Genomic Insights into Zika Virus Emergence and Spread.

The emergence and spread of Zika virus in the Americas continues to challenge our disease surveillance systems. Virus genome sequencing during the epidemic uncovered the timescale of Zika virus transmission and spread. Yet, we are only beginning to explore how genomics can enhance our responses to emerging viruses.

Ancient Plasmodium genomes shed light on the history of human malaria.

Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia BCE, respectively; for P. vivax, this evidence pre-dates textual references by several millennia3. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.

Genotyping, sequencing and analysis of 140,000 adults from Mexico City.

The Mexico City Prospective Study is a prospective cohort of more than 150,000 adults recruited two decades ago from the urban districts of Coyoacán and Iztapalapa in Mexico City1. Here we generated genotype and exome-sequencing data for all individuals and whole-genome sequencing data for 9,950 selected individuals. We describe high levels of relatedness and substantial heterogeneity in ancestry composition across individuals. Most sequenced individuals had admixed Indigenous American, European and African ancestry, with extensive admixture from Indigenous populations in central, southern and southeastern Mexico. Indigenous Mexican segments of the genome had lower levels of coding variation but an excess of homozygous loss-of-function variants compared with segments of African and European origin. We estimated ancestry-specific allele frequencies at 142 million genomic variants, with an effective sample size of 91,856 for Indigenous Mexican ancestry at exome variants, all available through a public browser. Using whole-genome sequencing, we developed an imputation reference panel that outperforms existing panels at common variants in individuals with high proportions of central, southern and southeastern Indigenous Mexican ancestry. Our work illustrates the value of genetic studies in diverse populations and provides foundational imputation and allele frequency resources for future genetic studies in Mexico and in the United States, where the Hispanic/Latino population is predominantly of Mexican descent.

Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries.

This article provides an update on the global cancer burden using the GLOBOCAN 2020 estimates of cancer incidence and mortality produced by the International Agency for Research on Cancer. Worldwide, an estimated 19.3 million new cancer cases (18.1 million excluding nonmelanoma skin cancer) and almost 10.0 million cancer deaths (9.9 million excluding nonmelanoma skin cancer) occurred in 2020. Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer, with an estimated 2.3 million new cases (11.7%), followed by lung (11.4%), colorectal (10.0 %), prostate (7.3%), and stomach (5.6%) cancers. Lung cancer remained the leading cause of cancer death, with an estimated 1.8 million deaths (18%), followed by colorectal (9.4%), liver (8.3%), stomach (7.7%), and female breast (6.9%) cancers. Overall incidence was from 2-fold to 3-fold higher in transitioned versus transitioning countries for both sexes, whereas mortality varied <2-fold for men and little for women. Death rates for female breast and cervical cancers, however, were considerably higher in transitioning versus transitioned countries (15.0 vs 12.8 per 100,000 and 12.4 vs 5.2 per 100,000, respectively). The global cancer burden is expected to be 28.4 million cases in 2040, a 47% rise from 2020, with a larger increase in transitioning (64% to 95%) versus transitioned (32% to 56%) countries due to demographic changes, although this may be further exacerbated by increasing risk factors associated with globalization and a growing economy. Efforts to build a sustainable infrastructure for the dissemination of cancer prevention measures and provision of cancer care in transitioning countries is critical for global cancer control.

Evidence for European presence in the Americas in AD 1021.

Transatlantic exploration took place centuries before the crossing of Columbus. Physical evidence for early European presence in the Americas can be found in Newfoundland, Canada1,2. However, it has thus far not been possible to determine when this activity took place3-5. Here we provide evidence that the Vikings were present in Newfoundland in AD 1021. We overcome the imprecision of previous age estimates by making use of the cosmic-ray-induced upsurge in atmospheric radiocarbon concentrations in AD 993 (ref. 6). Our new date lays down a marker for European cognisance of the Americas, and represents the first known point at which humans encircled the globe. It also provides a definitive tie point for future research into the initial consequences of transatlantic activity, such as the transference of knowledge, and the potential exchange of genetic information, biota and pathologies7,8.

Peopling of the Americas as inferred from ancient genomics.

