNs is simple and rapid, and should be performed in all patients hospitalised with suspected severe malaria.
\n \n\n \n \nThe organophosphate pirimiphos-methyl and the carbamate carbosulfan were evaluated in comparison to the pyrethroid alphacypermethrin and the 'near-pyrethroid' etofenprox against pyrethroid resistant Anopheles gambiae and Culex spp. in an experimental hut station located in central C\u00f4te d'Ivoire. Bednets were impregnated with the above mentioned compounds and randomly allocated to the huts. On 40 consecutive mornings, after sleepers had occupied the huts overnight, mosquitoes were collected from the huts, identified and scored as live or dead (including delayed mortality). An. gambiae s.l. that had been collected were tested for the presence of the kdr allele in heterozygous or homozygous form. Both non-pyrethroid treatments caused very high mortality, whereas mortality with alpha-cypermethrin and etofenprox generally did not differ from the levels observed with untreated control nets in this experiment. The nets had holes cut in them and there was considerable bloodfeeding on the sleepers, which was only significantly reduced for An. gambiae by carbosulfan and alpha-cypermethrin. PCR genotyping suggested that there was selection for the kdr resistance allele by the pyrethroid treated nets. Organophosphates and carbamates may therefore present an alternative to be used on bednets especially in areas of pyrethroid resistance, but the safety of these insecticides will have to be carefully considered.
\n \n\n \n \nBackground: Case-based surveillance of antimicrobial resistance (AMR) provides more actionable data than isolate- or sample-based surveillance. We developed A Clinically Oriented antimicrobial Resistance surveillance Network (ACORN) as a lightweight but comprehensive platform, in which we combine clinical data collection with diagnostic stewardship, microbiological data collection and visualisation of the linked clinical-microbiology dataset. Data are compatible with WHO GLASS surveillance and can be stratified by syndrome and other metadata. Summary metrics can be visualised and fed back directly for clinical decision-making and to inform local treatment guidelines and national policy. Methods: An ACORN pilot was implemented in three hospitals in Southeast Asia (1 paediatric, 2 general) to collect clinical and microbiological data from patients with community- or hospital-acquired pneumonia, sepsis, or meningitis. The implementation package included tools to capture site and laboratory capacity information, guidelines on diagnostic stewardship, and a web-based data visualisation and analysis platform. Results: Between December 2019 and October 2020, 2294 patients were enrolled with 2464 discrete infection episodes (1786 community-acquired, 518 healthcare-associated and 160 hospital-acquired). Overall, 28-day mortality was 8.7%. Third generation cephalosporin resistance was identified in 54.2% (39/72) of E. coli and 38.7% (12/31) of K. pneumoniae isolates. Almost a quarter of S. aureus isolates were methicillin resistant (23.0%, 14/61). 290/2464 episodes could be linked to a pathogen, highlighting the level of enrolment required to achieve an acceptable volume of isolate data. However, the combination with clinical metadata allowed for more nuanced interpretation and immediate feedback of results. Conclusions: ACORN was technically feasible to implement and acceptable at site level. With minor changes from lessons learned during the pilot ACORN is now being scaled up and implemented in 15 hospitals in 9 low- and middle-income countries to generate sufficient case-based data to determine incidence, outcomes, and susceptibility of target pathogens among patients with infectious syndromes.
\n \n\n \n \nScrub typhus is a mite-borne disease caused by a Gram-negative obligately intracellular bacillus, Orientia tsutsugamushi. The disease is endemic in the Asia\u2013Australia\u2013Pacific region, including Thailand. Scrub typhus generally manifests as acute undifferentiated febrile fever along with myalgia, rash, and lymphadenopathy. An eschar can be a valuable diagnostic clue, but this skin lesion may be missed in some patients. The disease symptoms resemble those of other febrile illnesses such as leptospirosis, typhoid, murine typhus, malaria, and dengue fever, making a laboratory diagnosis necessary for the definitive diagnosis. In this study, we expressed a recombinant protein derived from 56-kDa type-specific antigen of O. tsutsugamushi Karp serotype and tested its ability to detect and differentiate scrub typhus infection. IgM and IgG antibodies were determined in sera from scrub typhus (n = 92) and other febrile illness patients (murine typhus (n = 25), melioidosis (n = 36), leptospirosis (n = 42), and dengue (n = 35)) from Thailand. Sensitivities of 87.0% and 59.8% with a specified assay cut-off were obtained for IgM and IgG indirect ELISAs, respectively, with a specificity of 100% in both tests. The sensitivity was increased to 95.7% when a combination of IgM and IgG ELISAs results was considered. Our study suggested a potential of the 56-kDa recombinant protein for further development and evaluation for use in scrub typhus serodiagnosis.
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