Groundbreaking genetic mapping studies by Cavalli-Sforza have shown a sharp gradient in gene frequencies centered in the area around the Sea of Japan, suggesting that the area was a center of expansion for the ancestral Jomon-Ainu populations (thought to have occurred during the Jomon period although the studies cannot fix clear dates). This expansion of populations is thought to be the third most important genetic movement in Eurasia (after the “Great expansion” from the African continent, to Arabia and adjacent parts of the Middle East, as well as to the northern regions of Eurasia, (particularly Siberia from regions to the south).

According to genetic tests, the Ainu people belong mainly to Y-DNA haplogroup D2 (a haplogroup that is found uniquely in and frequently throughout Japan including Okinawa with its closest relations being Tibetans and Andaman Islanders in the Indian Ocean). On the paternal side, the vast majority (87.5%) of the Ainu were, according to a 2004 study to be of Asian-specific YAP+ lineages (Y-haplogroups D-M55* and D-M125), that were only distributed in the Japanese Archipelago. The Ainu exhibited no other Y-haplogroups (i.e. none of the common East Asian C-M8, O-M175*, and O-M122* haplogroups) and shared no other Y-DNA in common in mainland Japanese and Okinawans.

According to a study led by Hammer, one of the most useful and widely studied Y-linked polymorphisms is known as the “Y Alu polymorphic” (YAP) element (Hammer 1994). This polymorphism has resulted from the single and stable insertion of a member of the repetitive Alu family at a specific site (locus DYS287) on the long arm of the human Y chromosome during the past 29,000-334,000 years.

The frequency of Y chromosomes carrying the YAP element (YAP+) varies greatly among human populations from different geographic locations: Global surveys have shown that sub-Saharan African populations have the highest overall frequency of YAP chromosomes, followed by populations from northern Africa, Asia, Europe, the New World, and Oceania. However, an intriguing finding by Hammer (1997) that the ancestral YAP haplotype is the Asian haplotype 3 from which other haplotypes 4 and 5 evolved and derived, suggesting the possibility that YAP haplotype 3 originated in Asia and migrated to Africa. This hypothesis is supported by the finding of high frequencies of haplotype 3 in some Asian populations (i.e., -50% in Tibet) and by the observation of higher levels of diversity (based on the number and frequency of alleles at the DYS1 9 microsatellite locus) associated with Asian versus African haplotype 3 chromosomes. Chandrasekhar et al. 2007, also argued for the Asian origin of the YAP+ on the basis of evidence from the presence of the YAP insertion in Northeast Indian tribes and Andaman Islanders with haplogroup D that suggests that some of the M168 chromosomes gave rise to the YAP insertion and M174 mutation in South Asia. Others such as Underhill and Bravi stand by an African origin for YAP+. The prevalence of the YAP+ allele in central Asian populations was alternatively suggested by some (Altheide and Hammer 1997; Jin and Su 2000; Karafet et al. 2001) to point to a genetic contribution to the east Asian populations from the northwest, probably from central Asia. In Japan, the frequency of the YAP element ranges from 33% in Shizuoka to 56% in Okinawa, with an intermediate frequency of 39% in Aomori. The frequency is significantly higher in Okinawa than in Shizuoka (Fisher’s exact test, P = .0284), but the Okinawa frequency is not significantly different from the Aomori frequency (P= .2196). However, the frequency in Okinawa is significantly higher than in the combination of the two Honshu prefectures (P = .0256). 87.5% of the Ainu were, according to a 2004 study to be of Asian-specific YAP+ lineages. By contrast, YAP was absent from Korean male samples. This result is consistent with previous surveys that showed the YAP element to be polymorphic in Japan but absent in other Asian and Oceanic populations. In terms of antiquity as well as the relationship of the different YAP+ lineages, another interesting conclusion was made by the Hammer analysis: “All pairwise F., values were calculated on the basis of YAP allele frequencies in Japan and Taiwan, as well as in 13 other populations (Hammer 1994; Spurdle et al. 1994b). The neighbor-joining method was used to generate a clustering diagram (fig. 2). All Asian and Oceanic populations, except the Japanese, form a single group that is closely allied with the European populations. The greatest genetic distance is the one that separates these Eurasian