Genetic Characterization of Diverse HIV-1 Strains in an Immigrant Population Living in New York City

Abstract

New York City (NYC) is one of the original foci of the HIV-1 epidemic and has a greater number of AIDS cases than any other city in the United States. NYC also hosts the highest number of immigrants among the nation's cities: more than 2 million among a total population of 8 million. Such a high rate of immigration could act as a potential source for introducing and disseminating novel HIV-1 strains into the United States. Our current study focuses on the genetic characterization of HIV-1 strains circulating in an immigrant population in NYC. Of the 505 HIV-1-positive specimens obtained, 196 were available for viral sequencing from the C2 to V3 region of env. Phylogenetic analysis using maximum-likelihood and neighbor-joining methods demonstrated that non-B subtypes and circulating recombinant forms (CRFs) accounted for 43.4% (85 of 196 cases), whereas the remaining 56.6% (111 of 196) cases had viral variants similar to the typical North American subtype B virus. Of those non-B subtypes and CRFs, subtype A and CRF02 dominated (63.5% combined); other subtypes, including C, D, F1, G, CRF01_AE, and CRF06_cpx, were also detected. Two HIV-1 sequences do not cluster with any known subtypes or CRFs. Furthermore, the distribution of non-B subtypes and CRFs was consistent with the countries of origin, suggesting that many of the study subjects were likely infected in their home country before they entered the United States. Subtype B viruses identified in the immigrant population showed no significant differences from the typical North American B subtype, however, indicating that a significant proportion of the immigrants must have been infected after they came to the United States. Public health officials and physicians should be aware of the growing genetic diversity of HIV-1 in this country, particularly in areas with sizable immigrant populations.

T-Cell Vaccine Strategies for Human Immunodeficiency Virus, the Virus with a Thousand Faces

“…A global vaccine is a daunting challenge given HIV diversity, but it is motivated by several factors. First, even in a regional epidemic dominated by a single subtype, such as the B-clade epidemic in the United States, pockets of HIV with greater genetic diversity can be found (61,85). Second, most nations have complex epidemics and would not benefit from a single-subtype vaccine (Fig.…”

Reliability of Rapid Subtyping Tools Compared to That of Phylogenetic Analysis for Characterization of Human Immunodeficiency Virus Type 1 Non-B Subtypes and Recombinant Forms

“…An increasing number of non-B subtypes have been reported throughout Europe and in areas of North America with large numbers of immigrants. Local transmission of non-B subtypes and CRF have already been documented (1,5,14). In Spain, almost all HIV-1 subtypes have been identified (7,15), and multiple recombinants, mostly CRF02_AG variants, are currently in circulation (6,8,9).…”

Large-Scale Analysis of the Prevalence and Geographic Distribution of HIV-1 Non-B Variants in the United States

“…Most studies have focused on specific populations, such as military personnel, immigrants, or blood donors (25)(26)(27)(28)(29)(30)(31). There is evidence of increasing non-B prevalence in the United States, and it may be higher than generally recognized (29,(32)(33)(34).…”

“…Most studies have focused on specific populations, such as military personnel, immigrants, or blood donors (25)(26)(27)(28)(29)(30)(31). There is evidence of increasing non-B prevalence in the United States, and it may be higher than generally recognized (29,(32)(33)(34). Although data are limited, studies have shown that the prevalence of non-subtype B varies greatly depending on the population analyzed, ranging from 0.6% in a northern California clinic-based setting (35) to 95% in African-born immigrants in Minneapolis, MN (28,36), and New York City (27).…”