CoVID-19重症化リスクをもたらす3番染色体上の遺伝子

CoVID-19が広がって1年経ちますが、未だに国によって、感染率が大きく違います。

交絡因子が多く、環境要因、特に言語による飛沫の量や肥満度などが影響していて、遺伝的要因が影響していることを証明するのは難しいことです。

しかし間違いなく遺伝的要因はあるはずです。

その中で分かった一つの遺伝子はネアンデルタール人からもたらされたものです。

誤解して欲しくないのはネアンデルタール人は決して野蛮だとか知能が低いということは無く、脳の容積はホモサピエンス男性の1400mLに対して、ネアンデルタール人男性は1600mLでした。

（因みにアインシュタインは2000mLあったそうです。）

ネアンデルタールは絵を描き、小集団で狩りを行い、火を起こすことができ、抽象的な記号を書き、病人を看病して食事を与えていたことも分かっています。

身長は男性で160cm程度と低かったですが、全身の筋力は凄くて握力は平均で80kg程度あったようです。

ホモサピエンスが突然変異によって、言語を使う能力が急速に伸び、それによって文化を伝承し、工夫を積み重ねることができるようになりました。

走る能力と言語能力以外ではホモサピエンスの方が劣っていたのです。

医師や科学者の中にも「アフリカ人の遺伝子は〜」という奇妙な言い方をする人がいるので、以下のページでホモサピエンスの歴史を概観しました。

→ ＜ホモサピエンスに至る歴史＞

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＜Abstract＞

最近の遺伝子関連研究1は、SARS-CoV-2に感染した後の呼吸不全のリスク遺伝子座として3番染色体上の遺伝子クラスターを特定しました。 COVID-19の入院患者3,199人と対照者を含む別の研究（COVID-19 Host Genetics Initiative）は、このクラスターがSARS-CoV-2感染および入院後の重篤な症状の主要な遺伝的危険因子であることを示しました 。

ここでは、ネアンデルタール人から受け継がれ、南アジアの人々の約50％、ヨーロッパの人々の約16％が担っている、サイズが約50キロベースのゲノムセグメントによってリスクがもたらされることを示します。

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https://www.nature.com/articles/s41586-020-2818-3

Abstract

The COVID-19 pandemic has caused considerable morbidity and mortality, and has resulted in the death of over a million people to date3. The clinical manifestations of the disease caused by the virus, SARS-CoV-2, vary widely in severity, ranging from no or mild symptoms to rapid progression to respiratory failure4. Early in the pandemic, it became clear that advanced age is a major risk factor, as well as being male and some co-morbidities5. These risk factors, however, do not fully explain why some people have no or mild symptoms whereas others have severe symptoms. Thus, genetic risk factors may have a role in disease progression. A previous study1 identified two genomic regions that are associated with severe COVID-19: one region on chromosome 3, which contains six genes, and one region on chromosome 9 that determines ABO blood groups. Recently, a dataset was released by the COVID-19 Host Genetics Initiative in which the region on chromosome 3 is the only region that is significantly associated with severe COVID-19 at the genome-wide level (Fig. 1a). The risk variant in this region confers an odds ratio for requiring hospitalization of 1.6 (95% confidence interval, 1.42–1.79)

Main

The genetic variants that are most associated with severe COVID-19 on chromosome 3 (45,859,651–45,909,024 (hg19)) are all in high linkage disequilibrium (LD)—that is, they are all strongly associated with each other in the population (r2 > 0.98)—and span 49.4 thousand bases (kb) (Fig. 1b). This ‘core’ haplotype is furthermore in weaker linkage disequilibrium with longer haplotypes of up to 333.8 kb (r2 > 0.32) (Extended Data Fig. 2). Some such long haplotypes have entered the human population by gene flow from Neanderthals or Denisovans, extinct hominins that contributed genetic variants to the ancestors of present-day humans around 40,000–60,000 years ago6,7. We therefore investigated whether the haplotype may have come from Neanderthals or Denisovans.

The index variants of the two studies1,2 are in high linkage disequilibrium (r2 > 0.98) in non-African populations (Extended Data Fig. 3). We found that the risk alleles of both of these variants are present in a homozygous form in the genome of the Vindija 33.19 Neanderthal, an approximately 50,000-year-old Neanderthal from Croatia in southern Europe8. Of the 13 single nucleotides polymorphisms constituting the core haplotype, 11 occur in a homozygous form in the Vindija 33.19 Neanderthal (Fig. 1b). Three of these variants occur in the Altai9 and Chagyrskaya 810 Neanderthals, both of whom come from the Altai Mountains in southern Siberia and are around 120,000 and about 60,000 years old, respectively (Extended Data Table 1), whereas none of the variants occurs in the Denisovan genome11. In the 333.8-kb haplotype, the alleles associated with risk of severe COVID-19 similarly match alleles in the genome of the Vindija 33.19 Neanderthal (Fig. 1b). Thus, the risk haplotype is similar to the corresponding genomic region in the Neanderthal from Croatia and less similar to the Neanderthals from Siberia.

