Single-strand conformation polymorphism analysis for the study of adenoviral diversity in urban rivers.
The diversity of human adenoviruses (AdVs) in river waters was studied by single-strand conformational polymorphism (SSCP) analysis. Water samples were collected between 2002 and 2003 from 4 rivers in the Gyeonggi Province, South Korea. Forty-six (79.3%) of the 58 samples were positive for AdVs as determined on PCR amplification. Nine different SSCP profiles (profiles A to I) were detected in all the AdVs-positive samples by SSCP analysis, and most of the AdVs-positive samples (38 of 46 samples; 82.6%) showed the SSCP profile D. Nine different sequences were obtained in the SSCP profiles; sequence alignments and phylogenetic analysis identified 5 different sequences that were closely related to the human AdV type 41, and the 4 different sequences that were closely related to human AdV types 3, 4, 12, and 40. Two AdVs genomic variants were detected (types 3 and 41 in A, types 12 and 41 in B, and 2 genomic variants of type 41 in C) in SSCP profiles A, B, and C, respectively. SSCP analysis could be a useful technique for the identification of genetic variants of AdVs and for studying AdVs diversity in urban rivers.
Lee
Cheonghoon
C
School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, South Korea.
Kim
Sang-Jong
SJ
D000260:Adenoviruses, Human / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D004784:Environmental Monitoring / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D018807:Polymorphism, Single-Stranded Conformational; D056910:Republic of Korea; D045483:Rivers / Q000821:virology*; D014871:Water Microbiology