On January 28th, a paper reporting evidence of rapid progression associated with a recently identified HIV-1 recombinant circulating in Cuba (CRF19_cpx) was published online by the journal EBioMedicine. CRF stands for circulating recombinant form, and CRF19_cpx represents a combination of HIV-1 subtypes A, D and G. Last week, the authors issued a press release about the study, and since then media coverage has gradually ballooned. Most of the coverage takes its lead from the press release headline: “An aggressive form of HIV uncovered in Cuba.” The immediate problem is that the data are very preliminary, and it is way too soon to declare—as fact—that what has been uncovered is “an aggressive form of HIV.” It may or may not be, additional evidence is needed in order to make that determination. Many media stories also state that HIV CRF19_cpx causes AIDS within three years, which is potentially very misleading because what the study reports is that this rapid pace of progression was observed in a total of nine untreated people who were found to be infected with the strain; this does not prove that all people infected with HIV CRF19_cpx will progress at this rate. There is no evidence to suggest that HIV CRF19_cpx would not respond to treatment.
The study was prompted by anecdotal reports from clinicians in Cuba that they are seeing more cases of rapid progression from HIV infection to AIDS. Starting in November 2007, a total of 95 untreated HIV-positive individuals who were “attending the Institute for Tropical Medicine ‘Pedro Kourí’ (IPK) for medical care” were recruited to participate in the study. A total of 52 were defined as rapid progressors based on a diagnosis of AIDS within three years of the estimated date of seroconversion (estimated as the mid-point between last seronegative HIV test and the first HIV-positive test). Criteria for an AIDS diagnosis were a CD4 count <200 cells, CD4 percentage <14% or the presence of an opportunistic infection. For the purposes of the study, rapid progressors were required to have met the CD4 T cell criteria for an AIDS diagnosis and have an opportunistic infection, or met the CD4 T cell criteria for an AIDS diagnosis and had at least two prior CD4 T cell counts <350. Of the remaining 43 participants, 21 had been followed for more than three years after seroconversion and had not progressed to AIDS (categorized as “non-AIDS”) while 22 had received an AIDS diagnosis three years or more after seroconversion (categorized as “chronic-AIDS”; these individuals had been followed since around 2001 and had retrospective data available).
Of the 52 cases of rapid disease progression, a total of nine were infected with HIV CRF19_cpx. The crux of the study is that this recombinant was not detected in any of the participants in the non-AIDS or chronic-AIDS groups, so it was overrepresented among rapid progressors. Using a Bayesian statistical model, the researchers demonstrate that infection with HIV CRF19_cpx was associated with rapid progression, as well as an increased likelihood of having oral thrush, higher levels of the chemokine RANTES, and greater prevalence of X4 tropism (as inferred from virus genotyping). There was also an association between HIV CRF19_cpx infection and having a higher viral load at diagnosis compared to other subtypes, but this analysis only involved six out of the nine participants. The fitness of HIV CRF19_cpx was estimated to be high, but based only on inference from genetic sequencing and not any assessments of virus replication.
The study results certainly call for additional investigation of disease progression rates in larger numbers of individuals infected with HIV CRF19_cpx. In the discussion section of the paper, several limitations are noted, including the absence of any information on the genetics of the study participants. The fact that 43 out of the 52 rapid progressors had other strains of HIV is consistent with the literature showing that non-viral factors such as immune responses and immune response genes play a key role in determining progression rates. These factors might have contributed to the outcomes in the individuals infected with HIV CRF19_cpx. One issue the paper does not address explicitly is why so many study participants progressed to AIDS without receiving treatment; in some cases, presumably, HIV infection and AIDS were diagnosed simultaneously, but it seems unlikely that this occurred in all the individuals (update: the senior author Anne-Mieke Vandamme has since explained via email that "all patients were treated according to the prevailing Cuban/WHO treatment guidelines" and the final version of the paper is being edited to include this information). The study offers absolutely no reason to believe that HIV CRF19_cpx wouldn't be suppressed by antiretroviral therapy just as effectively as any other HIV strain.
