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PubMed2026

Tracing the evolution and diversity of human parvovirus B19 across human history.

Human parvovirus B19 (B19V) is an ubiquitously spread, exclusively human pathogen, mainly posing risks to children, as well as pregnant and immunocompromised individuals. Despite evidence of B19V infection of human populations as far back as 7,000 years, the evolutionary history of B19V remains poorly understood. In this study, we present B19V genomic data from the remains of 53 globally distributed individuals spanning more than 8,000 years, including 7 children. Our findings suggest that the most recent common ancestor of all present B19V lineages existed around 12,000 years ago, at the end of the last Ice Age. Additionally, we identified an extinct Eurasian clade that participated in the recombination event that led to the emergence of B19V genotype 2 (GT-2). We date this event to ∼3,200-1,800 BP, potentially in the greater Mediterranean area. Our study shows aspects of how ancient parvovirus variants arose, disseminated, and impacted human health through time.

ancient DNA↗
PubMed2026

Ancient DNA and Human Physiology.

Ancient DNA (aDNA) enables the reconstruction of chronologically sampled genomes from ancient humans, animals, plants, pathogens, and microorganisms, as well as environmental DNA, providing a record of biological changes through time. Improvements in short and degraded DNA extraction methods and low-cost sequencing now enable the generation of broad, cross-regional datasets that expand evolutionary analyses from past population demography to biological mechanisms. By tracking temporal shifts of allele frequencies, integrating functional genomics resources (e.g., gene expression, chromatin structure variation), modeling population demography to separate selection from genetic drift, and aligning genetic changes with archaeological, cultural, and climatic data, aDNA has the potential to link sequence variation to physiological function within their temporal and environmental contexts. In this review, we summarize illustrative case studies from aDNA research spanning complex traits, dietary adaptations, and responses to pathogens and other environmental changes, showing how human biology has evolved under multiple selective pressures through time. These dated signals help triage experimental work and expose mechanisms that are rare or absent in living cohorts. Although some challenges remain, such as geographic and temporal sampling disparities, limitations in data resolution and variant detection, and genotype-phenotype uncertainties, rapid methodological progress and stronger ethical frameworks are expanding what can be inferred, making aDNA a promising tool for refining physiological pathways, their timing, and their drivers.

Humans↗
PubMed2026

Genomic insights into preantibiotic osteomyelitis pathogens and their link to current resistant hospital strains.

OBJECTIVES: Osteomyelitis is a severe bone infection that was frequently fatal before the introduction of antibiotics and remains a significant healthcare burden today. Staphylococcus aureus is the most common cause, alongside other hospital-acquired pathogens. Despite their clinical importance, the evolutionary history of these bacteria remains poorly understood. We investigated historical osteomyelitis specimens to identify causative pathogens and characterise their genomes, virulence and antimicrobial resistance (AMR). METHODS: Seven osteomyelitis-affected bones from adults dating to 19th-20th century Germany were analysed using ancient DNA (aDNA) approaches. After sequencing and screening, candidate pathogens were prioritised based on authentic aDNA damage patterns, established association with osteomyelitis and exclusion as environmental contaminants. Identified species were characterised by phylogenetics, multilocus sequence typing and virulence/AMR profiling. RESULTS: In four patients, we detected authentic aDNA from Acinetobacter baumannii, S. aureus or Streptococcus pyogenes. Detected taxa in the remaining three patients did not fulfil the criteria for further analysis. Two patients carried A. baumannii genomes clustering closely with modern avian and freshwater isolates. Both harboured virulence genes, alongside intrinsic efflux pumps and β-lactamases. One patient carried an S. aureus strain belonging to the globally disseminated clonal complex 30, responsible for outbreaks since the 1950s. Molecular dating indicated that this strain diverged from the wider lineage around 1800, placing it among the earliest members of this group. It encoded multiple virulence genes, but no methicillin resistance genes. The fourth patient carried an S. pyogenes strain related to modern epidemic lineages from North America, encoding conserved virulence factors, but no AMR genes. CONCLUSIONS: These specimens provide a window into the evolution of osteomyelitis pathogens. Although modern developments such as widespread antibiotic use have intensified the global resistance crisis, our findings indicate that the genetic foundations for pathogenicity and resistance were already present more than 100 years ago.

Ancient DNA↗
PubMed2026

An ancient alpharetrovirus lineage in bats: Evolutionary insights and possible roles in reproduction.