In less than a decade, analyses of ancient genomes have transformed our understanding of the Indigenous peopling and population history of the Americas. These studies have shown that this history, which began in the late Pleistocene epoch and continued episodically into the Holocene epoch, was far more complex than previously thought. It is now evident that the initial dispersal involved the movement from northeast Asia of distinct and previously unknown populations, including some for whom there are no currently known descendants. The first peoples, once south of the continental ice sheets, spread widely, expanded rapidly and branched into multiple populations. Their descendants-over the next fifteen millennia-experienced varying degrees of isolation, admixture, continuity and replacement, and their genomes help to illuminate the relationships among major subgroups of Native American populations. Notably, all ancient individuals in the Americas, save for later-arriving Arctic peoples, are more closely related to contemporary Indigenous American individuals than to any other population elsewhere, which challenges the claim-which is based on anatomical evidence-that there was an early, non-Native American population in the Americas. Here we review the patterns revealed by ancient genomics that help to shed light on the past peoples who created the archaeological landscape, and together lead to deeper insights into the population and cultural history of the Americas.

Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry.

Modern humans appeared in Europe by at least 45,000 years ago1-5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.

Across two continents: The genomic basis of environmental adaptation in house mice (Mus musculus domesticus) from the Americas.

Replicated clines across environmental gradients can be strong evidence of adaptation. House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Multiple aspects of climate, such as temperature, vary predictably across latitude in the Americas. Past studies of North American populations across latitudinal gradients provided evidence of environmental adaptation in traits related to body size, metabolism, and behavior and identified candidate genes using selection scans. Here, we investigate genomic signals of environmental adaptation on a second continent, South America, and ask whether there is evidence of parallel adaptation across multiple latitudinal transects in the Americas. We first identified loci across the genome showing signatures of selection related to climatic variation in mice sampled across a latitudinal transect in South America, accounting for neutral population structure. Consistent with previous results, most candidate SNPs were in putatively regulatory regions. Genes that contained the most extreme outliers relate to traits such as body weight or size, metabolism, immunity, fat, eye function, and the cardiovascular system. We then compared these results with the results of analyses of published data from two transects in North America. While most candidate genes were unique to individual transects, we found significant overlap among candidate genes identified independently in the three transects. These genes are diverse, with functions relating to metabolism, immunity, cardiac function, and circadian rhythm, among others. We also found parallel shifts in allele frequency in candidate genes across latitudinal gradients. Finally, combining data from all three transects, we identified several genes associated with variation in body weight. Overall, our results provide strong evidence of shared responses to selection and identify genes that likely underlie recent environmental adaptation in house mice across North and South America.

A comprehensive demographic profile of the US evicted population.

Millions of American renter households every year are threatened with eviction, an event associated with severe negative impacts on health and economic well-being. Yet we know little about the characteristics of individuals living in these households. Here, we link 38 million eviction court cases to US Census Bureau data to show that 7.6 million people, including 2.9 million children, faced the threat of eviction each year between 2007 and 2016. Overall, adult renters living with at least one child in their home were threatened with eviction at an annual rate of 10.4%, twice that of adults without children (5.0%). We demonstrate not only that the average evicted household includes one child, but that the most common age to experience eviction in America is during childhood. We also find that previous studies have underestimated racial disparities in eviction risk: Despite making up only 18.6% of all renters, Black Americans account for 51.1% of those affected by eviction filings and 43.4% of those evicted. Roughly one in five Black Americans living in a renter household is threatened with eviction annually, while one in ten is evicted. Black-White disparities persist across levels of income and vary by state. In providing the most comprehensive description to date of the population of US renters facing eviction, our study reveals a significant undercount of individuals impacted by eviction and motivates policies designed to stabilize housing for children and families.

The age of the opening of the Ice-Free Corridor and implications for the peopling of the Americas.

SignificanceThe Ice-Free Corridor (IFC) has long played a key role in hypotheses about the peopling of the Americas. Earlier assessments of its age suggested that the IFC was available for a Clovis-first migration, but subsequent developments now suggest a pre-Clovis occupation of the Americas that occurred before the opening of the IFC, thus supporting a Pacific coastal migration route instead. However, large uncertainties in existing ages from the IFC cannot preclude its availability as a route for the first migrations. Resolving this debate over migration route is important for addressing the questions of when and how the first Americans arrived. We report cosmogenic nuclide exposure ages that show that the final opening of the IFC occurred well after pre-Clovis occupation.

