This page serves to bring together virus migration markers (JC Virus, HPVirus, BKVirus) which are today becoming relevant for analyzing the migration paths and origins of human populations, specifically related to Japan, East Asia and the Americas.
The geographic distribution patterns of the different subtyped-subgroups suggest a close relationship between the studied virus and human populations. Indeed, co‐migration of viruses such as BKV, HPV and human populations and can be used to identify clear distribution patterns for the viral subtypes and corresponding disease incidence. Thus, virus (and other types of disease markers) can serve as a means of tracing human migrations on earth, or at least clarifying or confirming the more commonly used Y-chromosome and mtDNA migration and population models.
Population substructure and differing origins of Ainu ancestors may be inferred from Huai-Ying Zhen’s 2005 Two distinct genotypes (MY-x and MX) of JC virus previously identified in Hokkaido Ainu
Genotyping the urinary JC virus (JCV) DNA is a useful means to gain new insights into the origin of ethnic groups. We recently detected thirteen JCV isolates from the Ainu, an indigenous population living on Japan’s northernmost island (Hokkaido). Based on phylogenetic analysis, these isolates were classified into five genotypes: two (MX and MY-x) were first identified in the Ainu, two (EU-a/Arc and EU-c) are prevalent in northeastern Siberians and an Arctic tribe, and one (MY-b) is widespread among Hondo Japanese, i.e. contemporary Japanese excluding the Ainu. Although these findings have several potential implications for the development of the modern Ainu, further studies are required to reach a definite conclusion. In this report, an isolate in a forensic subject whose ethnic origin was Ainu belonged to the MX genotype and two isolates recently identified in South Koreans and grouped as Native American isolates belonged to the MY-x genotype. The present findings suggest that the MX genotype of JCV is unique to the Ainu, whereas MY-x is spread among some Northeast Asian populations.
Using phylogenetic analysis, Yogo et al. (2003) recently analyzed thirteen JCV isolates from the Ainu, an indigenous population living on Hokkaido, the northernmost island of Japan, and classified them into five genotypes: two (MX and MY-x) were first identified in the Ainu, two (EU-a/Arc and EU-c) were prevalent in northeastern Siberians and an Arctic tribe, and one (MY-b) was widespread among Hondo Japanese (i.e. contemporary Japanese, excluding the Ainu). Although two new genotypes were recognized in Yogo et al.’s (2003) study, the data size was too small for them to draw definite conclusions about the ethnic distribution of these genotypes. In the present study, we performed a detailed phylogenetic analysis of three unique JCV isolates, one identified by ourselves in an Ainu subject and two detected by Cui et al. (2004)in Koreans living in Seoul, South Korea. The latter two isolates were described as Type 2A2, which is characteristic of Native Americans (Cui et al., 2004).
Based on the resulting tree (Figure 1), we conclude that ANF and two isolates (AN-9 and AN-13) that had previously been detected in the Ainu (Yogo et al., 2003) formed a distinct clade (designated MX), with a high bootstrap probability (100%). In contrast, the Korean isolates (255A and 256A) together with an isolate (AN-1) from an Ainu formed another distinct clade (MY-x) with a 100% BP (Figure 1). MY-x and the other MY subgroups (MY-a to MY-g) constituted a superclade, designated MY. As previously shown (Yogo et al., 2003), the MX and MY grouping has been demonstrated with a significantly high BP (83%; Figure 1).
Yogo et al. (2003) detected MY-x and MX in only one or a few subjects. Therefore, the ethnic distribution of these genotypes required further study. In the present study, we demonstrated the presence of the MX genotype in a forensic subject whose origin was Ainu. MX was previously detected at two distant sites (Asahikawa and Shiraoi) on Hokkaido (Yogo et al., 2003). In the present study, we detected MX in a subject from another site on Hokkaido (i.e. Makubetsu), which suggests that the MX genotype of JCV is widespread among the Ainu, albeit at a lower frequency.
