Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.

ABSTRACT: The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has emphasized the vulnerability of human populations to novel viral pressures, despite the vast array of epidemiological and biomedical tools now available. Notably, modern human genomes contain evolutionary information tracing back tens of thousands of years, which may help identify the viruses that have impacted our ancestors-pointing to which viruses have future pandemic potential. Here, we apply evolutionary analyses to human genomic datasets to recover selection events involving tens of human genes that interact with coronaviruses, including SARS-CoV-2, that likely started more than 20,000 years ago. These adaptive events were limited to the population ancestral to East Asian populations. Multiple lines of functional evidence support an ancient viral selective pressure, and East Asia is the geographical origin of several modern coronavirus epidemics. An arms race with an ancient coronavirus, or with a different virus that happened to use similar interactions as coronaviruses with human hosts, may thus have taken place in ancestral East Asian populations. By learning more about our ancient viral foes, our study highlights the promise of evolutionary information to better predict the pandemics of the future. Importantly, adaptation to ancient viral epidemics in specific human populations does not necessarily imply any difference in genetic susceptibility between different human populations, and the current evidence points toward an overwhelming impact of socioeconomic factors in the case of coronavirus disease 2019 (COVID-19).

SUBMITTER: Souilmi Y

PROVIDER: S-EPMC8223470 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Ancient genomics in insular East Asia

Project description:Ancient genomics reveals tripartite origins of Japanese populations

| PRJEB43762 | ENA

Ancient genome from Devil's Gate (East Asia)

Project description:7,700 year-old, low coverage (<0.1X in total) early Neolithic genomes from the Devil's Gate Cave in the Russian Far East.

| PRJEB14817 | ENA

Earliest domestication of common millet (Panicum miliaceum) in East Asia extended to 10,000 years ago.

Project description:The origin of millet from Neolithic China has generally been accepted, but it remains unknown whether common millet (Panicum miliaceum) or foxtail millet (Setaria italica) was the first species domesticated. Nor do we know the timing of their domestication and their routes of dispersal. Here, we report the discovery of husk phytoliths and biomolecular components identifiable solely as common millet from newly excavated storage pits at the Neolithic Cishan site, China, dated to between ca. 10,300 and ca. 8,700 calibrated years before present (cal yr BP). After ca. 8,700 cal yr BP, the grain crops began to contain a small quantity of foxtail millet. Our research reveals that the common millet was the earliest dry farming crop in East Asia, which is probably attributed to its excellent resistance to drought.

| S-EPMC2678631 | biostudies-literature

East Asia is most at risk of human flu epidemic, experts say.

Project description: Not available

| S-EPMC1261177 | biostudies-literature

Type 2 diabetes epidemic in East Asia: a 35-year systematic trend analysis.

Project description:Facing the challenge of effective prevention type 2 diabetes (T2DM) in China (as part of global health) requires knowledge about both the temporal trend and risk factors variation in T2DM. We searched the PubMed, CNKI, WANFANG, and International Diabetes Federation (IDF) databases for data on the prevalence of T2DM/ IGT (impaired glucose tolerance) published from January 1, 1980 to December 31, 2014 in China, Japan and Korea. The prevalence of T2DM was estimated with 95% confidence intervals (CIs) using random-effects meta-analysis. T2DM prevalence trend in the next 10 years was estimated by using a time series regression model based on the 35 years of data. The 621 articles covered 11.8 million Chinese people, 1.64 million Japanese, and 37.69 million Koreans. The aggregate prevalence of T2DM in China has increased sharply from 1.3% in 1980-1989 to 4.5% in 1990-1999, 6.8% 2000-2009, and 8.7% in 2010-2014. We estimated that by 2025, T2DM prevalence will have grown to 12.5%. Central obesity is the largest preventable cause of T2DM. We also found that female having a very high BMI (body mass index, ≥28 kg/m2) and being an older (≥50 years old) female are next-highest risk factors for T2DM compared with male. Consistent with the patterns characterized for China, T2DM prevalence in Japan increased with aging, and men were more likely to develop T2DM. It was the same as Korea. In the Far East, especially in China, T2DM prevalence will continue to increase until 2025. Statistical analyses were conducted using Stata 12.0 and SPSS 19.0.

| S-EPMC5805508 | biostudies-literature

Ancient inland human dispersals from Myanmar into interior East Asia since the Late Pleistocene.

Project description:Given the existence of plenty of river valleys connecting Southeast and East Asia, it is possible that some inland route(s) might have been adopted by the initial settlers to migrate into the interior of East Asia. Here we analyzed mitochondrial DNA (mtDNA) HVS variants of 845 newly collected individuals from 14 Myanmar populations and 5,907 published individuals from 115 populations from Myanmar and its surroundings. Enrichment of basal lineages with the highest genetic diversity in Myanmar suggests that Myanmar was likely one of the differentiation centers of the early modern humans. Intriguingly, some haplogroups were shared merely between Myanmar and southwestern China, hinting certain genetic connection between both regions. Further analyses revealed that such connection was in fact attributed to both recent gene flow and certain ancient dispersals from Myanmar to southwestern China during 25-10?kya, suggesting that, besides the coastal route, the early modern humans also adopted an inland dispersal route to populate the interior of East Asia.

| S-EPMC4379912 | biostudies-literature

Mitochondrial genomes from modern and ancient Turano-Mongolian cattle reveal an ancient diversity of taurine maternal lineages in East Asia.

