Two Percent of HIV-Positive U.S. Blood Donors Are Infected with Non-subtype B Strains ABSTRACT

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1 AIDS RESEARCH AND HUMAN RETROVIRUSES Volume 19, Number 12, 2003, pp Mary Ann Liebert, Inc. Two Percent of HIV-Positive U.S. Blood Donors Are Infected with Non-subtype B Strains ERIC L. DELWART, 1,2 SHARYN ORTON, 3 BHARAT PAREKH, 4 TRUDY DOBBS, 4 KENNETH CLARK, 5 and MICHAEL P. BUSCH 1,6 ABSTRACT To estimate the prevalence of HIV strains other than the predominant HIV-1B subtype in the U.S. blood donor population we genetically and serologically characterized HIV in infected blood donations collected throughout he United States from 1997 to mid Using a combination of DNA heteroduplex mobility and DNA sequence analyses of the env and gag regions of HIV-1 we determined that 285 of 312 infections were caused by HIV-1B and six by non-subtype B HIV-1 (four HIV-1C, one HIV-1AE, one HIV-1A). Genetic distances of greater than 14% in the envelope V3 V5 region of the four HIV-1C strains indicated that they did not share a recent common origin. HIV-1 group M, N, and O, and HIV-2 specific peptide serological testing of the 20 PCR-negative samples determined that one infection was caused by HIV-2 and none by HIV-1 group N and O. The major risk factor for infection with a non-hiv-1b strain was sex with an HIV-infected person from Africa although three of seven non-hiv-1b-infected subjects did not fit that category. For four of seven non-hiv-1b-infected subjects the subtype detected was consistent with the African country of origin of the infected person or of their sexual partner. The frequency of genetically confirmed non-subtype-b HIV infection in a geographically dispersed group of infected U.S. blood donors in was therefore 2.0% (6/312). INTRODUCTION THE GENETIC DIVERSITY OF HIV within the United States is of interest for tracking the spread of imported variant strains, ensuring the sensitivity of serological screening and viral RNA quantitation methods, and may possibly influence the efficacy of HIV-1B-based vaccine immunogen. 1 7 Unlike Europe, where multiple subtypes of HIV-1 cocirculate, 8 10 a single subtype (subtype B) of the main (M) group of HIV-1 (HIV-1B) still predominates in the United States. 11 An early and rapid spread of HIV-1B, possibly from a point source introduction in the midto late 1970s, 12 may account for the predominance of a single HIV-1 subtype in the United States. Nevertheless recent analyses have detected nonsubtype B HIV-1 in the United States. Subtypes A, C, D, E, F, G, A/J, as well as HIV-1 group O infections have been reported in non-national U.S. residents and in U.S. citizens likely to have been infected abroad Transmissions of non-hiv-1b that appeared to have occurred in the United States include 3A, 1F, 1E, 1B/F, 1A/B, and 1 A/B/E recombinant subtype viruses As part of a continuing effort to monitor the genetic diversity of HIV in the United States we attempted to genetically subtype 316 HIV strains from blood donors identified in U.S. blood collection sites as anti-hiv-1 and/or HIV-2 seropositive on the basis of routine laboratory screening of whole-blood donations given between 1997 and 2000, and subsequently enrolled in the CDC HIV Donor Study. 23 Subjects MATERIALS AND METHODS A total of 7.2 million blood donations were collected in from the 18 participating blood centers located 1 Blood Systems Research Institute, San Francisco, California Department of Medicine, University of California, San Francisco, California. 3 Transmissible Diseases Department, American Red Cross Holland Laboratory, Rockville, Maryland. 4 HIV Immunology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia. 5 Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia. 6 Department of Laboratory Medicine, University of California, San Francisco, California. 1065