We found that two isolates from Seoul belonged to MY-x, a subgroup within genotype MY (Yogo et al., 2003). These isolates were previously described as belonging to the Native American subgroup of MY (named Type 2A2; Cui et al., 2004), but the result of our analysis suggests that this classification should be revised. Although MY-x was distributed in two distinct human populations (i.e. the Ainu and Koreans), further division of the MY-x isolates was not demonstrated. This suggests that peoples carrying the MY-x genotype migrated to the Korean Peninsula and Hokkaido relatively recently (i.e. not earlier than 10000 years ago
Yoshiaki Yogo, Phylogenetic analysis of JC Virus DNAs defected for Ainu
Both major JCV genotypes showed regional differences in their geographic distribution(Table 1 and Figure 3). In the southwestern area from Miyako Jima to Kofu, the frequency of CY ranged from 65% at Kumamoto to 100% at Kume Jima. In contrast, in the northeastern area from Yonezawa to Goshogawara, the frequency of MY ranged from 64% at Yonezawa and Hirosaki to 100% at Koromogawa. Between the two areas lay an intermediate area where both genotypes were almost equally prevalent. (These distribution patterns of CY and MY are illustrated in Figure 1.) Thus, CY is more prevalent in the southwest, whereas MY is more prevalent in the northeast.
Similarly, the three minor JCV genotypes showed regional differences in geographic distribution. Eight SC isolates were found in the southwestern area (Okinawa Island, Kagoshima, Nishisonoki and Fukuoka), but no SC was detected in the other areas. Six B1-a isolates were found in the southwestern area (Kagoshima, Nishisonoki and Kofu) and a single B1-a isolate was found in the intermediate area (Takaoka). Four EU isolates were found in the southwestern area (Isahaya, Amagasaki and Kaizuka), a single EU isolate was found in the intermediate area (Ueda), and eleven EU isolates were found in the northeastern area (Yonezawa, Sendai, Akita, Hirosaki and Goshogawara). In summary, SC and B1-a are prevalent in the southwestern area, whereas EU is more prevalent in the northeastern area.
Previous studies have shown that approximately 2000 to 3000 years ago, a variant of ALDH2 was present within the Chinese population. Citing historical evidence , researchers speculated that people with this ALDH2 variant migrated to western Japan 2000 to 3000 years ago. Oota et al.  claimed that based on actual DNA evidence, this ALDH2 variant was a young haplotype associated with low levels of genetic diversity. Therefore, it may be possible that this mutation of the ALDH2 gene and the Yayoi migration from China to Japan happened in roughly the same period.
The JC virus (JCV), one of the polyomaviruses, is a useful marker in tracing the dispersal of human populations . This is because once an individual is infected asymptomatically with JCV during childhood [23, 24], the initially infected JCV strain persists in renal tissue for life, and other strains of JCV are unable to infect the already infected individual [2, 13, 29]. There are more than 20 main JCV genotypes that are distributed in geographically distinct domains throughout the world . Two major types of JCV genotypes, CY and MY, are found in the Japanese archipelago  (Fig. 2a). The genotype CY is commonly distributed in western Japan, northeast China, and Korea [5, 6] and is not found in other places [27, 32]. Earlier studies suggested that the Chinese might have brought the CY genotype JCV to Japan when they migrated from China . The genotype MY is commonly distributed in eastern Japan and among Native Americans [27, 32].
This JCV distribution may support the dual structure model of the Japanese population. However, there have been no studies verifying the correlation between the distribution of the CY genotype JCV and the dual structure model.
Therefore, through the detection of the ALDH2 mutation among JCV-positive Japanese samples, we investigated its correlation with the CY genotype JCV, and we discuss whether the dual structure model is also supported by JCV genotype in this study.
The ALDH2 polymorphism among 66 JC virus-positive samples was analyzed, and it was found that the ALDH2 variant is significantly higher in the population with CY genotype JCV (51.5 %) than in the population with the MY genotype (24.2 %) (p < 0.05).
From these findings, it may be inferred that the ALDH2 mutation, which is related to the Yayoi, is related to CY genotype JCV. When the [proto-]Yayoi [ancestor]migrated to the Japanese archipelago, they brought the ALDH2 mutation as well as the CY genotype JCV.
A chart from HWZheng 2007, shows the distribution of the different genotypes of the BK virus and the Relationship between BK Virus and human populations
Phylogenetic analyses of complete genome sequences have identified several geographically distinct subgroups of subtypes I and IV. To explain how the geographical distribution patterns of BKV subtypes and subgroups were formed, this study hypothesized that BKV co-migrated with human populations (the co-migration hypothesis), …The frequency of subtype I was always the highest throughout the populations, but that of subtype IV was variable among populations. A subgroup of subtype I (I/b-2) was detected primarily in all of the European and American populations, whereas subgroup I/c was predominant in the Asian populations (the observed difference was statistically significant). Additionally, all of the five fully sequenced subtype IV isolates from the American and European populations belonged to subgroup IV/c-2, whereas all subtype IV isolates from the Asian populations belonged to the other subgroups. Collectively, the current findings provide support for the co- migration hypothesis.
