The hemoglobinopathies, disorders of hemoglobin structure and production, protect against death from malaria 1 . In sub-Saharan Africa, two such conditions occur at particularly high frequencies: presence of the structural variant hemoglobin S and α + -thalassemia, a condition characterized by reduced production of the normal α-globin component of hemoglobin. Individually, each is protective against severe Plasmodium falciparum malaria 2-4 , but little is known about their malaria-protective effects when inherited in combination. We investigated this question by studying a population on the coast of Kenya and found that the protection afforded by each condition inherited alone was lost when the two conditions were inherited together, to such a degree that the incidence of both uncomplicated and severe P. falciparum malaria was close to baseline in children heterozygous with respect to the mutation underlying the hemoglobin S variant and homozygous with respect to the mutation underlying α + -thalassemia. Negative epistasis could explain the failure of α + -thalassemia to reach fixation in any population in subSaharan Africa.The mutation underlying the hemoglobin S variant (HbS) is a prototypical example of a balanced polymorphism: its frequency in populations is determined both by positive selection for heterozygosity (HbAS) 5 and negative selection for homozygosity (HbSS), which causes sickle cell disease, a debilitating condition associated with chronic anemia and premature death. Negative selection has not been shown to affect the frequency of α + -thalassemias. Perhaps as a consequence, these conditions approach fixation in a number of populations; for unknown reasons, however, frequencies remain relatively low in much of sub-Saharan Africa 1 .Despite conclusive evidence that both HbAS and α + -thalassemia protect against severe and fatal P. falciparum malaria 2-4 , the mechanisms underlying this protection are poorly 6,7 , and parasite-infected HbAS erythrocytes also seem to be targeted for premature destruction by the spleen 6,8,9 . These hypothetical mechanisms are supported by both the reduced incidence of clinical malaria and the lower parasite densities observed in children with HbAS erythrocytes when they suffer from clinical attacks 3,10 . Much less is known about α + -thalassemia. Although both heterozygosity (-α/αα) and homozygosity (-α/-α) with respect to the underlying mutation protect against severe and fatal malaria 2,4 , neither protects against uncomplicated malaria 11 or affects parasite densities during incident episodes 2,12 . We believe that a better understanding of how these conditions protect against malaria might provide insights into both the pathophysiology of severe malaria and the hostparasite relationship more generally 10 . Accordingly, we studied the effects of both HbAS and α + -thalassemia on the epidemiology of malaria in children living on the coast of Kenya.We measured the incidence of P. falciparum malaria in two cohorts of children from Kilifi District, where al...

Neisseria meningitis is a human commensal bacterium that occasionally causes life-threatening disease. As with a number of other bacterial pathogens, meningococcal populations comprise distinct lineages, which persist over many decades and during global spread in the face of high rates of recombination. In addition, the propensity to cause invasive disease is associated with particular ''hyperinvasive'' lineages that coexist with less invasive lineages despite the fact that disease does not contribute to host-to-host transmission. Here, by combining a modeling approach with molecular epidemiological data from 1,108 meningococci isolated in the Czech Republic over 27 years, we show that interstrain competition, mediated by immune selection, can explain both the persistence of multiple discrete meningococcal lineages and the association of a subset of these with invasive disease. The model indicates that the combinations of allelic variants of housekeeping genes that define these lineages are associated with very small differences in transmission efficiency among hosts. These findings have general implications for the emergence of lineage structure and virulence in recombining bacterial populations.bacteria ͉ meningococcus ͉ population structure ͉ strain ͉ mathematical model A spectrum of population structures has been identified among bacterial pathogens by multilocus studies of genetic variation in housekeeping genes (1, 2). It ranges from the extremely low diversity observed in Yersinia pestis (3) and Salmonella enterica var Typhi (4) to the very high levels of unstructured diversity found in Helicobacter pylori (5). The majority of pathogenic bacteria investigated to date, however, occupy an intermediate position within this spectrum, being composed of distinct cocirculating lineages that constitute a small subset of the possible allele combinations (6). These intermediate population structures exhibit apparently conflicting signals of both clonal descent and genetic exchange, and the mechanisms whereby they arise and are maintained remain incompletely understood (7).Neisseria meningitidis, the meningococcus, was one of the first bacteria where such an intermediate population structure was described (8-10). Populations of this highly recombining bacterium (11), which has an essentially commensal relationship with the human host, also present the intriguing feature that only certain lineages, the so-called hyperinvasive lineages, are associated with disease (12). These observations present two conceptual challenges: first, how does lineage structure arise in the face of the observed high rates of recombination; and, second, why are some lineages especially virulent, when invasive disease confers no benefit in terms of host-to-host spread (13)?Here, we address these questions by means of a survey of 1,108 meningococci isolated from asymptomatic carriage and disease in the Czech Republic over a 27-year period. The isolates were characterized at seven housekeeping loci by multilocus sequence typing (MLST) (14) and...

