There is an increasing scientific consensus that individuals infected with HIV may be at risk of acquiring other strains of HIV. As discussed in The Origins of AIDS, at least eight major subtypes of HIV–1 have already been identified, and one major subtype of HIV–2 has also been identified. It has recently been established that:

• Individuals can be infected with two different subtypes at once.
• Individuals can be infected with wild-type virus after initially being infected with drug-resistant virus
• Chimpanzees can be infected with one subtype of HIV after having already seroconverted in response to another sub–type. This suggests that an immune response to one sub–type may not be protective against another sub–type, and that re–infection is a theoretical possibility
• Subtypes of HIV can re–combine to form new subtypes. For example, subtype E is believed to have been a product, or `mosaic', of co–infection with subtypes B and F at some point in the history of the epidemic. Subtypes G and I are also recombinants related to subtype A. It is unknown whether different subtypes have different biological properties such as greater infectiousness or speedier disase progression (although see The strain of virus above for discussion of this issue).

At the XIII International AIDS Conference in Durban, Dr Francine McCutcheon presented evidence that the number of recombinant viruses is growing, and that these viruses are particularly common in West  and Central Africa. Some recombinants appear to contain genetic information from up to six different viruses, she reported, indicating a far rate of re-infection than hitherto imagined. However, high levels of recombinant viruses in the population appears to be associated with a lower HIV prevalence, suggesting that these viruses may not be transmitted as efficiently as `purer' viruses.

• Re–infection with the same subtype may also be cause for concern even in populations where one subtype predominates, especially if it is possible for drug resistant viruses to pass to hosts already infected with HIV. This raises the prospect of drug-resistant HIV being transmitted within the HIV–positive population.
• Transmission of drug resistant HIV could also lead to the recombination of HIV variants resistant to several different drugs, leading to the faster emergence of multiple drug resistant HIV.

Persuasive evidence which seems to support these theories was presented to the XIV International AIDS Conference in Barcelona. Two cases of documented superinfection with different strains of HIV were reported. In one case a man presented to doctors with an acute retroviral syndrome (the flu-like illness which develops when a person first develops antibodies to HIV after infection with the virus) following a number of unprotected sexual contacts. The man was already known to be HIV-positive and had been on HAART for over two years. Tests after a viral rebound indicated that the man had originally been infected with subtype AE, but was also infected with subtype B. The possibility that he was infected with subtype B before the rebound was eliminated by performing a polymerase chain reaction (PCR) test, which confirmed the absence of subtype B before the viral rebound. In addition, the type of subtype B the man was infected with closely related to subtypes found in Brazil, where the man had had recent unprotected sexual contacts.

In a second similar case, a man was found to be superinfected despite having a strong and effective immune response to his exisiting HIV infection. The case involved a man who had been enrolled on a treatment interruption study, and after three cycles of treatment and interruption had mounted an effective immune response to HIV. When a viral rebound occurred, detailed analysis of the man’s viral profile revealed that he had been superinfected with a new strain of subtype B. Despite having a strong immune response to the original strain of subtype B, the man’s immune system was less able to recognise the new strain leading to uncontrolled viral replication.

The May 2nd edition of the journal AIDS carried a case report of a man who has been superinfected with wild-type (drug-sensitive) HIV after initial infection with drug-resistant virus.

The patient was enrolled in a cohort of people who were initially infected with drug-resistant HIV. Four months later, however, a separate and distinct wild-type viral population was detected.

At enrollment the man had a CD4 cell count of 711 cells/mm³ and viral load of 2,413 copies/ml. Plasma and peripheral blood mononuclear cell samples were taken in order to identify resistance mutations. Resistance mutations in reverse transcriptase codons 181 and 184 were identified.

However, the presence of a second, distinct viral population was confirmed four months later by the sequencing of the 1302 bp fragment of the gag-pol region. It showed that, unlike the initial strain of HIV detected in the man, the second strain was drug-sensitive at codons 181 and 184 of HIV reverse transcriptase where drug resistance was initially detected.

