Analysis of a markedly larger, higher-coverage, and geographically diverse whole-genome sequencing dataset from 529 ancient individuals sheds important light on the demographic impact of major sociohistorical changes that occurred during the late Medieval period in Scandinavia and the Baltic region and link Christianisation to increased diversity in ancestry before the pandemic.
One of the most devastating events in human history, the Black Death (c.1347-1353), marked the beginning of the Second Plague Pandemic. After initially receding, plague returned in intermittent outbreaks throughout Europe, beginning with the pestis secunda. Despite its significance, the post-Black Death epidemiology of Yersinia pestis remains poorly understood. Here, we report 23 new Y. pestis genomes recovered from Second Plague Pandemic contexts across Scandinavia, the Netherlands, Iceland, and Armenia, spanning approximately 270 years. Applying a reproducible mutation-filtering pipeline to assess genetic diversity, we report both Black Death and post-Black Death lineages and document multiple waves of plague at individual cemetery sites. We identify four pestis secunda genomes, including three from Armenia, supporting the eastward dissemination of this lineage prior to its disappearance from Europe. We also resolve a previously under-characterised Branch 1A sub-lineage of Y. pestis and provide the first genomic evidence of plague in Iceland, resolving longstanding uncertainty over its presence on the island. Finally, by calling variants against a reconstructed ancestral reference, we identify clade-defining mutations, including nonsynonymous changes in metabolic and biofilm-related genes with predicted structural effects that may have contributed to shaping the epidemiological dynamics of the Second Plague Pandemic.
Cameron Ferguson, Å. J. Vågene, Marcel Keller et al.· bioRxiv· 0 citations
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.
Plague, caused by Yersinia pestis, has affected human societies for millennia, yet the timing, scale and biological shifts underlying its earliest spread remain unclear. Here, we screened 1,400 ancient human remains from eastern Eurasia (8,000-400 cal. BP) and recovered three prehistoric Y. pestis genomes, including one from East Asia. Integrating these data with 136 published ancient and modern Y. pestis genomes, we resolved a trans‑Eurasian polytomy dated to ~5.3 ka BP that links Scandinavia, Central Europe, and northern China. Low SNP distances and tip-dating indicate splits over century‑scale intervals across > 7,500 km (median lower-bound dispersal rate of 32.9 km yr⁻¹), consistent with rapid long-distance dispersal. Mapping variation onto the deep phylogeny showed that the basal stem of the LNBA⁺ lineage is the only one of the seven deep phases examined to show significant enrichment of disruptive genomic remodeling relative to the genome-wide background distribution of mutation categories, including acquisition of the ymt gene and multiple gene‑disrupting indels and gene losses. This phylogenetic concentration is consistent with an early episode of adaptation associated with later flea-adapted lineages. Our results extend the prehistoric record of plague into East Asia and refine the timing and scale of its earliest trans-Eurasian expansion. Plague, caused by the pathogen Yersinia pestis, has affected human societies for millennia. Here, the authors screened 1,400 ancient human remains from eastern Eurasia and recovered three prehistoric Y. pestis genomes, extending the prehistoric record of plague into East Asia and refining the timing and scale of its earliest trans-Eurasian expansion.
Mpox has re-emerged as a significant global zoonotic threat, driven mainly by two large waves the 2022 worldwide Clade IIb outbreak and the 2024 Clade Ib epidemic in Central Africa. This review examines the challenges of interpreting this evolving virus from molecular, epidemiological, and bioinformatics perspectives, with a focus on global health workforce preparedness. Clade IIb largely moved through sexual transmission across countries, but Clade Ib has appeared in a wider population-women, children, and individuals infected through household spread without any sexual contact. Early case series suggest that Clade Ib may cause a more severe disease burden, but more research is needed to directly compare severity and fatality rates with Clade IIb due to the limited number of current studies. The review examines the virus's strategies for evading the host's immune defenses throughout its ~197 kbp genome, including how it disrupts interferon signaling and creates decoy receptors. This review summarizes the clinical findings of PALM007 and STOMP, noting that neither trial achieved its main efficacy endpoint making routine tecovirimat use less compelling-while leaving open whether it helps particular high-risk groups. A further point is that immunity from the MVA-BN vaccine wanes with time, leading to the growing adoption of booster vaccinations. In conclusion, the review calls for a One Health approach pairing genomic tracking with ecological intelligence and including wastewater surveillance to fill existing gaps in knowledge and enhance the global handling of new orthopoxvirus threats.
Rajtilak Detroja, Muktesh Chandra· Journal of Microbiological M...· 0 citations
Genetic evidence indicates that most humans descend from a single tribe that 70,000–40,000ya rapidly replaced the
entire Eurasian population while also gradually expanding within Africa. This rapid expansion of one tribe is supported by five
lines of genetic evidence: (1) Y-chromosome data tracing most non-African male lineages to haplogroup CT 70,000ya; (2)
mitochondrial DNA, which shows that most non-Africans descend from haplogroup L3 and its M and N branches that spread across
Eurasia 70,000ya; (3) nuclear DNA analyses confirming that all non-Africans derive from a single migration event 70,000–50,000ya;
(4) evidence of genetic bottleneck; (5) 2% Neanderthal DNA in all non-Africans, showing interbreeding before Eurasian dispersal.
What social, cognitive, or technological advantage enabled this extraordinary expansion? The discovery of three discrete levels of
language comprehension in modern individuals suggests the possibility that this ancestral tribe experienced a leap from the
Modifier to the Syntactic Phenotype, unlocking unprecedented capacities for coordination, strategizing, and deception.
A. Vyshedskiy· Evolutionary Linguistic Theo...· 0 citations
Influenza A(H1N1)pdm09 remains one of the predominant seasonal influenza viruses worldwide and continues to evolve under the combined effects of host immunity, vaccination, and changing epidemiological conditions. However, the long-term impact of the COVID-19 pandemic on its evolutionary dynamics remains poorly understood. We investigated the genetic variability and phylodynamic evolution of the hemagglutinin (HA) and neuraminidase (NA) genes of Italian A(H1N1)pdm09 viruses collected between 2009 and 2026. Time-calibrated phylodynamic analyses, Bayesian Skyline Plots (BSPs), Lineages Through Time (LTT) graphs, principal component analysis (PCA), and codon-based selection analyses were used to characterize long-term evolutionary patterns. Both HA and NA followed continuous evolutionary trajectories, with a marked post-2020 genetic shift associated with the emergence of 6B.1A.5a.2-related clades. HA showed greater evolutionary variability than NA, whereas selection analyses identified only one positively selected site in HA and none in NA, consistent with reduced adaptive diversification in recent strains. Phylodynamic analyses revealed a marked decline in effective population size and lineage accumulation during the COVID-19 pandemic, followed by renewed expansion after 2022. Overall, Italian A(H1N1)pdm09 viruses exhibited reduced genetic diversity, limited evidence of positive selection, and coordinated genomic restructuring following the pandemic. These findings provide new insights into the long-term evolutionary dynamics of A(H1N1)pdm09 in Italy and reinforce the importance of sustained genomic surveillance for anticipating evolutionary changes and informing evidence-based public health strategies.
Maria Perra, Ilaria Deplano, I. Azzena et al.· Pathogens· 0 citations
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