The bacterial pathogen, Streptococcus pneumoniae (the pneumococcus), is a leading cause of life-threatening illness and death worldwide. Available conjugate vaccines target only a small subset (up to 13) of >90 known capsular serotypes of S. pneumoniae and, since their introduction, increases in non-vaccine serotypes have been recorded in several countries: a phenomenon termed Vaccine Induced Serotype Replacement (VISR). Here, using a combination of mathematical modelling and whole genome analysis, we show that targeting particular serotypes through vaccination can also cause their metabolic and virulence-associated components to transfer through recombination to non-vaccine serotypes: a phenomenon we term Vaccine-Induced Metabolic Shift (VIMS). Our results provide a novel explanation for changes observed in the population structure of the pneumococcus following vaccination, and have important implications for strain-targeted vaccination in a range of infectious disease systems.

Efforts to suppress transmission of SARS-CoV-2 in the UK have seen non-pharmaceutical interventions being invoked. The most severe measures to date include all restaurants, pubs and cafes being ordered to close on 20th March, followed by a “stay at home” order on the 23rd March and the closure of all non-essential retail outlets for an indefinite period. Government agencies are presently analysing how best to develop an exit strategy from these measures and to determine how the epidemic may progress once measures are lifted. Mathematical models are currently providing short and long term forecasts regarding the future course of the COVID-19 outbreak in the UK to support evidence-based policymaking. We present a deterministic, age-structured transmission model that uses real-time data on confirmed cases requiring hospital care and mortality to provide up-to-date predictions on epidemic spread in ten regions of the UK. The model captures a range of age-dependent heterogeneities, reduced transmission from asymptomatic infections and produces a good fit to the key epidemic features over time. We simulated a suite of scenarios to assess the impact of differing approaches to relaxing social distancing measures from 7th May 2020 on the estimated number of patients requiring inpatient and critical care treatment, and deaths. With regard to future epidemic outcomes, we investigated the impact of reducing compliance, ongoing shielding of elder age groups, reapplying stringent social distancing measures using region based triggers and the role of asymptomatic transmission. We find that significant relaxation of social distancing measures from 7th May onwards can lead to a rapid resurgence of COVID-19 disease and the health system being quickly overwhelmed by a sizeable, second epidemic wave. In all considered age-shielding based strategies, we projected serious demand on critical care resources during the course of the pandemic. The reintroduction and release of strict measures on a regional basis, based on ICU bed occupancy, results in a long epidemic tail, until the second half of 2021, but ensures that the health service is protected by reintroducing social distancing measures for all individuals in a region when required. Our work confirms the effectiveness of stringent non-pharmaceutical measures in March 2020 to suppress the epidemic. It also provides strong evidence to support the need for a cautious, measured approach to relaxation of lockdown measures, to protect the most vulnerable members of society and support the health service through subduing demand on hospital beds, in particular bed occupancy in intensive care units.

Background: The progression and geographical distribution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the United Kingdom (UK) and elsewhere is unknown because typically only symptomatic individuals are diagnosed. We performed a serological study of blood donors in Scotland in the spring of 2020 to detect neutralising antibodies to SARS-CoV-2 as a marker of past infection and epidemic progression. Aim: Our objective was to determine if sera from blood bank donors can be used to track the emergence and progression of the SARS-CoV-2 epidemic. Methods: A pseudotyped SARS-CoV-2 virus microneutralisation assay was used to detect neutralising antibodies to SARS-CoV-2. The study comprised samples from 3,500 blood donors collected in Scotland between 17 March and 18 May 2020. Controls were collected from 100 donors in Scotland during 2019. Results: All samples collected on 17 March 2020 (n = 500) were negative in the pseudotyped SARS-CoV-2 virus microneutralisation assay. Neutralising antibodies were detected in six of 500 donors from 23 to 26 March. The number of samples containing neutralising antibodies did not significantly rise after 5-6 April until the end of the study on 18 May. We found that infections were concentrated in certain postcodes, indicating that outbreaks of infection were extremely localised. In contrast, other areas remained comparatively untouched by the epidemic. Conclusion: Although blood donors are not representative of the overall population, we demonstrated that serosurveys of blood banks can serve as a useful tool for tracking the emergence and progression of an epidemic such as the SARS-CoV-2 outbreak.