2 1066 throughout the United States. Seven hundred thirty-two donors (0.01%) were confirmed as HIV positive using standard blood banking criteria, i.e., repeat reactive by an HIV-1/HIV-2 enzyme immunoassay (3A77 EIA, Abbott Laboratories, Abbott Park, IL) and confirmed by Western Blot (Biotech; Rockville, MD) using CDC/FDA criteria (two bands from p24, gp41, and/or gp120/160). These donors were counseled and invited to participate in the study. If the donor was willing to participate (n 5 428), consent was obtained at that time for the following activities: willingness to participate in an interview about their sexual practices, drug use, and knowledge of AIDS and HIV transmission; blood draw for a complete blood count (CBC), white blood cell (WBC), and lymphocyte subset determination; and storage of blood for future testing when new research tests are developed. All the available demographic characteristics of the enrolled and nonenrolled subjects were identical (p $ 0.05 for age, gender, first time or repeated blood donor, year of donations, regions, hepatitis B core, hepatitis B surface antigen, syphilis, hepatitis C virus (HCV), and human T cell leukemia virus (HTLV) I/II antibody reactivities). Because the race/ethnicity of donors was not routinely determined by most participating blood banks during the initial blood donation and was removed from the record of the nonenrolled subjects a comparison of the race/ethnicity of the enrolled and nonenrolled subjects was not possible. Subjects whose HIV were genetically and serologically analyzed here did not significantly differ from the other enrolled subjects in any of the above demographic characteristics including race/ethnicity. The study protocol was reviewed and approved by the Committee on Human Research at the University of California, San Francisco. PCR, genetic analysis, and serology DNA was extracted from dimethyl sulfoxide (DMSO)-preserved buffy coat or peripheral blood mononuclear cell (PBMC) preparations using a DNA extraction kit (QIAGEN, San Clarita, CA). One microgram of genomic DNA was used to initiate nested polymerase chain reaction (npcr) using previously described primer pairs (ED5 ED12 followed by ES7 ES8) amplifying a 700-bp V3 V5 envelope fragment. 24 When amplifications of env genes remained negative following multiple attempts, a nested set of primers directed at the gag region designed to amplify all subtypes of HIV-1 M group was used. 25 Plasma was obtained from the subjects whose PBMC DNA remained PCR negative. Viral RNA was extracted from 140 ml of plasma using a viral RNA extraction kit (QIAGEN, San Clarita, CA) and resuspended in 30 ml of water with 3 U of RNasin (Promega, Madison, WI); 11.5 ml RNA was reverse transcribed using RNase H negative reverse transcriptase (Gibco BRL, Gaithersburg, MD) and 1.5 mg of six-nucleotide-long random oligonucleotides (Gibco BRL Life technologies, Rockville, MD) to prime reverse transcription. Five of the 20 ml of cdna so generated was used to initiate env or gag npcrs. HMA subtype classification was based on the electrophoretic mobility of DNA heteroduplexes formed between the PCR amplicons from each infected blood donor and amplicons derived from prototypes of HIV-1 from each of the major HIV- 1 subtypes Maximum likelihood phylogenetic trees were constructed with the PHYLIP dnaml program with global rearrangements and randomized input orders ( genetics.washington.edu/phylip.html). 27 Evidence for intersubtype recombination in the untypable variant (U-US35) was tested using the subtyping subtype/subprehiv1.html) and RIP ( RIPsubmit.html) programs on the NCBI and Los Alamos National Laboratory HIV database website. Sequence information is reported as GenBank accession numbers AF to AF and AY to AY V3 peptides from HIV- 1 group M, N, and O were used to detect HIV-1 M-, N-, or O- specific antibodies in non-pcr amplifiable samples. Immunodominant gp41 or gp36 peptides from HIV-1 or HIV-2 were also used for serotyping HIV-1 and HIV-2 infections. 21,28 Peptides were coated on microwells of 96-well plates at 0.5 mg/well. 28 Plasma specimens were diluted 1:400 and used to detect peptide-specific antibodies. RESULTS DELWART ET AL. Blood samples from a total of 316 HIV-positive donors enrolled in this study were tested for PCR amplifiable HIV-1 sequences. PBMC DNA was first analyzed by PCR using primer pairs amplifying an env V3 V5 region fragment. 24 These nested env primers pairs used have been shown to amplify all known subtypes of the M (main) group of HIV-1. 