Project description:Turano-Mongolian cattle are a group of taurine cattle from Northern and Eastern Asia with distinct morphological traits, which are known for their ability to tolerate harsh environments, such as the Asian steppe and the Tibetan plateau. Through the analysis of 170 mitogenomes from ten modern breeds, two sub-lineages within T3 (T3119 and T3055) were identified as specific of Turano-Mongolian cattle. These two T3 sub-lineages, together with the previously identified T4, were also present in six Neolithic samples, dated to ~3900 years BP, which might represent the earliest domestic taurine stocks from Southwest Asia. The rare haplogroup Q, found in three Tibetan cattle, testifies for the legacy of ancient migrations from Southwest Asia and suggests that the isolated Tibetan Plateau preserved unique prehistoric genetic resources. These findings confirm the geographic substructure of Turano-Mongolian cattle breeds, which have been shaped by ancient migrations and geographic barriers.

| S-EPMC8178343 | biostudies-literature

Tobacco control challenges in East Asia: proposals for change in the world's largest epidemic region.

Project description:East Asia is one of the world's largest tobacco epidemic regions. Although several international studies have evaluated the status of tobacco control in this region, the findings have not been integrated with knowledge on domestic activities at the national and municipal levels. We analysed the current tobacco control situation in three East Asian countries, Japan, China and the Republic of Korea, using both international and domestic data sources. We collected data between 2008 and 2011 in each country according to the framework of WHO's MPOWER (Monitoring, Protect, Offer, Warn, Enforcement and Raise) approach for guiding implementation of the WHO Framework Convention on Tobacco Control. Analysis revealed that 37-53% of adult men were current smokers and that smoking prevalence among middle-aged men reached 63%. Less than 20% of male smokers plan to quit and the use of nicotine replacement drugs was 14% at maximum. Forty-six percent or more of men and 20% or more of women were exposed to passive smoking at workplaces and at home, respectively. Many tobacco industry activities remain unrestricted and prevalent. Our findings indicate an urgent need for the following set of policies: raise cigarette prices to increase the quit attempt rate, particularly among adult men; develop a multi-component quitting assistance system to provide adequate assistance for smoking cessation; implement effective smoke-free policies in workplaces and public places to reduce exposure to passive smoking; and rebuild the administrative structure to denormalise tobacco industry activities. The importance of these standard approaches should be reaffirmed by all tobacco control policymakers in East Asia.

| S-EPMC4078676 | biostudies-literature

Palaeoproteomic analysis of Pleistocene cave hyenas from east Asia

Project description:Spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances being found between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. This marks the first proteomic data generated from cave hyenas, adding new molecular data to the east Asian populations. Phylogenetic analysis based on these protein sequences reveals two different groups of cave hyenas in east Asia, one of which could not be distinguished from modern spotted hyenas from northern Africa, tentatively the result of previously suggested gene flow between these lineages. With developments of instrumentation and analytical methods, proteomics holds promising potential for the phylogenetic reconstruction of ancient fauna previously thought to be unreachable using ancient DNA.

2020-10-19 | PXD020530 | Pride

A20 Haploinsufficiency in East Asia.

Project description:A20, encoded by the TNFAIP3 gene, is a negative regulator of tumor necrosis factor (TNF)-nuclear factor-κB signaling. It was recently demonstrated that A20 haploinsufficiency (HA20), caused by a heterozygous mutation in the TNFAIP3 gene, can present as an early onset autoinflammatory disease resembling Behçet's disease (BD). In addition to autoinflammatory symptoms, HA20 was also reported to be associated with autoimmune diseases and immunodeficiency. Because the phenotypes associated with HA20 are broad, with different severities observed even among individuals in the same family with identical mutations, it has been assumed that the symptoms of HA20 may depend on genetic background and environmental factors. In this review, we summarize the characteristics of patients with HA20 in East Asia and compare these with patients in other regions, mainly the USA and Europe. Patients with HA20 in East Asia developed recurrent fever more frequently than patients in other regions, but were less likely to develop typical BD symptoms such as skin rashes and genital ulcers. In addition, patients with HA20 in East Asia had low rates of complication with autoimmune diseases and low autoantibody detection rates. While anti-TNF-α agents were the primary treatments for severe HA20 in East Asia, anti-interleukin-1 agents and Janus kinase inhibitors were also administered in other regions. Future studies will need to establish methods for analyzing the pathophysiology of HA20 and determining optimal treatment strategies for each patient.

| S-EPMC8664410 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data