Asian Genotypes of JC Virus in Japanese-Americans Suggest Familial Transmission

DOI: 10.1128/JVI.76.19.10074-10078.2002

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FIG. 1.
NJ phylogenetic tree relating 84 complete JCV DNA sequences. An NJ phylogenetic tree was constructed from the complete sequences, excluding regulatory sequences, reported in this and previous studies. The phylogenetic tree was visualized by using TREEVIEW. As there is no reliable out-group, the tree was rooted by using subtype Af1 as the out-group. The symbols for isolates are shown in Table 2 and have been described elsewhere (2-5, 12, 19, 25, 35). Isolates identified in Southern Californians and second- and third-generation Japanese-Americans are indicated by asterisks. The numbers at the nodes in the tree indicate the bootstrap confidence levels (percent) obtained by 1,000 replicates (only values of >50% are shown). Superclusters (types A, B, and C) (35) and subtypes (Af1, Af2, EU, etc.) are indicated. MY/Jpn, a cluster containing MY isolates from native Japanese and Japanese-Americans; MY/Am, clusters containing MY isolates from Southern Californians and other Americans.

TABLE 1.

JCV genotypes detected in various populations

Genotype^a	Major domain in the eastern hemisphere^b	Incidence (%) of genotype^c in:
Genotype^a	Major domain in the eastern hemisphere^b	Southern Californians	Second-generation Japanese-Americans	Third-generation Japanese-Americans
EU (types 1 and 4)	Europe, Mediterranean areas	17/33 (52)^e	1/35 (3)	0/18 (0)
Af2 (type 3)	Africa, West Asia	0/33 (0)	1/35 (3)	1/18 (6)
B1-c (type 2B)	Europe	1/33 (3)	0/35 (0)	0/18 (0)
B1-d	Saudi Arabia, Greece	1/33 (3)	0/35 (0)	0/18 (0)
CY (type 7B)	Japan, South Korea, North China, Mongolia	2/33 (6)	25/35 (71)^f	12/18 (67)^f
MY (type 2A)	Japan, South Korea	6/33 (18)	8/35 (23)	4/18 (22)
SC (type 7A)	Southeast Asia, South China, Pacific Islands	4/33 (12)	0/35 (0)	0/18 (0)
Other	ND^d	2/33 (6)	0/35 (0)	1/18 (6)

↵ a Genotypes designated by Guo et al. (13) and Sugimoto et al. (34) and those (in parentheses) designated by Agostini et al. (6) are indicated.
↵ b References 13, 31, and 34.
↵ c Identified according to a phylogenetic tree (not shown) constructed from IG sequences.
↵ d ND, not detected in the eastern hemisphere.
↵ e Significantly different from values obtained with second- and third-generation Japanese-Americans (P < 0.01).
↵ f Significantly different from value obtained with Southern Californians (P < 0.01).

TABLE 2.

Twenty JCV isolates whose complete DNA sequences were determined in this study and analyzed by using the whole-genome approach

Population	Isolate	Genotype^a	Accession no.^b
Second-generation Japanese-Americans	J2-10	CY	AB081600
Second-generation Japanese-Americans	J2-24	MY	AB081601
Third-generation Japanese-Americans	J3-3	MY	AB081604
Third-generation Japanese-Americans	J3-7	CY	AB081605
	J3-8	MY	AB081606
	J3-9	CY	AB081607
	J3-11	CY	AB081602
	J3-13a	CY	AB081603
Southern Californians	LA-2	SC	AB081611
	LA-4	SC	AB081616
	LA-11	MY	AB081608
	LA-13	EU	AB081609
	LA-17	CY	AB081610
	LA-27	MY	AB081612
	LA-28	B1-d	AB081613
	LA-29	MY	AB081614
	LA-31	EU	AB081615
Native Japanese^c	MS	CY	AB081654
	SI	CY	AB081617
	UA	CY	AB081618

↵ a Determined according to a phylogenetic analysis using the whole-genome approach (Fig. 1).
↵ b GSDB, DDBJ, EMBL, and NCBI nucleotide sequence databases.
↵ c Reported previously (40).