populations from the Japanese and African populations. The Okinawan and Honshu populations are separated; the former population clusters in the middle of the African groups, and the latter population clusters between the African and Eurasian samples.” In other tests of two out of a sample of sixteen – i.e. 12.5% of Ainu men were found to belong to Haplogroup C3, which is the most common Y-chromosome haplogroup among the indigenous populations of the Russian Far East and Mongolia. A separate test (a sample of four Ainu men) found that one in four Ainu men belonged to haplogroup C3. The presence of the C3 haplogroup is believed to reflect the genetic influence of the nomadic Nivkhs people of northern Sakhalin Island, with whom the Ainu have long-standing cultural interactions. Relationship to other populations While Y-chromosome haplogroup markers D2 and mtDNA D4 and M7a (and M7a1) indicate that Ainu are related to other Japanese populations in the rest of Japan, the various mtDNA studies may indicate that Ainu men took wives from a variety of locations throughout Central Asia, Siberia and the Russian Far East. East Asian genes M7 has been detected so far in China, Vietnam, the West Siberian Mansi, Mongols and island Southeast Asia, apart from from the Korean peninsula and Japanese islands where the subclades expanded. Haplogroup M7a has been found in Southeast Asia-Taiwan, but mainly among Japanese and Ryukyuans. Haplogroup M7 is seen as characteristically distributed in East Asia while M7a is regarded as its daughter group specific for (pre-Jomon to Jomon) Japanese populations (while M7b2 is specific for Korean populations). The 2002 study puts the estimated settlement times for M7a, M7b and M7c at between 6,000 and 18,000 years … although it suggests that the M7a and M7b pioneer settlers may have entered even earlier ~ 30,000 years at a time when the Yellow Sea had fallen dry and was more like a large lake , but that the populations became bottle-necked toward the Last Glacial Maximum (LGM). Beyond the ancestral M7, it has been noted that M7 nested subclades are not shuffled between the Koreans and Japanese, so the M7a, M7b and M7c starlike clades are thought to represent the post LGM resettlement process, with M7a in the area of the southern Japanese Sea. This settlement event would have been contemporary with the spread of microblades, e.g. of the Suyanggae-type and before the onset of the Jomon culture. It has also been noted that the Ainu of today are not pure descendants of the Jomon, but rather from the Jomon-Yayoi mixture of the Satsumon/Emishi people. The Emishi were Jomon descendants with Yayoi assimilated cultural traits. It is believed from place names in Tohoku that the Emishi spoke the Ainu language as well. As the Yayoi people pushed north, it is thought that the Emishi people advanced on Hokkaido, infusing the Jomon culture in Hokkaido with an agrarian society and with metal-using traits from the Yayoi culture. Citing Gary Crawford, Paula Nielsen writes in “Origins of the Ainu People of Northern Japan” that “the Satsumon culture recently discovered in Hokkaido was descended from the Tohoku Emishi of northeastern Honshu who migrated to Hokkaido, bringing a fused culture of the Middle Yayoi, along with the ancient physical traits of the Jomon”. And although the Ainu of Japan have traditionally considered descendants of the Jomon or post-Jomon Satsumon people (indicated by the D or D2 gene marker), they have been found to carry the Y-chromosome DNA haplogroup C3 showing a paternal lineage from North Asia including Sakhalin. mtDNA haplogroups Y – An origin in the neighbouring Amur tribes of the contiguous zones? Genetic testing showed a varied picture of the maternal lines, with the presence of mitochondrial DNA – haplogroup Y (21.6%), haplogroup M7a (and M7a1) (15.7%), haplogroup D – especially D4, and haplogroup G. MtDNA haplogroup Y is thought to have been likely the genetic influence from the Nivkhs, (although it is also present in the Tungusic peoples, Koreans, Mongols (including Kalmyks and Buryats), Tajiks, Chinese and other Central Asians, South Siberian Turkic peoples (e.g. Tuvans, Todjins, Soyots). The presence of Y1 lineages (Y is restricted to Northeast Asians and Ainu) among the Ainu also points to the migration route, from Siberian populations to the northernmost populations of the Japanese islands (fitting well with the archaeological record) but poses separate events from the settlement by M7a and M7b peoples. A 2020 study of the maritime tribes of the Northeast Pacific coast, “identified the novel haplogroup N9b1 in Primorye, which implies