It has been proposed that subtype IV of BKV originated in East Asia (Chen et al., 2006; Nishimoto et al., 2007), but the occurrence of minor subtype IV populations in Europe appears contradictory to this viewpoint (Nishimoto et al., 2007). However, as most of the European subtype IV isolates belong to subgroup IV/c-2 (this subgroup is also found in North-east Asia, e.g. Mongolia), it can be assumed that a North-east Asian population carrying IV/ c-2 diverged into multiple subpopulations, some expanding into East Asia, but some migrating to Europe, probably via Central Asia (Nishimoto et al., 2007). [Hun/Mongol expansion?] This scenario is based on the co-migration hypothesis and is now realistic, as the current study provides substantial support for this hypothesis.
Co-migration of BKV and the human race suggests that, like JCV (Agostini et al., 2001; Sugimoto et al., 1997), BKV may be used as a population marker in genetic anthropology.
S Zhong et al., Even distribution of BK polyomavirus subtypes and subgroups in the Japanese Archipelago, 2007
Based on nucleotide sequence variation, subtype I is fur- ther classified into four subgroups (Ia, Ib-1, Ib-2 and Ic), each of which have a close relationship to a particular human population. To clarify the re- lationships between BKV and human populations, we investigated the distribution patterns of BKV subtypes and subgroups in the modern Japanese population, which was formed from two distinct ethnic groups. Urine samples were collected from immunocompetent elderly patients in six regions along the Japanese Archipelago. The 287-bp VP1 region of the viral genome from these samples was amplified using the polymerase chain reaction. The amplified VP1 regions were sequenced and a neigh- bor-joining phylogenetic tree was reconstructed to classify the BKV isolates. We observed a similar pattern of subtype distribution throughout the Japa- nese Archipelago, with subtype I always detected at high rates (67–75%), followed by subtype IV (19– 31%), with rare or no detection of subtypes II and III. Based on phylogenetic and single nucleotide polymorphism analyses, the subtype I isolates were divided into subgroups; the percentage of the Ic subgroup was high in all geographic regions (88– 100%). These results suggest that BKV subtypes and subgroups are evenly distributed in the Japanese Archipelago. We discuss the implications of these findings for the relationships between BKV and human populations.
Distribution of BKV subtypes in Japan
The numbers of isolates classified as belonging to each subtype for individual geographic areas are shown in Table 4 (subtype identification was based on phylogenetic analysis). The findings can be summarized as follows. (i) Subtype I was prevalent in all geographic regions, with rates varying from 67% (OKN) to 75% (NEA, NEB, and NGY). (ii) Subtype IV occurred at the second-highest rate in each geographic region, with rates from 19% (FUK) to 31% (OKN). (iii) Subtype III occurred only rarely in all geographic areas and subtype II did not occur in any region. The ratios of subtype IV to subtype I did not differ significantly among the geographic regions (P>0.2).
Distribution of subtype-I subgroups in Japan
Table 5 shows the numbers of isolates classi- fied into each subtype-I subgroup for individual geographic regions. Subgroup identification was based on phylogenetic (Figs. 2 and 3) and SNP analysis . Subgroup Ic was the most prevalent throughout Japan, with rates ranging from 88% (NEA) to 100% (NAR and FUK), and some minor subgroups were also identified: I-b1 (NEB, NGY, and OKN) and I-b2 (NEA). Subgroup Ia was not detected.
We previously reported that BKV subtype I occurred far more frequently than subtype IV in two central areas of Japan, although in most East Asian regions subtype IV is more prevalent than or as prevalent as subtype I . In this study, we observed essentially the same BKV subtype distribution throughout Japan, with subtype I being most prevalent, followed by subtype IV (with subtypes II and III rarely being found).
