Roughly 50,000-70,000 years ago, the ancestors of most present-day non-Africans interbred with Neanderthals as they migrated out of Africa into Eurasia. That mixing left a permanent, traceable signature in the human genome. Any individual today carries only around 2% Neanderthal DNA — but because different people carry different surviving fragments, geneticists estimate over 50% of the entire Neanderthal genome is still floating around somewhere across the modern human population, just distributed in pieces.
For years, this was mostly framed as ancestry trivia — a fun percentage on a report, evidence of an epic prehistoric love story. Then COVID-19 happened, and researchers accidentally discovered that one specific chunk of inherited Neanderthal DNA was the single strongest genetic risk factor for severe illness.
The discovery that changed how scientists think about archaic DNA
In 2020, a team led by Svante Pääbo and Hugo Zeberg found that a roughly 50-kilobase segment on chromosome 3 — inherited directly from Neanderthals — was the major genetic risk factor for developing severe COVID-19. Carrying one copy of this variant was associated with nearly double the risk of severe illness. The segment is carried by around 16% of Europeans and, strikingly, around 50% of people in South Asia — a massive difference in prevalence that likely contributed to real, measurable differences in pandemic outcomes across populations.
Chromosome 3 segment
Increases risk of severe COVID-19 illness. Carried by ~50% of South Asians, ~16% of Europeans, rare or absent in East Asians and Africans.
Chromosome 12 segment
A separate Neanderthal-inherited region found in a follow-up study — this one appears protective, reducing risk of needing intensive care by roughly 22%.
The same research group found the effect isn't uniformly bad news — a different Neanderthal-derived segment on chromosome 12 appears to modestly protect against severe outcomes, illustrating that "Neanderthal DNA" isn't a single monolithic risk category. Some inherited fragments raise risk, some lower it, and most do essentially nothing detectable at all.
Beyond COVID: pain, immunity, and more
The COVID findings opened the door to a broader look at what surviving Neanderthal DNA actually does in modern humans. Some of the more established findings:
- Pain sensitivity: A Neanderthal-derived variant in the SCN9A gene, a sodium channel involved in pain signaling, has been linked to a lower pain threshold in people who carry it.
- Immune system shaping: Neanderthal-derived HLA alleles — genes central to immune recognition — are estimated to make up a substantial share of some HLA variation in non-African populations, likely because they offered early modern humans protection against local pathogens Neanderthals had already adapted to.
- Skin tone, hair, and circadian patterns: Multiple studies have linked Neanderthal-derived variants to skin and hair pigmentation and to differences in sleep chronotype (a stronger tendency toward "morning person" traits in some analyses).
See exactly which Neanderthal segments you carry
A basic ancestry percentage tells you almost nothing about which functional variants you actually inherited. Whole genome sequencing captures the specific regions — including the chromosome 3 and chromosome 12 segments tied to COVID severity.
Get Your Whole Genome Sequenced → Use code GENOME for 10% off at Dante LabsThe takeaway
Neanderthal ancestry percentages make for a great party-fact headline, but the more interesting story is underneath: specific, identifiable pieces of that ancient DNA are doing real, measurable work in your immune system, your pain pathways, and — as an entire pandemic demonstrated — potentially in how sick you get from a novel virus. That's a very different kind of "ancestry" than the version most consumer DNA tests present.