a link between a component of the Udegey ancestry and the Hokkaido Jomon. … The Udegey group is found to consist of two mtDNA haplogroups: N9b and M7a2 (see Table 1 and Additional file 6: Figures S5 and Additional file 7: Figure S6). Aside from the Udegey originating in the villages of Gvasygi and Agzu in the Sikhote-Alin/Primorye region, we sampled the Udegey individuals who married into Ulchi and Nivkhi families dispersed along the reaches of the Lower Amur [22]. Haplogroup N9b is represented mainly by lineages of four major subhaplogroups: N9b1, N9b2, N9b3, and N9b4 [34,35,36]. We identified a novel N9b1 mitogenome (MH807371) in one individual from Primorye (Agzu), hence expanding the established geographical scope of the N9b1 haplogroup and disclosing a link between a component of the Udegey ancestry and the Hokkaido Jomon from Japan [36,37,38]. The second prevalent haplogroup is M7a2a3a, which was detected in 8/46 (17.4%) of the Udegey samples (Table 1, Additional file 7: Figure S6). The Udegey, as well as the Hokkaido Jomon, lack subhaplogroup M7a1, which is the predominant subhaplogroup in modern Japanese and Korean populations “ The study also proposed: “mtDNA haplogroup Y (a descendant of haplogroup N9) is proposed to indicate matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations in the Far East [22, 25,26,27,28,29]. Within Siberia, the majority of contemporary Y1 carriers cluster into Y1a marked by the coding change m.7933A > G (aged ~ 10.6 kya), whereas Y1b and Y1c are confined to continental China, Japan, and Korea (Additional file 2: Figure S1). Accordingly, two offshoots arose from the Y1a founding haplotype for this haplogroup. On one side, the newly refined Y1a1 haplotype defined by m.12732 T > C is well represented in Tungusic-speaking groups (e.g., Evenki, Udegey), while the other side harbors a back mutation at np m.16189 T > C relative to the Reconstructed Sapiens Reference Sequence (RSRS). Sequence diversification within the Y1a-m.16189 T > C! haplogroup is characteristic (at most) of the Nivkhi from Sakhalin. The updated network analysis includes 10 Y1a2 sequences defined by m.12397A > G, of which 7 are new from the coastal Koryak. … we extended the survey of major mitochondrial lineages dispersed across the Russian Far East. Several components may be delineated in this regard. The first component traces back to East Eurasian hunter-gatherers and represents lineages belonging to subdivisions of haplogroups N9b and M7a2. The second is well represented by Y1a and G1b and points to the Lower Amur as the ancestral homeland for this and other haplogroups. The third comprises D4e5, which establishes an association between the Oroki and interior eastern Eurasian populations. Last, rare D4m2a mtDNA exhibited by modern Siberians may have roots in Primorye, at the eastern edge of the continent, rather than a South-Central Siberian source.“ Influx of Siberian genes? G1b a marker of the Okhotsk tribes, and the Tokarev ancestor Haplogroup G has been found most frequently among indigenous populations of easternmost Siberia, but it is also common in the Altai-Sayan region of southern Siberia, and Central Asia. According to a 2002 study, D and G stem from a common source or node, but G1 is restricted to Northeast Siberia while G2a is highest among Central Asians (8.8%) and occurs at above 3% in Tibetans and Ainu. Based on non-metric cranial traits studies, the Ainu people occupy an intermediate position between Jomon and Northeast Asians (the Okhotsk) on the one hand, and between and to a lesser extent the recent Hokkaido Ainu. Both genetic and cranial measurement studies support the recent consensus view that the Ainu originated in the merger of the Satsumon and Okhotsk cultures around 1200 CE. The Ainu are also considered to occupy an intermediate position between Jomon and Northeast Asians on the one hand, and between Jomon and the Native Americans on the other. Thus studies on the variations among the three Ainu series from Sakhalin Island, the northeast Hokkaido coast, and central/south Hokkaido shown in the study, conclude that there has been admixture between the ancestors of recent Ainu and northern groups such as the Okhotsk people in the post-Jomon periods. Sato’s 2009 study of the Okhotsk mtDNA concluded that there was gene flow from the Sakhalin Okhotsk people into the Ainu. A 2019 study found that the ancestors of the Tokarev culture of the Kolymar basin, belonged to the G1b haplogroup and that the Tokarev culture (at the Spafaryev site) was probably associated with the migration of the migration of ancient Amur tribes to the north.