We next investigated whether the core 49.4-kb haplotype might be inherited by both Neanderthals and present-day people from the common ancestors of the two groups that lived about 0.5 million years ago9. The longer a present-day human haplotype shared with Neanderthals is, the less likely it is to originate from the common ancestor, because recombination in each generation will tend to break up haplotypes into smaller segments. Assuming a generational time of 29 years12, the local recombination rate13 (0.53 cM per Mb), a split between Neanderthals and modern humans of 550,000 years9 and interbreeding between the two groups around 50,000 years ago, and using a published equation14, we exclude that the Neanderthal-like haplotype derives from the common ancestor (P = 0.0009). For the 333.8-kb-long Neanderthal-like haplotype, the probability of an origin from the common ancestral population is even lower (P = 1.6 × 10−26). The risk haplotype thus entered the modern human population from Neanderthals. This is in agreement with several previous studies, which have identified gene flow from Neanderthals in this chromosomal region15,16,17,18,19,20,21 (Extended Data Table 2). The close relationship of the risk haplotype to the Vindija 33.19 Neanderthal is compatible with this Neanderthal being closer to the majority of the Neanderthals who contributed DNA to present-day people than the other two Neanderthals10.

A Neanderthal haplotype that is found in the genomes of the present human population is expected to be more similar to a Neanderthal genome than to other haplotypes in the current human population. To investigate the relationships of the 49.4-kb haplotype to Neanderthal and other human haplotypes, we analysed all 5,008 haplotypes in the 1000 Genomes Project22 for this genomic region. We included all positions that are called in the Neanderthal genomes and excluded variants found on only one chromosome and haplotypes seen only once in the 1000 Genomes Project data. This resulted in 253 present-day haplotypes that contained 450 variable positions. Figure 2 shows a phylogeny relating the haplotypes that were found more than 10 times (see Extended Data Fig. 4 for all haplotypes). We find that all risk haplotypes associated with severe COVID-19 form a clade with the three high-coverage Neanderthal genomes. Within this clade, they are most closely related to the Vindija 33.19 Neanderthal.

Among the individuals in the 1000 Genomes Project, the Neanderthal-derived haplotypes are almost completely absent from Africa, consistent with the idea that gene flow from Neanderthals into African populations was limited and probably indirect20. The Neanderthal core haplotype occurs in south Asia at an allele frequency of 30%, in Europe at an allele frequency of 8%, among admixed Americans with an allele frequency of 4% and at lower allele frequencies in east Asia23 (Fig. 3). In terms of carrier frequencies, we find that 50% of people in South Asia carry at least one copy of the risk haplotype, whereas 16% of people in Europe and 9% of admixed American individuals carry at least one copy of the risk haplotype. The highest carrier frequency occurs in Bangladesh, where more than half the population (63%) carries at least one copy of the Neanderthal risk haplotype and 13% is homozygous for the haplotype. The Neanderthal haplotype may thus be a substantial contributor to COVID-19 risk in some populations in addition to other risk factors, including advanced age. In apparent agreement with this, individuals of Bangladeshi origin in the UK have an about two times higher risk of dying from COVID-19 than the general population24 (hazard ratio of 2.0, 95% confidence interval, 1.7–2.4).

It is notable that the Neanderthal risk haplotype occurs at a frequency of 30% in south Asia whereas it is almost absent in east Asia (Fig. 3). This extent of difference in allele frequencies between south and east Asia is unusual (P = 0.006, Extended Data Fig. 5) and indicates that it may have been affected by selection in the past. Indeed, previous studies have suggested that the Neanderthal haplotype has been positively selected in Bangladesh25. At this point, we can only speculate about the reason for this—one possibility is protection against other pathogens. It is also possible that the haplotype has decreased in frequency in east Asia owing to negative selection, perhaps because of coronaviruses or other pathogens. In any case, the COVID-19 risk haplotype on chromosome 3 is similar to some other Neanderthal and Denisovan genetic variants that have reached high frequencies in some populations owing to positive selection or drift14,26,27,28, but it is now under negative selection owing to the COVID-19 pandemic.

It is currently not known what feature in the Neanderthal-derived region confers risk for severe COVID-19 and whether the effects of any such feature are specific to SARS-CoV-2, to other coronaviruses or to other pathogens. Once the functional feature is elucidated, it may be possible to speculate about the susceptibility of Neanderthals to relevant pathogens. However, with respect to the current pandemic, it is clear that gene flow from Neanderthals has tragic consequences.

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