Factors influencing terrestriality in primates of the Americas and Madagascar.

Among mammals, the order Primates is exceptional in having a high taxonomic richness in which the taxa are arboreal, semiterrestrial, or terrestrial. Although habitual terrestriality is pervasive among the apes and African and Asian monkeys (catarrhines), it is largely absent among monkeys of the Americas (platyrrhines), as well as galagos, lemurs, and lorises (strepsirrhines), which are mostly arboreal. Numerous ecological drivers and species-specific factors are suggested to set the conditions for an evolutionary shift from arboreality to terrestriality, and current environmental conditions may provide analogous scenarios to those transitional periods. Therefore, we investigated predominantly arboreal, diurnal primate genera from the Americas and Madagascar that lack fully terrestrial taxa, to determine whether ecological drivers (habitat canopy cover, predation risk, maximum temperature, precipitation, primate species richness, human population density, and distance to roads) or species-specific traits (body mass, group size, and degree of frugivory) associate with increased terrestriality. We collated 150,961 observation hours across 2,227 months from 47 species at 20 sites in Madagascar and 48 sites in the Americas. Multiple factors were associated with ground use in these otherwise arboreal species, including increased temperature, a decrease in canopy cover, a dietary shift away from frugivory, and larger group size. These factors mostly explain intraspecific differences in terrestriality. As humanity modifies habitats and causes climate change, our results suggest that species already inhabiting hot, sparsely canopied sites, and exhibiting more generalized diets, are more likely to shift toward greater ground use.

Population Genomic Evidence of Adaptive Response during the Invasion History of Plasmodium falciparum in the Americas.

Plasmodium falciparum, the most virulent agent of human malaria, spread from Africa to all continents following the out-of-Africa human migrations. During the transatlantic slave trade between the 16th and 19th centuries, it was introduced twice independently to the Americas where it adapted to new environmental conditions (new human populations and mosquito species). Here, we analyzed the genome-wide polymorphisms of 2,635 isolates across the current P. falciparum distribution range in Africa, Asia, Oceania, and the Americas to investigate its genetic structure, invasion history, and selective pressures associated with its adaptation to the American environment. We confirmed that American populations originated from Africa with at least two independent introductions that led to two genetically distinct clusters, one in the North (Haiti and Colombia) and one in the South (French Guiana and Brazil), and an admixed Peruvian group. Genome scans revealed recent and more ancient signals of positive selection in the American populations. Particularly, we detected positive selection signals in genes involved in interactions with hosts (human and mosquito) cells and in genes involved in resistance to malaria drugs in both clusters. Analyses suggested that for five genes, adaptive introgression between clusters or selection on standing variation was at the origin of this repeated evolution. This study provides new genetic evidence on P. falciparum colonization history and on its local adaptation in the Americas.

So many Nigerians: why is Nigeria overrepresented as the ancestral genetic homeland of Legacy African North Americans?

The genetics of African North Americans are complex amalgamations of various West and Central African peoples with modest gene flow from specific European and Amerindian peoples. A comprehensive understanding of African North American biohistory is a prerequisite for accurate interpretations of the ancestral genetics of this population. Too often, genetic interpretations falter with ahistorical reconstructions. The recently reported overrepresentation of Nigerian lineages in African North Americans reflects pronounced limitations in the African genomic database, the artificiality of the colonial maps of Africa, the contributions of multiple African empires and kingdoms into the transatlantic trade in enslaved Africans, and the overrepresentation of Yoruba peoples in the existing limited representation of West Africans in public genomic databases. This Matters Arising paper is in response to Micheletti et al. (2020), published in The American Journal of Human Genetics. See also the response by Micheletti et al. (2020), published in this issue.

Two Randomized Trials of Neutralizing Antibodies to Prevent HIV-1 Acquisition.