We have previously suggested that subtype I, which originally occurred in the ancestors of mod- ern humans, was dispersed to most human populations after the ‘‘Out of Africa’’ migrations of modern humans . In contrast, subtype IV BKV, which is now circulating among humans, was derived from ancient East Asians infected with this virus . Subtype IV in geographic regions other than East Asia may have been transmitted from East Asia, probably in association with human migrations . Therefore, it appears that the pattern of BKV subtype distribution in Japan (subtype I is highly prevalent, with subtype IV at a lower frequency) is due to reduced introduction of sub- type IV.
We recently reported that a single subtype-I sub- group (Ic) primarily occurs in central regions of Japan . In this study, we observed essentially the same pattern of subtype-I subgroup distribution throughout the Japanese Archipelago. However, we also detected a small number of two other sub- groups (Ib-1 and Ib-2) in some geographic regions. Since these subgroups occur mainly in areas other than Japan (Ib-1 in Southeast Asia, Ib-2 in Europe), it is likely that they were recently introduced into Japan by foreigners.
It is generally thought that the modern Japanese population was formed by two human populations of different origins [3, 5]. Indeed, Kitamura et al.  investigated the distribution patterns of JCV lineages in various regions of Japan, including most regions studied here, and found that patterns of JCV lineages were different among regions (i.e. lineage MY occurred more frequently in Northeast Japan including NEA and NEB, while lineage CY occurred more frequently in Southwest Japan including NAR, FUK and OKN). It is assumed that CY was brought to Japan by Northeast Asians who immigrated to Japan about 2000 years ago, whereas MY persisted in the indigenous Japanese popula- tion, the Jomonese . If a correlation also exists between BKV subgroups and human populations, the patterns of BKV subgroup distribution should differ between northeastern and southwestern parts of Japan. However, we found essentially the same pattern of subtype-I subgroups throughout Japan, with the rate of a single subgroup (Ic) being consistently high.
We previously noted that the number of BKV subtype-I subgroups is small (only four), compared to that of JCV lineages . To explain this, we hypothesized that human populations may some- times lose their intrinsic BKV strains, allowing infection with BKV strains from neighboring human populations. The same explanation can be applied to the even distribution of a single subtype-I subgroup (Ic) in the Japanese Archipelago. Sub- group Ic frequently occurs in Northeast China and South Korea, as well as in Japan, and it appears that this subgroup was introduced into Japan by North- east Asian immigrants, as was the JCV lineage CY (see above). This subgroup may have spread among Jomonese people (the indigenous Japanese), probably because the Jomonese were susceptible to a foreign subtype I BKV due to the lack of their own subtype I virus.
In summary, we demonstrated that not only BKV subtypes but also subtype-I subgroups are evenly distributed in the Japanese Archipelago. To explain this, we hypothesize that human populations may sometimes lose their intrinsic BKV strains, allow
BKV is widespread among humans, infecting children asymptomatically and then persisting in renal tissue. Based on the serological or phylogenetic method, BKV isolates worldwide are classified into four subtypes (I-IV), with subtypes I and IV further divided into several genetically-distinct subgroups. Since, similarly to JCV, a close relationship exists between BKV lineages and human populations, BKV should be useful as a marker to trace human migrations. To elucidate ancient human migrations in northeast Asia, urine samples were collected from immunocompetent elderly patients in Shanghai, China; Anyang, South Korea; and various locations in Japan. Partial and complete BKV genomes from these samples were amplified and sequenced using PCR, and the determined sequences were classified into subtypes and subgroups by phylogenetic and SNP analyses. In addition, based on an SNP analysis, the major subtype I subgroup (I/c) was classified into two subdivisions, I/c/Ch and I/c/KJ. The distribution patterns of BKV subgroups and subdivisions among the three regions were compared. Some aspects of the subgroup and subdivision distribution were more similar between Korea and Japan, but others were more similar between China and Korea or between China and Japan. Based on these findings, we inferred various northeast Asian migrations. Most of the JCV-based inferences of northeastern Asian migrations were consistent with those based on BKV…
Subtype I is divided into four subgroups (I/a, I/b1, I/b2 and I/c), each of which has a unique geographic distribution pattern: I/a is most prevalent in Africa, I/b1 in Southeast Asia and China, I/b2 in Europe, and I/c in northeast Asia (8–10). Subtype IV is subdivided into six subgroups (IV/a1, IV/a2, IV/b1, IV/b2, IV/c1 and IV/c2) based on phylogenetic analyses (11). Most subtype IV subgroups, excluding c2, are found in distinct areas of East Asia, but c2 is prevalent mainly in Mongolia and Europe, suggesting that the subtype IV of BKV now prevalent in modern humans is derived from a virus that infected ancestral Asians (11).