A 2007 study investigated the phylogenetic status of the Okhotsk people that were distributed in northern and eastern Hokkaido as well as southern Sakhalin during the fifth to the thirteenth centuries, DNA was carefully extracted from human bone and tooth remains excavated from archaeological sites, see 2007, Origins and genetic features of the Okhotsk people, revealed by ancient mitochondrial DNA analysis, Journal of Human Genetics 52(7):618-27 DOI – 10.1007/s10038-007-0164-z: 16 mtDNA haplotypes were identified from 37 individuals of the Okhotsk people. Of the 16 haplotypes found, 6 were unique to the Okhotsk people, whereas the other 10 were shared by northeastern Asian people that are currently distributed around Sakhalin and downstream of the Amur River. The phylogenetic relationships inferred from mtDNA sequences showed that the Okhotsk people were more closely related to the Nivkhi and Ulchi people among populations of northeastern Asia. In addition, the Okhotsk people had a relatively closer genetic affinity with the Ainu people of Hokkaido, and were likely intermediates of gene flow from the from the northeastern Asian people to the Ainu people. These findings support the hypothesis that the Okhotsk culture joined the Satsumon culture (direct descendants of the Jomon people) resulting in the Ainu culture, as suggested by previous archaeological and anthropological studies. DNA updates – aDNA of Ainu of the Edo era: A study of Edo era Ainu DNA throws light on regional differences in Ainu origins: A 2018 study of mitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era concluded that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations; the study: a. confirmed that the genetic influence of the Okhotsk culture people on the Ainu is significant. The proportion of Okhotsk‐type haplogroups in the Edo Ainu was 35.1%, which is as high as that of the Jomon‐type haplogroups (30.9%). This suggests that the Okhotsk culture people were one of the main genetic contributors to the formation of the Ainu. b. indicated that while the Ainu still retain the matrilineage of the Hokkaido Jomon people, the Siberian influence on this population is far greater than previously recognized. Siberian‐type haplogroups are observed in the Edo Ainu. Although their frequency is low (7.3%), as described earlier, the existence of these haplogroups may hint at the continuity of the genetic relationship between the Ainu and native Siberians even after the Okhotsk culture disappeared from Hokkaido. However, the number of Okhotsk people who were genetically analyzed is still small (n = 37; Sato et al., 2009), so it is possible that these haplogroups will be identified in the Okhotsk people in further study. c. ***It also found that the influence of mainland Japanese is evident PRIOR to the Meiji period, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan. Intriguingly, a genetic contribution of the mainland Japanese to the Edo Ainu is evident (28.1%), which is almost as considerable as those of the Jomon and the Okhotsk culture people. Conventionally, the genetic influence of the mainland Japanese on the Ainu is considered to have been limited until the Meiji government started sending settlers to Hokkaido as a national policy in 1869. However, our findings cast doubt on this accepted notion. d. Regional differences of the Ainu were observed as follows (excerpt from study below): By classifying the mtDNA haplogroups into four types as described earlier, regional differences of the Ainu people were highlighted. Judging from the data shown in Table 2, the high frequencies of Jomon‐type haplogroups in northeastern/central Hokkaido (44.2%) and the high frequencies of mainland Japanese‐type haplogroups in southwestern Hokkaido (37.3%) might be plausible reasons for these regional differences. This result is consistent with the result of a morphological analysis by Ossenberg et al. (2006). They described that, among the Ainu in Hokkaido, individuals in southeastern Hokkaido (this area is contained within our category of “northeastern/central Hokkaido”) are the closest to the Jomon people, whereas the individuals in western Hokkaido (this area is included within our category of “southwestern Hokkaido”) are the closest to mainland Japanese. This result is considered reasonable, given the geographical proximity of southwestern Hokkaido to the main island of Japan. ***However, surprisingly, there were no regional differences in the frequencies of the Okhotsk‐type haplogroups (35.3% in southwestern Hokkaido and 34.9% in northeastern/central Hokkaido). This indicates that the genetic influence of the Okhotsk culture people diffused rapidly in the fledgling Ainu. As described earlier, Segawa (2007) stated that the invasion of the Satsumon culture people into the areas inhabited