BACKGROUND: Whether a broadly neutralizing antibody (bnAb) can be used to prevent human immunodeficiency virus type 1 (HIV-1) acquisition is unclear. METHODS: We enrolled at-risk cisgender men and transgender persons in the Americas and Europe in the HVTN 704/HPTN 085 trial and at-risk women in sub-Saharan Africa in the HVTN 703/HPTN 081 trial. Participants were randomly assigned to receive, every 8 weeks, infusions of a bnAb (VRC01) at a dose of either 10 or 30 mg per kilogram (low-dose group and high-dose group, respectively) or placebo, for 10 infusions in total. HIV-1 testing was performed every 4 weeks. The VRC01 80% inhibitory concentration (IC80) of acquired isolates was measured with the TZM-bl assay. RESULTS: Adverse events were similar in number and severity among the treatment groups within each trial. Among the 2699 participants in HVTN 704/HPTN 085, HIV-1 infection occurred in 32 in the low-dose group, 28 in the high-dose group, and 38 in the placebo group. Among the 1924 participants in HVTN 703/HPTN 081, infection occurred in 28 in the low-dose group, 19 in the high-dose group, and 29 in the placebo group. The incidence of HIV-1 infection per 100 person-years in HVTN 704/HPTN 085 was 2.35 in the pooled VRC01 groups and 2.98 in the placebo group (estimated prevention efficacy, 26.6%; 95% confidence interval [CI], -11.7 to 51.8; P = 0.15), and the incidence per 100 person-years in HVTN 703/HPTN 081 was 2.49 in the pooled VRC01 groups and 3.10 in the placebo group (estimated prevention efficacy, 8.8%; 95% CI, -45.1 to 42.6; P = 0.70). In prespecified analyses pooling data across the trials, the incidence of infection with VRC01-sensitive isolates (IC80 <1 µg per milliliter) per 100 person-years was 0.20 among VRC01 recipients and 0.86 among placebo recipients (estimated prevention efficacy, 75.4%; 95% CI, 45.5 to 88.9). The prevention efficacy against sensitive isolates was similar for each VRC01 dose and trial; VRC01 did not prevent acquisition of other HIV-1 isolates. CONCLUSIONS: VRC01 did not prevent overall HIV-1 acquisition more effectively than placebo, but analyses of VRC01-sensitive HIV-1 isolates provided proof-of-concept that bnAb prophylaxis can be effective. (Supported by the National Institute of Allergy and Infectious Diseases; HVTN 704/HPTN 085 and HVTN 703/HPTN 081 ClinicalTrials.gov numbers, NCT02716675 and NCT02568215.).

Progress Toward Elimination of Mother-to-Child Transmission of Hepatitis B Virus - Region of the Americas, 2012-2022.

In 2022, an estimated 5 million persons in the World Health Organization Region of the Americas (AMR) were living with chronic hepatitis B virus (HBV) infection, the leading cause of hepatocellular carcinoma and cirrhosis worldwide. Most chronic infections are acquired through mother-to-child transmission (MTCT) or horizontal transmission during childhood and are preventable with hepatitis B vaccination, including a birth dose (HepB-BD), followed by 2-3 additional doses (HepB3) in infancy. The Pan American Health Organization (PAHO) Elimination of MTCT of HBV infection strategy is intended to reduce chronic HBV infection (measured by hepatitis B surface antigen [HBsAg] seroprevalence) to ≤0.1% among children by achieving 1) ≥95% coverage with HepB-BD and HepB3; and 2) ≥80% of pregnant women received testing for HBsAg, and provision of hepatitis B immunoglobulin to HBV-exposed neonates. By 2012, all 51 AMR countries and territories (countries) provided HepB3 nationwide, and by 2021, 34 (67%) provided HepB-BD nationwide. Mathematical models estimate that HBsAg seroprevalence in children is ≤0.1% in 14 (28%) of 51 countries and at the regional level. Three (6%) of 51 countries met the 95% coverage targets for both HepB3 and HepB-BD during both 2021 and 2022. Of these, two have likely met criteria for the elimination of MTCT of HBV infection. However, in 2022, HepB3 coverage had declined by ≥10 percentage points in 15 (37%) of 41 countries with 2012 coverage data for comparison. These declines in HepB3 coverage, as well as the absence of HepB-BD in the routine immunization schedules in 17 countries, threaten PAHO's progress toward the elimination of MTCT of HBV infection. Efforts to introduce HepB-BD and maintain high HepB3 and HepB-BD coverage are needed.

Proceedings of the second international meeting on endemic mycoses of the Americas (IMEMA) and first international symposium on implantation mycoses (ISIM).