The geographic distribution patterns of subtype‐I and ‐IV subgroups suggest a close relationship between BKV and human populations. Indeed, co‐migration of BKV and human populations has recently been shown by identifying similar distribution patterns for BKV subtypes and subgroups for Europeans and European‐Americans (12). Thus, it can be assumed that, similarly to JCV (13–15), BKV could serve as a means of tracing human migrations on earth. To elucidate ancient human migrations in northeast Asia, here we compared the patterns of distribution of BKV subtypes and subgroups in Shanghai, China; Anyang, South Korea; and various locations in Japan. A previous study by Zheng et al. (10) has shown that BKV subtype profiles are roughly similar among the three countries, subtype I occurring at the highest rates followed by subtype IV. Therefore, a more detailed comparison of BKV lineages among the three countries is needed to gain an insight into the dispersals of northeastern Asians. In this study, we subdivided subtype I into four subgroups (I/a, I/b1, I/b2 and I/c) and subtype IV into six subgroups (IV/a1, IV/a2, IV/b1, IV/b2, IV/c1 and IV/c2). In addition, we sub‐classified subgroup I/c into two subdivisions, I/c/Ch and I/c/KJ. We hoped that comparison of the distribution patterns of BKV subgroups and subdivisions among the three countries would allow us to make inferences regarding the dispersals of northeast Asians..
Distribution of subtype I subgroups in northeast Asia
Table 4 shows the numbers of isolates classified as belonging to each subtype I subgroup for the three geographic areas (subgroup identification was based on both phylogenetic and SNP analyses, as noted above). The findings can be summarized as follows.
- 1 In each geographic area, subgroup I/c [the subgroup prevalent in northeast Asia (10)] occurred at the highest incidence, ranging from 71% to 94%.
- 2 I/b1 [the subgroup prevalent in Southeast Asia and South China (10)] occurred at the second highest rate (27%) in Shanghai, China, while it was not found in Anyang, South Korea (0%) and rarely occurred at various sites in Japan (5%). The differences in the incidence of I/b1, as compared to I/c, between Shanghai, China and Anyang, South Korea and between Shanghai, China and various sites, Japan were all statistically significant (P < 0.01).
- 3Subgroup I/a [the subgroup prevalent in Africa (10)] and subgroup I/b2 [the subgroup prevalent in Europe (10)] did not occur, or rarely occurred, in each geographic area.
Geographic distribution of the subdivisions of subgroup I/c
The phylogenetic tree (Fig. 3) based on complete genome sequences revealed a cluster of eight Korean isolates together with two reference sequences from Japan (BP, 74%). This observation suggested that the I/c subgroup might be classified into a few regionally distinct subdivisions ….
Ancient human migrations from the Korean Peninsula to the Japanese Archipelago
It is generally accepted that modern Japanese were developed from two distinct ethnic groups; the Jomon people (“Jomonese”) who colonized Japan in the Neolithic period, and later immigrants (the Yayoi immigrants) who came from the Asian continent during the Aeneolithic Yayoi and the prehistoric Kofun periods (reviewed in 29). Using the JCV method, Zheng et al. (30) examined the route by which the Yayoi immigrants migrated to the Japanese Archipelago. Two JCV lineages, MY and CY, are mainly distributed in the Japanese Archipelago, with CY linked to the Yayoi immigrants and MY linked to the Jomonese (16, 31). Based on nucleotide variations in the JCV genome, Zheng et al. (30) classified CY into two sub‐lineages, CY‐a and CY‐b, and found that the ratio of CY‐a to CY‐b diverged among northeast Asian populations, with CY‐a more abundant in Chinese and Japanese populations, and CY‐b more abundant in Koreans. This finding, suggesting a closer affinity between Chinese and Japanese than between Koreans and Japanese, was considered to provide support for the hypothesis that the Yayoi immigrants migrated directly from China to Japan rather than through the Korean Peninsula (30). However, an alternative hypothesis: that the [proto-] Yayoi immigrants came from the Korean Peninsula, has been suggested by studies in different disciplines, that is, archaeology (29) and genetic anthropology (32), and therefore the hypothesis remained to be confirmed by other approaches using symbiotic microorganisms, which could include BKV.