Alpharetroviruses are an important group of pathogens known to cause leukemias and tumors, and were historically considered to be restricted to avian hosts. The identification of alpharetrovirus-like envelopes in bat genomes has hinted at a potentially wider host range, although their relations to modern alpharetroviruses and distribution remains unclear. Through a paleovirological screening of 818 vertebrate genomes we identified CHIRalphaEnv, a lineage that belongs firmly within alpharetroviruses, and emerged from a cross-class transmission from saurian hosts. We determine that CHIRalphaEnv envelope genes have been co-opted across bats on eight separate occasions between 43.8 and 18.9 million years ago and are preserved in most bat genomes screened. CHIRalphaEnv elements encode full-length envelope proteins and have been maintained under purifying selection, demonstrating multiple instances of exaptation by their bat hosts and a likely ubiquitous function. We observe high expression levels of CHIRalphaEnv envelopes in endometrium tissue from Carollia perspicillata, suggesting an involvement in reproductive function. We find CHIRalphaEnv sequence relatives in multiple mammalian clades (Afrotherians, rodents and bats), expanding the host range and extending origins of alpharetroviruses beyond 43 million years. We also propose the first mammalian co-opted Endogenous retrovirus (ERV) derived from an Alpharetrovirus envelope and explore the convergent functional recruitment of CHIRalphaEnv in hemochorial placentation in bats, elephant shrews and spiny mice. These findings highlight alpharetroviruses as a previously underappreciated source of functional exaptation in mammals.

Animals↗
PubMed2026

Ten millennia of purifying selection on HLA-B27 reveals an ancient epidemic-scale burden of spondyloarthritis in West Eurasia.

HLA-B27 exemplifies an evolutionary trade-off between protection against infection and susceptibility to inflammatory disease. To investigate its long-term population history, this study examined three HLA-B27-tagging variants-rs116488202, rs4349859, and rs116666910-in present-day populations from UK biobank and 1000 Genomes Project, and in 15,836 ancient West Eurasian individuals. The estimated frequency of HLA-B27 reached 49.0% approximately 8500 years before present, then declined progressively to 3.9% in the present-day reference population. Comparison with genome-wide association study (GWAS) data for ankylosing spondylitis (AS) showed that HLA-B27-linked alleles conferring increased disease risk had negative selection coefficients, indicating sustained selection against HLA-B27 over the past 10,000 years. The decline coincided with major Holocene changes in settlement and subsistence patterns, microbial exposure, and enteric infection, which may have increased the inflammatory costs of HLA-B27. Because previous paleopathological studies have largely been limited to identifying advanced skeletal manifestations of AS, this ancient genetic study may provide currently the most sensitive population-level record of an otherwise largely undetectable, epidemic-scale disease burden in antiquity. These findings support the hypothesis that HLA-B27-associated spondyloarthritis was sufficiently prevalent and severe to influence human evolution in prehistoric West Eurasia.

Humans↗
PubMed2026

Ancient DNA as a temporal lens: reconstructing evolution, migration, and disease dynamics.

Ancient DNA (aDNA) has transformed evolutionary biology and anthropology by providing direct, chronologically validated genetic evidence over millennia. This review synthesizes significant findings from the paleogenomic era (2010-2025), demonstrating how ancient DNA has resolved persistent debates across four interconnected themes: (i) human migration and admixture, revealing complex population transitions from archaic hominins to Holocene expansions; (ii) adaptation, tracking allele frequency changes during domestication and selection; (iii) pathogen history, clarifying the origins of pandemics and the evolution of microbiomes; and (iv) ecosystem dynamics, identifying extinction causes through sedimentary DNA and conservation genomics. We contend that scientific rigor and ethical stewardship are crucial for accurate conclusions, given ancient DNA study requires the destructive collection of culturally significant remains. This review argues that continued advancement will depend on the integration of genomic data with archaeological, isotopic, and proteomic evidence, and highlights the necessity for equitable involvement with descendant communities. By conceptualizing the past as a continuum of dynamic processes rather than static events, ancient DNA provides a revised historical narrative and insights relevant to contemporary concerns in conservation, health, and social justice.

Evolution↗
PubMedDate not supplied

[Changes in the positive P.A.S. reaction of the cytoplasm of giant cells. Role of etiologic factors and the giant cell reaction].