by the Okhotsk culture people and the subsequent decline of Okhotsk culture occurred rapidly. The Okhotsk culture people were considered to have been assimilated rapidly into the Satsumon culture during this process, and became part of the basis of the Ainu. The Native American connection Current molecular genetic evidence suggest that the initial founders of the Americas emerged from an ancestral population of less than 5,000 individuals that evolved in isolation, likely in Beringia, from where they dispersed south after approximately 17 kya. Recent findings about the peopling of northern Asia reconstructed by archaeologists suggest that modern humans (haplogroups C and D) colonized the southern part of Siberia around 40 thousand years ago (kya, pre-LGM) and the far northern parts of Siberia and ancient Beringia, by approximately 30 kya. Haplogroup D4, the most represented of D clades, is subdivided into fifteen principal subclades (D4a–D4j, D4k’o’p’, D4l–D4n, D4q), which range from ~6 to ~28 kya when using the sequence variation of the entire genome and from ~3 to ~42 kya but all subclades are found in eastern Asia, with the eastern Asian lineages the oldest among them. The ancient mtDNA D4 have been found in the vicinity of Devil’s Gate, i.e. Northeast Asia, the 2017 study of 7700 bp neolithic hunter-gatherers from Devil’s Gate concluded D4 continuity through to today.: “The mitochondrial genome of the individual with higher coverage (DevilsGate1) could be assigned to haplogroup D4; this haplogroup is found in present-day populations in East Asia (11) and has also been found in Jomon skeletons in northern Japan … Modern populations that live in the same geographic region as Devil’s Gate have the highest genetic affinity to our ancient genomes (Fig. 2), with a progressive decline in affinity with increasing geographic distance (r2 = 0.756, F1,96 = 301, P < 0.001; Fig. 3), in agreement with neutral drift leading to a simple isolation-by-distance pattern. The Ulchi, traditionally fishermen who live geographically very close to Devil’s Gate and are the only Tungusic-speaking population from the Amur Basin sampled in Russia (all other Tungusic speakers in our panel are from China), are genetically the most similar population in our panel. Other populations that show high affinity to Devil’s Gate are the Oroqen and the Hezhen—both of whom, like the Ulchi, are Tungusic speakers from the Amur Basin—as well as modern Koreans and Japanese. Given their geographic distance from Devil’s Gate (Fig. 3), Amerindian populations are unusually genetically close to samples from this site, in agreement with their previously reported relationship to Siberian and other north Asian populations.” mtDNA haplogroup D is found frequently throughout East Asia, in higher frequencies in Northeast Asia, Siberia and Central Asia. A previous view is Derenko’s who is in favour of an East Asian homeland: A 2010 Russian Derenko study clarified that D4 has an age of 24–28 kya and is further subdivided into fifteen principal subclades (D4a–D4j, D4k’o’p’, D4l–D4n, D4q), which range from ~6 to ~28 kya. These D4 subclades have a very distinctive geographic distribution, which is highly informative about the demographic history of the northern Asia. The study showed that all the subclades are found in eastern Asia and that they had already expanded before the LGM, with their oldest lineages being present in the eastern Asia. In particular, most of the eastern Asian subclades of haplogroup D show coalescence ages of between 15 and 42 kya, thus suggesting that some of them were already present here before the LGM. The mitochondrial DNA gene marker (Y-haplogroup C-M217*) are genetic characteristics also shared by the Nivkhi in northern Sakhalin, and Koryaks in the Kamchatka Peninsula. Hence, the Ainu can be said to be related to the Nivkhi and the Koryaks. However, since the Nivkhi do not carry haplogroup D which has a dominant presence in the Ainu, the migration is seen to have occurred unidirectionally, from the North into Hokkaido. This appears to be confirmed by the research of the Saitou laboratory at the National Institute of Genetics, which concluded that the Ainu of Hokkaido (as well as ancient Jomon) showed the closest genetic affinity to native Okinawans. Another 2020 study on the neolithic Boisman culture observed continuity going back 8,000 years of the D4 ancestry in the Amur River Basin, as well as its affinity with the Jomon: “The individuals from the ~5000 BCE Neolithic Boisman culture and the ~1000 BCE Iron Age Yankovsky culture together with the previously published ~6000 BCE data from Devil’s Gate cave19 are genetically very similar, documenting a continuous presence of this ancestry profile in the Amur River Basin stretching back at least to eight thousand years ago (Figure 