In this study, we found that Korea and Japan shared two features with respect to the distribution of BKV lineages. First, a subdivision (I/c/KJ) of subgroup I/c was mainly detected in Korea and Japan, whereas another subdivision (I/c/Ch) occurred predominantly in China. Second, of various subtype IV subgroups, IV/b2 occurred predominantly or at the highest rate in Korea and Japan, whereas it rarely occurred in China. Since BKV co‐migrated with the human race (12), the present findings on BKV lineages support a migration route through the Korean Peninsula (29, 32).
If the BKV lineage data obtained in this study accurately represent the population history of northeast Asia, it follows that the ratio of CY‐a to CY‐b is not necessarily a reliable marker with which to evaluate the affinity among human populations. These sub‐lineages of CY were estimated to have been separated about 10 000 years ago (30), and it is conceivable that, after such a long time, the ratio of CY‐a to CY‐b in present‐time populations may have significantly drifted from the original ratio.
Other northeast Asian migrations based on BKV data
Various northeast Asian migrations inferred on the basis of the present findings are illustrated in Figure 4. Migration from Korea to Japan was inferred based on the findings regarding subdivision I/c/KJ and subgroup IV/b2 as described in the preceding section. Other migrations shown in Figure 4, except for the one based on IV/b1 (see below for a discussion on the origin of IV/b1), were inferred by assuming that migration occurred from the homeland (i.e. the major domain of a subgroup or subdivision) to an adjacent area where the subgroup or subdivision was detected less frequently. These included a migration from China to Korea inferred based on subdivision I/c/Ch or subgroup IV/c1; a migration from China to Japan based on subdivision I/c/Ch, subgroup I/b1 or subgroup IV/a2; and a migration from Southeast Asia to China based on subgroup I/b1, subgroup IV/a1 or subgroup IV/a2.
We emphasize that the migrations from Southeast Asia to China and from China to South Japan, both based on BKV lineages (see above), are consistent with those based on JCV lineages, as explained in the following. A JCV lineage named SC is prevalent in South China and Southeast Asia. Saruwatari et al. (33), who conducted a detailed phylogeographic analysis of SC isolates worldwide, found that although isolates belonging to a sub‐lineage (SC‐f) of SC are widespread in the world, most non‐SC‐f isolates, (excluding SC‐x spread in the Philippines), are restricted to an area of mainland Southeast Asia including Myanmar and Thailand. From these observations, they inferred that in an area of Southeast Asia including Myanmar and Thailand, an ancestral human population carrying proto‐SC may have diverged into various populations, each carrying a distinct variant of SC, and that of these human populations, only two (those carrying SC‐f and SC‐x) migrated out of the area. Thus, based on SC‐f, a migration from Southeast Asia to South China is inferred. In addition, since SC‐f occurs in South Japan at a low frequency, a minor migration from China (probably Taiwan) to South Japan is also inferred.
Since IV/b1 has not been detected in geographic regions other than Japan, the origin of this subgroup remains unclear. As all subtype IV subgroups, excluding IV/b1, occur in the Asian continent, it seems reasonable to assume that IV/b1 originated in the continent and migrated from there to Japan. IV/b1 may have been associated with the indigenous people in Japan, the Jomonese, who are probably derived from the Upper Paleolithic northeast Asians (34), since no BKV lineage has been implicated with this ethnic group (17).
Zhong S., et al., Even distribution of BK polyomavirus subtypes and subgroups in the Japanese archipelago. Arch Virol. 2007;152(9):1613-21. Epub 2007 Jun 1. .