The search for alpha-amylase resistant, P.A.S. positive cytoplasm has been carried out in 206 giant cell lesions with or without specific inflammatory features and with neogenetic and degenerative plasmodia. It allowed to distinguish: --P.A.S. positivity in inflammatory cells of any nature, however with quantitative variations linked to etiologic factors (pathogen agent and disposition), to site, to the age of the plasmodia, and particularly, with negativation of the reaction in ancient lesions;--negativity of the neogenetic and degenerative plasmodia, save the giant cell articular lesions. Cells containing glycogen particularly (muscular tumors, renal or placental) are easily identified thanks to enzymatic digestion tests. Variations observed in the inflammatory cells seem to be the reflect of an active metabolism bringing about resorption phenomena but probably also immunization processes acting at the level of the cellular microenvironment.

Cytoplasm↗
PubMed1979

[Seasonal and periodic rhythms of infectious diseases (author's transl)].

The causes of epidemics are plainly not the pathogens alone as was initially assumed by Koch's school, predisposition and constitution of the population proved to be equally important. Ever since ancient times problems linked with the "constitutio epidemica" have been topical; the "physis", the "natura hominis" and the invironment of man play an increasingly important role in the symptomatology of disease, as can be gathered from such early documents as the "Corpus hippocraticum". Fracastoro distinguished between contagious and non-contagious epidemics. The casual organisms were considered to be miasmas -- noxious emanations -- or "contagia" i.e. likewise toxic substances. Questions concerning the origin of these miasmas turned attention to the environment (air, soil, water) and even led to astrological medicine. Not until the Renaissance were attempts made to differentiate the usual global words for epidemic, such as "loimos", "lues" and "pestis" with the result that a symptom was used more and more to designate a disease. For example, the symptom fever led to the designation "three-day fever" or "four-day fever", "typhus fever". This terminology made a differential diagnosis difficult to establish, thwarted selection measures to check epidemics and the medical world was thus helpless in explaining the causal agents and the phenomena of epidemics. This is illustrated by some epidemiological examples (ergotism, scurvy, yellow fever, English sweat, diphtheria and malaria). In this connection the "morbus novus", the transformation of the pathogen and the change of the pathogen is discussed. Many questions still left unanswered regarding the seasonal incidence, the fluctuation and disappearance of epidemics over decades or even centuries lead more frequently to sociomedical considerations with respect to the victims of epidemics, their predisposition, constitution and environment exposure term "hospital gangrene" with the modern term "hospitalism", we are not dealing with a transformation but a change of the pathogen. The impressive effects produced by antibiotics resulted in carelessness and along with the unprecedented advances in medicine and engineering we forgot to bear in mind that almost all great steps forward have an adverse side. Hygiene and practical medicine have only made a modest beginning in establishing the contact which should indeed be a matter of course in the hospital.

Adult↗
PubMed2026

[Syphilis and human treponemes: a long evolutionary history revealed by paleogenomics].

Recent discoveries in paleogenomics have revolutionized our understanding of syphilis and other human treponematoses. Far from being a pathogen that suddenly appeared in Europe in the late Middle Ages, we now know that Treponema pallidum has been circulated among human populations for millennia. Ancient genomes recovered from pre-Columbian contexts in the Americas show that major treponemal lineages had already diversified well before the modern era, often in the absence of recognizable skeletal lesions. Genomic analyses further indicate that treponemal diversity is not the result of extensive genetic acquisition, but rather of small-scale modulation of a highly conserved genome, notably via antigenic variation involving the tpr gene family. Combined with data on endemic treponematoses, congenital syphilis, and historical pathology collections, these findings support a model in which syphilis, yaws, and bejel represent context-dependent expressions of an ancient treponemal continuum, with implications for diagnosis, epidemiology, and vaccine design.

Humans↗
PubMed2026

Three thousand five hundred years of sheeppox virus evolution inferred from archaeological and codicological genomes.

Sheeppox virus (SPPV) is a major livestock pathogen causing economic hardship through reduced production and death of vulnerable sheep, with written descriptions of sheeppox-like disease recorded since antiquity. We report 21 novel ancient SPPV genomes spanning the Eurasian steppe Bronze Age (∼1700 BCE) to the Early Modern period in Western Europe, including multiple genomes obtained from medieval parchment. We estimate that major capripoxvirus lineages diverged ∼11,500 to 3700 years ago, overlapping known translocations and bio-cultural developments in sheep. Our dataset supports SPPV diverging first within the lineage leading to goatpox virus and lumpy skin disease virus, and that known gene inactivation events within SPPV and goatpox virus occur in our earliest SPPV genomes. These findings reveal that the food security of Eurasian communities has been threatened by sheeppox for more than 3700 years and provide insights into the genomic evolution and potential host adaptation of SPPV.