24,29 The genomic DNA samples that tested negative for HIV-1 env were further analyzed by npcr using gag specific primers also designed to amplify all subtypes of the HIV-1 group M. 25 When genomic DNA was negative for both env and gag, cdna generated from plasma was tested using the nested npcr primer sets for both regions. Using these methods 291 (92.0%) of the 316 cases yielded PCR amplicons (284 env and 7 gag), which were then subtyped by env and gag heteroduplex mobility analysis (HMA) ; 285 HIV-1 strains belonged to subtype B, four to subtype C, and two to subtype A. All four viruses subtyped as HIV-1C in the env HMA were also subtyped in the gag region. HMA showed these four viruses to have subtype C gag sequences and therefore they did not appear to be recombinant viruses. Env PCR fragments were also purified and directly sequenced. Sequence alignment followed by gap stripping and maximumlikelihood distance measurement between the four subtype C variants indicated that they diverged by.14% (Fig. 1). One subtype A virus could be amplified only in the gag region while the other subtype A virus was PCR positive only in the env region. Both PCR fragments were directly sequenced. The 10 sequences most closely related to the gag A variant in the Los Alamos HIV database belonged to the common recombinant form HIV-1CRF01-AE from Thailand. The subtype A env sequence (using HMA) was phylogenetically most closely related to subtype A env sequences from Africa. Because of its large degree of divergence from other subtype A env variants (including the new subsubtype A2 30 ), and its outlier status on the phylogenetic tree, this U.S. strain was labeled as an untyped (U) HIV-1 strain (Fig. 1). Trees constructed using the PHYLIP dnadist and neighbor programs produced trees with similar topologies (data not shown). The large degree of genetic divergence between these six non-b subtype HIV-1 strains indicated that they did not share a recent common ancestry and were therefore independently introduced into the United States. Based on V3 loop sequences

3 NON-HIV-1B SUBTYPES IN U.S. BLOOD DONORS 1067 FIG. 1. HIV-1 env V3 V5 sequences from non-hiv-1b-infected donors were aligned with sequences representative of different subtypes of group M HIV-1 and a phylogenetic tree derived by the maximum likelihood method. The 4 HIV-1C and the HIV-1U U.S. strains are highlighted in bold. all non-b viruses were inferred to be nonsyncytium-inducing, CCR5-dependent strains. 31 Plasma samples from the 25 subjects from which neither HIV-1 M env nor gag regions could be amplified from DNA or plasma RNA were tested for antibodies to HIV-1 group M, N, and O and HIV-2 peptides using an EIA serotyping assay. 28 Twenty of 25 plasma samples showed the presence of antibodies to HIV-1 group M peptides while one other sample reacted only to HIV-2 peptides. No antibody reactivity to HIV-1 groups N and O peptides were detected. Serotyping using HIV- 1 group M peptides from different subtypes 28 suggested the possible presence among the PCR-negative samples of nine subtype B serotypes, one subtype D serotype, one subtype C serotype, and nine samples whose HIV-1 group M serotype was indeterminate. Serotyping of the PCR-negative plasma samples therefore indicated the possible presence of one more subtype C and one subtype D infection. The inability to amplify HIV- 1 DNA and RNA from these 20 group M peptide reactive samples may reflect proviral and plasma viral loads that were too low to permit their amplification, sequence polymorphisms at PCR primer binding sites, or sample degradation. The five plasma samples that tested negative for HIV-1 group M, N, and O peptide antibodies were further tested for HIV antibody reactivity using the Genetic Systems combined HIV- 1/HIV-2 antibody EIA (Bio-Rad Laboratories, Redmond, WA), HIV-1 Western blots (Bio-Rad Laboratories, Hercules, CA), and for the presence of HIV-1 RNA using the Roche Amplicor HIV- 1 Monitor assay (v1.5 with a sensitivity of 400 copies/ml). Four of the five samples were negative on HIV-1/2 EIA and all were negative for HIV-1 viral RNA. The one HIV-1/2 EIA reactive sample was the same sample that was also reactive to the HIV- 2 peptide EIA. That sample had an indeterminate HIV-1 Western blot banding pattern, and was further classified as HIV-2 infected by specific serology using Select-1 and Select-2 EIAs (Biochem Immunosystems, Montreal, Canada), and an HIV-2 Western blot (GeneLabs, Singapore). Therefore, by all serological criteria tested, this blood donor appeared infected with HIV-2. The four remaining HIV-1 PCR-negative samples that tested negative by all serological (HIV-1 M, N, O group and HIV-2 peptides serotyping, combined HIV-1/2 peptide EIA, and anti-hiv- 1 Western blot) and virologic tests (HIV-1 amplicor RNA load, gag and env npcr with DNA and cdna) are therefore likely to represent falsely identified HIV-positive blood donations. Overall one infected donor (2%) of 50 tested from 1997 was found to be infected with a non-hiv-1b (one HIV-1C), two (1.8%) of 113 from 1998 were non-hiv-1b (one HIV-1C and one HIV-2), two (2.0%) of 97 from 1999 were non-hiv-1b (two HIV-1C), and two (6.0%) of the 33 from 2000 were non-hiv- 1B (one HIV-1CRF01_AE and one HIV-1U). A further two infections from 1998 and 2000 may also have been caused by non- HIV-1B viruses using the less stringent serotyping criterion The available demographics of the HIV-1B-infected, PCRnegative and non-hiv-1b-infected blood donors are shown in Table 1. The predominant risk factors for non-hiv-1b infection were having sex with a person from Africa. The HIV-2 infection was found in a male donor born in the Ivory Coast who acknowledged having sex with someone from the Ivory Coast, a country with a high rate of HIV-2 infection. 35 Subtype C infection was detected in a U.S.-born black male blood donor who acknowledged having sex with someone from Namibia, a black female born in Zimbabwe who acknowledged having had sex with someone from Zimbabwe, and a black female born in Ethiopia who reported having had sex with someone from Ethiopia. HIV-1C is the dominant subtype in these three African countries ( The fourth subtype C was found in a U.S.-born black female whose only identified risk factor was having sex with an intravenous drug user. The HIV-1U (or subtype A outlier variant) was found in a U.S.- born female of unknown race who acknowledged having sex with a bisexual man, while the HIV-1CRF01_AE virus was found in a U.S.-born white male with no identified risk factors.

4 1068 TABLE 1. TEMPORAL, DEMOGRAPHIC, AND RISK FACTOR CORRELATION OF GENETICALLY CONFIRMED HIV-1B AND NON-HIV-1B INFECTION IN U.S. BLOOD DONORS a HIV-1B PCR negative Non-HIV-1B b Year donation Demographic Gender Male Female Race Black Hispanic White Other Unknown Age, Location East North North East Puerto Rico South South East West Risk factors No identified risk Sex with IDU MSM Sex with HIV Sex with 4 1 bisexual IDU 9 0 MSM 1 IDU 2 0 Sex with someone from Africa Sex with someone from Haiti a Of samples analyzed 312 from a total of 732 HIV-1/2-positive infections identified by participating blood banks. Four subsequently identified HIV-seronegative samples not included. Association between demographic groups and non- HIV-1B infection was measured using Fisher s exact test. Only sex with someone from Africa was correlated with non-hiv- 1B infection (p, 0.05). IDU, intravenous drug user; MSM, men who have sex with men. b Serologically identified HIV-2 case included in non-hiv- 1B column. DISCUSSION DELWART ET AL. This study reports a genetically confirmed frequency of non- HIV-1B strains of HIV of 2.0% in infected blood donations collected from throughout the United States in Four of the seven cases of non-hiv-1b infections were likely acquired following sex with an HIV-positive African in the United States or abroad. For the remaining three cases the infected persons were U.S. born and did not report sex with someone from Africa, indicating that their viral strain may have already been transmitted within the United States. HIV-positive samples analyzed were detected using Food and Drug Administration (FDA)-approved blood bank serological tests and interpretive criteria. Blood banks employ the latest generation and highest sensitivity EIAs available, which are based on selected immunodominant HIV-1 and HIV-2 recombinant proteins detected using an antigen sandwich EIA configuration. These assays are validated to detect antibodies to all the different subtypes of the main (M) group of HIV-1, to HIV- 2, and to 90% of sera from HIV-1 group O-infected subjects, but they carry no FDA approved claim regarding their sensitivity to HIV-1 group N. 7,36 Hence it is possible that some infected donors with highly divergent HIV with poor cross-reactivity to antigens represented in FDA-licensed donor screening assays were not detected and therefore not included in our study. This would result in an underestimate of the frequency of non- HIV-1B-infected donors. A prior HIV-1 subtyping study of 142 hemophiliacs and blood donors identified as seropositive in 1985 showed the presence of only HIV-1B strains. 