BK polyomavirus (BKV) is ubiquitous among humans, infecting children asymptomatically and then persisting in renal tissue. BKV has four subtypes (I-IV) that can be identified by serological and genotyping methods. Subtypes I and IV are most prevalent in all countries examined to date. Based on nucleotide sequence variation, subtype I is further classified into four subgroups (Ia, Ib-1, Ib-2 and Ic), each of which have a close relationship to a particular human population. To clarify the relationships between BKV and human populations, we investigated the distribution patterns of BKV subtypes and subgroups in the modern Japanese population, which was formed from two distinct ethnic groups. Urine samples were collected from immunocompetent elderly patients in six regions along the Japanese Archipelago. The 287-bp VP1 region of the viral genome from these samples was amplified using the polymerase chain reaction. The amplified VP1 regions were sequenced and a neighbor-joining phylogenetic tree was reconstructed to classify the BKV isolates. We observed a similar pattern of subtype distribution throughout the Japanese Archipelago, with subtype I always detected at high rates (67-75%), followed by subtype IV (19-31%), with rare or no detection of subtypes II and III. Based on phylogenetic and single nucleotide polymorphism analyses, the subtype I isolates were divided into subgroups; the percentage of the Ic subgroup was high in all geographic regions (88-100%). These results suggest that BKV subtypes and subgroups are evenly distributed in the Japanese Archipelago
Virus Markers for the Americas
Osiowy Cet al., Distinct geographical and demographic distribution of hepatitis B virus genotypes in the Canadian Arctic as revealed through an extensive molecular epidemiological survey. J Viral Hepat.2011 Apr;18(4):e11-9. doi: 10.1111/j.1365-2893.2010.01356.x. Epub 2010 Aug 15.
Very little is known of hepatitis B virus (HBV) in Canadian Arctic indigenous populations, where HBV was considered endemic prior to the introduction of HBV vaccine. This study expands upon an HBV seroepidemiological survey conducted between 1983 and 1985 throughout the Canadian Arctic, to characterize HBV in this population. Archived hepatitis B surface antigen (HBsAg)-positive sera (n = 401) were processed for HBV DNA, followed by sequencing and phylogenetic analysis of the HBsAg- and HBcAg-coding regions. Sixty-nine per cent of samples (277/401) were DNA positive, with most having low viral load (median 3.4 log 10 IU/mL). The predominant HBV genotype observed was genotype B (HBV/B, 75%), followed by HBV/D (24%) and HBV/A (1%). All HBV/B strains clustered within subgenotype B6, a newly recognized HBV genotype among western circumpolar Inuit and Alaska Native people. HBV/D strains included both D3 (88%) and D4 (12%) subgenotypes, while all HBV/A strains were subgenotype A2. An association of HBV genotype B with Inuit living in the eastern Arctic and an association of genotype D with First Nation (Dene) living in the western Arctic was observed. This study establishes the high prevalence of HBV/B6 and HBV/D genotypes in Arctic populations and reveals their marked distribution within the Canadian Arctic based on geographical and demographic attributes
Yogo Y1, et al., Rev Med Virol. 2004 May-Jun;14(3):179-91.
A small DNA virus, named JC virus (JCV) and belonging to the Polyomaviridae, is attracting the attention of anthropologists worldwide, as JCV genotyping appears to be a novel means of elucidating human migrations and the origins of various ethnic groups. The basic properties of JCV, the regional distributions of JCV genotypes, and the phylogenetic relationships among various JCV genotypes are described. Then, a study is described in which the origin of the modern Japanese was extensively investigated using the JCV genotyping method. Based on JCV genotypes in neighboring areas, the origins of people who carried JCV genotypes to the Japanese Archipelago are discussed. Finally, the relationships between JCV genotypes and Y-chromosome haplogroups are examined, as genetic variation on the Y chromosome has recently been examined in detail to investigate ancient human migrations and the population structures of human groups.
JCV GENOTYPE PROFILE OF THE JAPANESE ARCHIPELAGO
The presence of two major JCV genotypes in Japan was first discovered in 1994, when DNA fragments amplified from JCV isolated in two distant areas of Japan were analysed using RFLP . These geno- types were named CY and MY after representative isolates in each genotype. This finding was greatly extended to clarify the overall distribution of JCV genotypes in the Japanese Archipelago .
Thus, urine samples were collected at 34 sites along the Japanese Archipelago, from the northern edge of Honshu (Goshogawara) down to one of the southernmost islands (Miyako-jima) (sites of urine collection are shown in Figure 4). The northern island, Hokkaido (Figure 4), was not included in this study, as the general population on this island mainly consists of descendants of recent immigrants from Honshu. It was reported else- where the genotypes of JCV detected in an aboriginal tribe (the Ainu) in Hokkaido . Amplified IG
Figure 4. Map showing the domains of the two major JCV geno- types (CY and MY) in Japan. Sites of urine collection are indi- cated by dots with site numbers, the names of which were described elsewhere . The areas in which CY and MY were found more frequently (i.e. at rates 5 75%) are indicated as CY- rich (or MY-rich) areas, respectively. The area designated an inter- mediate area is where CY and MY were found at almost the same frequencies.