2 and Figure S2). The genetic continuity is also evident in the prevailing Y chromosomal haplogroup C2b-F1396 and mitochondrial haplogroups D4 and C5 of the Boisman individuals, which are predominant lineages in present-day Tungusic, Mongolic, and some Turkic-speakers. The Neolithic Boisman individuals shared an affinity with Jomon as suggested by their intermediate positions between Mongolia_East_N and Jomon in the PCA and confirmed by the significantly positive statistic f4 (Mongolia_East_N, Boisman; Mbuti, Jomon). The expansion of haplogroup D4 settlers took place in northern Asia post LGM. Of the subclades shared with eastern Asians, D4b1a is thought to represent a separate Upper Paleolithic migration initiated northward from the Altai-Sayan region of southern Siberia around 11-20 kya. D4b1a falls into two branches, one of which, D4b1a2, is largely restricted to northern Asia and its major subclade, D4b1a2a, resulted from the earliest split from the Yukaghir mtDNA within D4b1a2.” The Paleolithic Siberian population expansions are also thought to be responsible for a migration to the Americas and that North America may have had ancestral relatives of the Jomon and Ainu among its early settlers. See Analysis of HLA genes and haplotypes in Ainu (from Hokkaido, northern Japan supports the premise that they descend from Upper Paleolithic populations of East Asia, Tissue Antigens. 2000 Feb;55(2):128-39: The Ainu people are assumed to be the descendants of pre-agricultural native populations of northern Japan, while the majority of population of present-day Japan (Hondo-Japanese) is considered to have descended mainly from post-neolithic migrants. Sequence-level polymorphisms of the HLA-class I (HLA-A and HLA-B) genes were investigated in DNA samples of 50 Ainu living in Hidaka district, Hokkaido. HLA-A*2402, A*0201, A*0206, A*2601, A*3101, B*1501, B*5101, B*3901, and B*3501 were observed at frequencies of more than 10% and most of these have previously been found in populations of not only Asians but also North and South American Indians. A*68012, which has not so far been detected in Hondo-Japanese, was found in the Ainu (3%). Correspondence and neighbor-joining analyses of various populations based on HLA-A, -B and -DRB1 gene frequencies enabled distinction between Asian, Native South American, European, and African populations. The Ainu, as well as Tlingit (Na-Dene), were placed midway between other East Asians, including Hondo Japanese, and Native South Americans (Amerindians) in the correspondence analysis. Furthermore, several HLA-A-B and HLA-B-DR-DQ haplotypes common in the Ainu, are shared with some Native American populations. These observations strongly suggest a unique place for the Ainu as descendants of some Upper Paleolithic populations of East Asia, from whom some Native Americans may have descended. The Ainu are thought to be connected to ancestry that might be in common with those of Native Americans – one connection lies in the detection of the common presence of Haplogroup X in both populations. Haplogroup X is traceable to ancient remains of Altaians in the Gobi desert, as well as to the Altai populations today, but ultimately to the Druze, Basque, and other European populations of the Caucasus. Although it is not at the moment, known how the Haplogroup X arrived in the Ainu ancestral lines, nor to Native American populations in ancient times, a 1998 study concluded that Native American founders may have had Caucasian ancestry. For more on this see DNA analyses and inferred genetic origins of the Ainu. On the other hand… A study on the HLA gene (alleles and haplotypes) frequencies on North, Meso, South American AmeriIndians showed that AmerIndians have little relatedness with Asians, according to genealogy studies except that North-Americans only share one haplotype (A*24-B*40-DRB1*1401-DQB1*0503) with Taiwanese and Japanese in low frequencies. More work should be done in interdisciplinary studies on virus and disease markers to study ancient migrations. Early work in one study shows that all type 2A JC Virus strains from North and South Americans are closely related to strains in present-day Japan. The strains of JC virus present in Navajo in New Mexico (speakers of an Athapaskan language in the Na-Dene language phylum) were found to be of a prototype type 2A strain of a northeast Asian genotype found in Japan. The partial VP1 gene sequences of the JC virus from the Salish people in Montana (speakers of a language in the Salishan group in the Amerind family) and from the Guarani Indians of Argentina (speakers of the Tupi-Guarani language and Equatorial branch of the Amerind family) were however shown to be closely related to several strains variants of strains found in Japan.

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