The second international meeting on endemic mycoses of the Americas (IMEMA) and the first international symposium on implantation mycoses (ISIM) took place in Santiago del Estero, Argentina, on September 25-27, 2023. The conference provided a platform for researchers, clinicians, and experts to discuss the latest developments in the field of endemic and implantation mycoses. Topics included epidemiology, diagnostic advances, treatment strategies, and the impact of environmental factors on the spread of these fungal diseases. IMEMA and ISIM contributed to the regional discourse on the mycoses, emphasizing the importance of international cooperation in addressing these public health challenges.

IMEMA/ISIM, held in Santiago del Estero, Argentina, convened experts to discuss endemic and implantation mycoses, covering topics such as epidemiology, diagnostics, treatment, and advocacy. The event highlighted ongoing efforts in combating these diseases.

Temporal trends of carbonated soft-drink consumption among adolescents aged 12-15 years from eighteen countries in Africa, Asia and the Americas.

Carbonated soft-drink consumption is detrimental to multiple facets of adolescent health. However, little is known about temporal trends in carbonated soft-drink consumption among adolescents, particularly in non-Western countries. Therefore, we aimed to examine this trend in representative samples of school-going adolescents from eighteen countries in Africa, Asia and the Americas. Cross-sectional data from the Global School-based Student Health Survey 2009-2017 were analysed. Carbonated soft-drink consumption referred to drinking carbonated soft-drinks at least once per day in the past 30 d. The prevalence of carbonated soft-drink consumption was calculated for each survey, and crude linear trends were assessed by linear regression models. Data on 74 055 students aged 12-15 years were analysed (mean age 13·9 (sd 1·0) years; 49·2 % boys). The overall mean prevalence of carbonated soft-drink consumption was 42·1 %. Of the eighteen countries included in the study, significant decreasing, increasing and stable trends of carbonated soft-drink consumption were observed in seven, two and nine countries, respectively. The most drastic decrease was observed in Kuwait between 2011 (74·4 %) and 2015 (51·7 %). Even in countries with significant decreasing trends, the decrease was rather modest, while some countries with stable trends had very high prevalence across time (e.g. Suriname 80·5 % in 2009 and 79·4 % in 2016). The prevalence of carbonated soft-drink consumption was high in all countries included in the present analysis, despite decreasing trends being observed in some. Public health initiatives to reduce the consumption of carbonated soft-drink consumption among adolescents are urgently required.

Income inequality as a determinant of neonatal mortality in the Americas during 2000-2019: implications for the attainment of Sustainable Development Goal target 3.2.

BACKGROUND: The work of the WHO Commission on the Social Determinants of Health has been fundamental to provide a conceptual framework of the social determinants of health. Based on this framework, this study assesses the relationship of income inequality as a determinant of neonatal mortality in the Americas and relates it to the achievement of the Sustainable Development Goal target 3.2 (reduce neonatal mortality to at least as low as 12 deaths per 1,000 live births). The rationale is to evaluate if income inequality may be considered a social factor that influences neonatal mortality in the Americas. METHODS: Yearly data from 35 countries in the Americas during 2000-2019 was collected. Data sources include the United Nations Inter-agency Group for Child Mortality Estimation for the neonatal mortality rate (measured as neonatal deaths per 1,000 live births) and the United Nations University World Institute for Development Economics Research for the Gini index (measured in a scale from 0 to 100). This is an ecological study that employs a linear regression model that relates the neonatal mortality rate (dependent variable) to the Gini index (independent variable), while controlling for other factors that influence neonatal mortality. Coefficient estimates and their robust standard errors were obtained using panel data techniques. RESULTS: A positive relationship between income inequality and neonatal mortality is found in countries in the Americas during the period studied. In particular, the analysis suggests that a unit increase in a country's Gini index during 2000-2019 is associated with a 0.27 (95% CI [- 0.04, 0.57], P =.09) increase in the neonatal mortality rate. CONCLUSION: The analysis suggests that income inequality may be positively associated with the neonatal mortality rate in the Americas. Nonetheless, given the modest magnitude of the estimates and Gini values and trends during 2000-2019, the findings suggest a potential limited scope for redistributive policies to support reductions in neonatal mortality in the region. Thus, policies and interventions that address higher coverage and quality of services provided by national health systems and reductions in socio-economic inequalities in health are of utmost importance.