The JCV genotype profile in modern Japanese thus established  is summarised below. (i) Two genotypes, CY and MY, are prevalent in modern Japanese. (ii) Both CY and MY have unique domains in the Japanese Archipelago. MY is more prevalent in Northeast Japan, while CY is more prevalent in Southwest Japan (see Figure 4). (iii) There are three minor genotypes (EU-a, B1-a and SC), each showing a unique regional dis- tribution pattern. EU-a occurs predominantly in northeastern areas facing the Japanese Sea; B1-a occurs in the central area of Honshu; and SC is localised to South Japan.
ANCESTRAL POPULATIONS THAT CONTRIBUTED TO THE FORMATION
OF MODERN JAPANESE
It is generally accepted by anthropologists that modern Japanese were formed by two distinct ethnic groups, the Jomon people who colonised Japan in the Neolithic period and later ‘immigrants’ from the Asian Continent during the Aeneolithic Yayoi and prehistoric Kofun periods [59,60]. Here, we infer the origin of modern Japanese based on the JCV genotype profile in Japan. As there are two major JCV genotypes (CY and MY) in Japan, it can be inferred that modern Japanese were formed mainly by two ancestral populations, carrying CY or MY. In general, this inference is in agreement with the ‘immigrants’ hypothesis on the formation of modern Japanese. Nevertheless, it was found that three minor JCV genotypes (EU-a, B1-a and SC) occur in the Japanese Archipelago. Two major genotypes (CY and MY) and two minor genotypes (B1-a and SC) belong to Type-B, while one minor genotype (EU-a) belongs to Type-A. As described above, people carrying Type-B JCVs excluding Af2 and B1-c correspond to Mongoloids, while those carrying Type-A JCVs correspond to Caucasoids. Thus, we may state that not only Mongoloids but also Caucasoids contributed to the formation of modern Japanese. …
Asian genotypes of JC virus in Native Americans and in a Pacific population: Viral markers of evolution and migration
The first point to stress is the geographical distribution of the 52 strains of types 1 and 4. Half of them were found in Europe. One strain was found in Morocco. Six strains were isolated in North America from individuals of European origin. Eight strains were isolated from autochthonous populations inhabiting the northeastern edge of Siberia, such as the Nanais, Koryaks, Chukchis, Luskys and Yukaghirs. Two strains were found in the Canadian Inuits, an indigenous Arctic populace speaking an Eskimo-Aleut language (Ruhlen, 1991). The remaining nine strains were found in Japan: four of them belong to the Ainu, a pre-agricultural native population of great anthropological interest (Bannai et al., 2000).
Since it has been proved that types 1 and 4 arose from type 6 as an independent lineage (Pavesi, 2003), its geographical distribution could reflect a prehistoric migration of humans from Africa into Europe and from there to northern Asia. The hypothesis that types 1 and 4 were acquired by modern humans when they migrated into Europe and came in contact with archaic populations (Homo neanderthalensis) seems to be rather unlikely. The transmission of JCV, in fact, requires close and prolonged contact between individuals living in the same ethnic group (Kunitake et al., 1995), as proved by the lack of transmission between populations inhabiting the same geographical area yet only occasionally intermingling with each other (Kato et al., 1997). The geographical distribution of the other lineage of JCV (East Africa, Eurasia, Asia, Americas, Oceania and the Pacific Islands) is compatible with the pattern of migration yielded by human genes (Cavalli-Sforza & Feldman, 2003).
The finding that the divergence of the Caucasian lineage of JCV (types 1 and 4) was accompanied by synonymous, rather than non-synonymous substitutions (Table 1T1) seems to exclude the hypothesis of a divergence due to selective pressures favouring adaptation to cold climates. The hypothesis of an additional early expansion of humans from Africa to the northern areas of the world (Fig. 4F4), previously suggested by synthetic maps (Pavesi, 2004) or phylogenetic trees (Yanagihara et al., 2002; Sugimoto et al., 2002a, b; Yogo et al., 2003), seems to be substantiated by the virtual lack of marks of natural selection in the divergence of types 1 and 4.