Based on their press release, it appears the researchers wanted to highlight the relevance of their study to HIV prevention, as they begin by noting that acquisition of multiple strains of HIV can lead to the emergence of new recombinants. The release also expounds on a hypothesis offered in the paper that the apparently increased prevalence of X4 tropism in the nine HIV CRF19_cpx-infected participants was related to the high levels of RANTES and played a causative role in their rapid disease progression. The theory is that because RANTES binds to CCR5, the high levels seen in HIV CRF19_cpx infection favored the emergence of X4-tropism. However, although X4 tropism is associated with rapid CD4 T cell decline and disease progression, the cause and effect relationship remains uncertain. There are rare case reports of individuals genetically lacking CCR5 (CCR5Δ32 homozygotes) who have acquired infection with X4-tropic HIV strains, and while precipitous loss of CD4 T cells from the blood has been documented, this has not necessarily equated to the rapid onset of clinical disease. Also, there were concerns that CCR5-blocking drugs such as maraviroc might lead to rapid disease progression by selecting for X4 tropic HIV but this does not appear to have occurred in instances where X4 virus has emerged during treatment. Furthermore, no explanation is offered in the paper as to how HIV CRF19_cpx might cause increased production of the chemokine RANTES by immune cells.
The bottom line is that the paper raises the possibility that HIV CRF19_cpx is a particularly pathogenic HIV variant, but lacks the evidence necessary to confirm that this is the case.
Available online 28 January 2015
In Press, Accepted Manuscript
Vivian Kouria, 1, Ricardo Khourib, c, , 1, Yoan Alemána, Yeissel Abrahantesa, Jurgen Vercauterenb, Andrea-Clemencia Pineda-Peñab, d, Kristof Theysb, Sarah Megensb, Michel Moutschene, Nico Pfeiferf, Johan Van Weyenberghb, Ana B. Péreza, Jorge Péreza, Lissette Péreza, Kristel Van Laethemb, Anne-Mieke Vandammeb, g
a Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
b KULeuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
c LIMI, Centro de Pesquisa Gonçalo Moniz, FIOCRUZ, Salvador-Bahia, Brasil
d Clinical and Molecular Infectious Diseases Group, Faculty of Sciences and Mathematics, Universidad del Rosario, Bogotá, Colombia
e AIDS Reference Center, Centre Hospitalier Universitaire de Liège, Liège, Belgium
f Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany
g Centro de Malária e outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
Received 17 October 2014, Revised 22 January 2015, Accepted 26 January 2015, Available online 28 January 2015
Clinicians reported an increasing trend of rapid progression (RP) (AIDS within 3 years of infection) in Cuba.
Recently infected patients were prospectively sampled, 52 RP at AIDS diagnosis (AIDS-RP) and 21 without AIDS in the same time frame (non-AIDS). 22 patients were sampled at AIDS diagnosis (chronic-AIDS) retrospectively assessed as > 3 years infected. Clinical, demographic, virological, epidemiological and immunological data were collected. Pol and env sequences were used for subtyping, transmission cluster analysis, and prediction of resistance, co-receptor use and evolutionary fitness. Host, immunological and viral predictors of RP were explored through data mining.
Subtyping revealed 25 subtype B strains, 6 C, 7 CRF18_cpx, 9 CRF19_cpx, 29 BG-recombinants and other subtypes/URFs. All patients infected with CRF19 belonged to the AIDS-RP group. Data mining identified CRF19, oral candidiasis and RANTES levels as strongest predictors of AIDS-RP. CRF19 was more frequently predicted to use the CXCR4 co-receptor, had higher fitness scores in the protease region, and patients had higher viral load at diagnosis.
CRF19 is a recombinant of subtype D (C-part of Gag,PR, RT and nef), subtype A (N-part of Gag, Integrase, Env) and subtype G (Vif, Vpr, Vpu and C-part of Env). Since subtypes D and A have been associated with respectively faster and slower disease progression, our findings might indicate a fit PR driving high viral load, which in combination with co-infections may boost RANTES levels and thus CXCR4 use, potentially explaining the fast progression. We propose that CRF19 is evolutionary very fit and causing rapid progression to AIDS in many newly infected patients in Cuba.