18,37 Analysis of 383 samples also collected throughout the United States from infected blood donors in showed a non-hiv-1b frequency of 0.8% (one HIV- 1A, one HIV-1CRF02_AG, and one HIV-1C). 18,37 In this study we identified seven non-hiv-1b among 292 samples subtyped (2.3%). When comparing the frequency of non- HIV-1B strains among hemophiliacs and/or blood donors in either and with that found in , a trend toward increasing frequency of non-hiv-1b strains was seen; however, this was not statistically significant with p-values of 0.06 and 0.08, respectively (Fisher s exact test). The 2.3% rate of non-hiv-1b viruses collected from blood donors throughout the United States in 1997 to 2000 was marginally higher than the 1.2% rate of non-hiv-1b reported for AIDS patients collected in in the Bronx, NYC 21 (Fisher s exact test p ) and the 0.6% rate of non-hiv- 1B detected at Stanford University Hospital in (Fisher s exact test p ). Continued monitoring of HIV genetic diversity in blood donors and other populations from throughout the United States will determine whether increasingly diverse strains of HIV are detected and transmitted, as has been seen in other regions of the world. Such surveillance is important for several reasons. Serological and nucleic acid screening and diagnostic monitoring assays need to be sensitive for detecting all circulating strains. Most tests currently licensed in the United States are based on early prototype U.S. HIV-1B isolates. The sensitivity of these tests to non-hiv-1b strains depends on the extent of serological cross-reactivity and nucleic acid sequence homology. A number of recent studies have documented failure of some an-

5 NON-HIV-1B SUBTYPES IN U.S. BLOOD DONORS 1069 tibody and RNA assays to sensitively detect or accurately quantify non-b HIV infections. 1,3 7,39 As these infections become more common it will be critical to ensure that assays with enhanced sensitivity for these infections are licensed and their use implemented. Second, the extent of diversity of HIV in a population is an important consideration in the development of candidate HIV vaccines. Similar to diagnostic assays, the earliest prototype HIV vaccines were based on envelope proteins from T cell line adapted U.S. HIV-1B isolates. These vaccines have shown to have very limited capacity to induce cross-neutralizing antibodies for primary strains of HIV-1B. 40 More recent vaccine candidates incorporate or express proteins from additional regions of the HIV-1B genome, as well as non-hiv-1b epitopes. It is possible that different vaccines may be needed to induce protective immunity for different subtypes of HIV-1 and HIV- 2, and therefore that regional HIV strain distributions will need to be monitored to appropriately target vaccines to each population. It is worth noting that the present study documented four cases in which donors were misdiagnosed as HIV infected. Follow-up testing of cells and plasma from these four donors showed no evidence of HIV antibodies or nucleic acids using a battery of serological and nucleic acid amplification assays. These donors also denied risk factors for HIV infection. False positive HIV results may be due to sample labeling error, sample cross-contamination, or nonspecificity of assays and interpretive criteria (i.e., the 1992 revision of Western blot interpretive criteria deleted the requirement for a p31 Western blot band.) 41 The rate of false-positive HIV-1 test results in the current study (four out of 320 HIV positive or 1.25%) is lower than the 4.8% (20 of 421) rate previously reported in a study of HIV-1 Western blot-positive U.S. blood donors identified from Nonetheless, each case of misdiagnosed HIV infection may have traumatic consequences for the donor. Hence, we agree strongly with the recommendation that repeat testing of a follow-up sample should occur prior to final diagnosis of HIV infection. 41,42 This is particularly important when testing low prevalence populations, when the Western blot band pattern is indeterminate, and when the subject denies risk factors following disclosure of the initial positive test results. 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