Animals↗
PubMed1992

Features of cholera and Vibrio parahaemolyticus diarrhoea endemicity in Calabar, Nigeria.

The clinical and epidemiological features of acute vibrio diarrhoeal disease were studied in 881 patients seen at the University of Calabar Teaching Hospital (UCTH), Calabar, Nigeria, between January and December 1989. Stools and rectal swabs of patients and randomly-selected control subjects were microscopically and culturally examined for the presence of enteric pathogens. Households of vibrio diarrhoea cases and matched controls were visited for ecologic studies. Of a total of 108 (12.3%) culturally-confirmed bacterial diarrhoeas, 47 (43.5%) were due to Escherichia coli, 33 (30.6%) to Vibrio cholerae-01 (classical and El Tor biotypes) and V. parahaemolyticus, while shigellae and salmonellae accounted for 29 (26.9%) and 9 (8.3%) cases, respectively. Most cholera case households clustered within the ancient neighbourhood of the inner city, characterized by poorly developed water and sewage disposal systems. A preponderance of vibrio diarrhoea patients were children < or = 10 years. Adult cases involved mostly females. The only case of diarrhoea-related death involved an eight-month old child with kwashiorkor and V. parahaemolyticus infection. Incidence of vibrio diarrhoeas was seasonal, with most cases occurring during the dry season followed by subsidence at the onset of rainy season. Bimodal peaks of vibrio diarrhoeal episodes observed over the period appeared to coincide with periods of acute water scarcity, high temperature, increased fishing activities and trade traffic on the Calabar River estuary. Of the environments sampled, only clam shells from a case household and river sediments yielded vibrio pathogens on culture. Ecological factors that are capable of stabilizing a focus of vibrio diarrhoea endemicity in this area are highlighted.

Adolescent↗
PubMed2024

Genomic insights from a deeply phenotyped highly consanguineous neurodevelopmental disorders cohort.

PURPOSE: The genetic underpinning of neurodevelopmental disorders (NDDs) in diverse ethnic populations, especially those with high rates of consanguinity, remains largely unexplored. Here, we aim to elucidate genomic insight from 576 well-phenotyped and highly consanguineous (16%) NDD cohort. METHODS: We used chromosomal microarray (CMA; N:247), exome sequencing (ES; N:127), combined CMA and ES (N:202), and long-read genome sequencing to identify genetic etiology. Deep clinical multivariate data were coupled with genomic variants for stratification analysis. RESULTS: Genetic diagnosis rates were 17% with CMA, 29.92% with ES, and 37.13% with combined CMA and ES. Notably, children of consanguineous parents showed a significantly higher diagnostic yield (P < .01) compared to those from nonconsanguineous parents. Among the ES-identified pathogenic variants, 36.19% (38/105) were novel, implicating 35 unique genes. Long-read sequencing of seizure participants unresolved by combined test identified expanded FMR1 trinucleotide repeats. Additionally, we identified 2 recurrent X-linked variants in the G6PD in 3.65% (12/329) of NDD participants. These variants were absent in large-population control cohorts and cohort comprising neurodevelopmental and neuropsychiatric populations of European descendants, indicating a possible associated risk factor potentially resulting from ancient genetic drift. CONCLUSION: This study unveils unique clinical and genomic insights from a consanguinity rich Bangladeshi NDD cohort.

Humans↗
PubMed2026

Ancestry, admixture, and pathogens in contemporaneous Neolithic farmers and foragers on the Island of Gotland.

Two archaeological cultural complexes; the Neolithic Funnelbeaker culture (FBC) and the Pitted ware culture (PWC), coexisted on Gotland for over 500 years, between ~3300 and 2800 calBCE. The ancestry of the FBC farmers and PWC marine foragers largely aligns with European Neolithic Farmers and European Mesolithic foragers, respectively, but the direct interactions between the groups on Gotland is not understood. We present a Middle Neolithic (MN) high-coverage genome and a Late Neolithic (LN) low-coverage genome from the Ansarve FBC dolmen. We investigate ancestry, admixture, and pathogens among these MN farmers (n&#x2009;=&#x2009;6), foragers (n&#x2009;=&#x2009;19), and the LN individual. We find that recent gene-flow between farmers and foragers could have taken place, although most gene-flow happened prior to their coexistence on the island. We also find evidence of different Yersinia pestis strains in the three cultural groups, showing that the pestis was widespread among groups with different subsistence strategies.

Humans↗