Vahey M, Nau M E, Barrick S, Cooley J D, Sawyer R, Sleeker A A, Vickerman P, Bloor S, Larder B, Michael N L, Wegner S A
Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland 20850, USA.
J Clin Microbiol. 1999 Aug;37(8):2533-7. doi: 10.1128/JCM.37.8.2533-2537.1999.
The performance of a silica chip-based resequencing method, the Affymetrix HIV PRT 440 assay (hereafter referred to as the Affymetrix assay), was evaluated on a panel of well-characterized nonclade B viral isolates and on isolates exhibiting length polymorphisms. Sequencing of human immunodeficiency virus type 1 (HIV-1) pol cDNAs from clades A, C, D, E, and F resulted in clade-specific regions of base-calling ambiguities in regions not known to be associated with resistance polymorphisms, as well as a small number of spurious resistance polymorphisms. The Affymetrix assay failed to detect the presence of additional serine codons distal to reverse transcriptase (RT) codon 68 that are associated with multinucleoside RT inhibitor resistance. The increasing prevalence of non-clade B HIV-1 strains in the United States and Europe and the identification of clinically relevant pol gene length polymorphisms will impact the generalizability of the Affymetrix assay, emphasizing the need to accommodate this expanding pool of pol genotypes in future assay versions.
在一组特征明确的非B亚型病毒分离株以及表现出长度多态性的分离株上，对基于二氧化硅芯片的重测序方法——Affymetrix HIV PRT 440检测法（以下简称Affymetrix检测法）进行了评估。对来自A、C、D、E和F亚型的人类免疫缺陷病毒1型（HIV-1）pol cDNA进行测序，结果发现在未知与耐药性多态性相关的区域出现了特定亚型的碱基识别模糊区域，以及少量虚假的耐药性多态性。Affymetrix检测法未能检测到与多核苷类逆转录酶抑制剂耐药性相关的、位于逆转录酶（RT）密码子68远端的额外丝氨酸密码子的存在。在美国和欧洲，非B亚型HIV-1毒株的流行率不断上升，以及临床相关的pol基因长度多态性的发现，将影响Affymetrix检测法的通用性，这凸显了在未来的检测版本中纳入这一不断扩大的pol基因型库的必要性。