Both strains of HIV were from the type B subtype, which is prevalent in the US. Further tests were conducted to rule out the possibility that the man had been initially infected with both a drug-sensitive and drug-resistant strain of HIV. These included clonal sequencing and genetic reconstruction of viral populations. These tests failed to detect a mixed population of HIV before or after the point at month four when the man was superinfected. Coinfection was further ruled out by analysis of the length polymorphism of the V4-V5 region of HIV gp120 which showed that the man was initially infected with a single strain of HIV.

Superinfection with the wild-type HIV had a negative impact on the man’s viral load and CD4 cell count. Coinciding with detection of the second strain of HIV the man’s viral load increased from a stable level of between 2,400 copies/ml and 7,000 copies/ml to a little over 34,000 copies/ml at month four, almost 200,000 copies/ml at month six and 170,000 copies at month nine. At the same time, the man’s CD4 cell count fell from almost 800 cells/mm³ to a low point of 283 cells/mm³ at eleven months.

"These data indicate that four months after infection by drug-resistant HIV this patient was infected by a second, drug-sensitive virus”, note the investigators.

The potential health implications of infection with two different viral populations, which are not equally susceptible to the patient’s immune system, are emphasised by the investigators, with the fitter wild-type virus causing “an abrupt increase in plasma viremia” in this patient.

Superinfection could also impact on the effectiveness of HAART. Standard tests to detect drug resistance would not reveal a drug resistant strain of HIV after superinfection with a second, fitter, wild-type strain. “Nevertheless, if the patient were to initiate therapy, it seems likely that drug-resistant virus would quickly re-emerge.”

At the 11^th Retrovirus Conference in 2004 (Smith 2004) a group of investigators from Los Angeles and San Diego provided long-awaited information on the incidence of sexually-acquired superinfection, concluding that, amongst their cohort of 78 recently infected individuals not on therapy, the annual rate of superinfection was 5%.

Smith and colleagues retrospectively analysed blood plasma samples from 78 individuals – the majority of whom (90%) were gay men – who were enrolled in the San Diego and Los Angeles Acute HIV Infection and Early Disease Research Programmes between December 1997 and June 2003, and looked for independent clusters of the pol gene. When superinfection was suspected, they rigourously tested the samples using four different lines of molecular investigation: clonal (V3) and dye-primer (pol) sequencing, and length polymorphism analysis (V1-2 and V4-5).

Three cases of superinfection were identified in the cohort. In each case, superinfection occurred between five to 13 months after the estimated date of initial infection. Each superinfecting HIV strain was associated with a change in susceptibility to antiretrovirals, even though none of the men were on therapy. Two were initially infected with drug-resistant HIV and then became superinfected with a wild-type strain, while the other was initially infected with a wild-type strain and then was superinfected with a drug-resistant strain. Within six months of acquiring the superinfecting strain, their viral loads increased by an average of 1.6 logs and their CD4 counts decreased by an average of 132 cells/mm³ (p< .05).

All three of the cases were gay men who had multiple sexual partners, making identification of the person who superinfected them (the index case) impossible. Without the index cases, the possibility of co-infection – that is, infection with two different viruses at the same time – cannot be completely ruled out. However, since the method they used to identify superinfection is considered to be somewhat conservative, Smith noted that their 5% annual rate may actually be an underestimate, although previous studies in chimpanzees and injection drug users found a similar 5% incidence rate.

However other doctors disagree as to the frequency of superinfection. At the seventh International Conference on Drug Therapy in HIV Infection Dr Mark Wainberg talked about instances of superinfection he had detected in a cohort of patients followed since primary HIV infection.

One patient out of the 31 in the PHI cohort was not only initially infected with a multi-drug-resistant virus but later acquired a second MDR virus some 30-40 weeks after his first infection. The superinfection was detected because the patient’s viral load, which had been very low (in the region of 200-1,000 copies) suddenly increased tenfold to several thousand copies/ml.

Genotyping showed that a different pattern of resistance mutations had taken over; while the first virus had thymidine analogue mutations, the second one lacked these, while still having the M184V mutation and the V108I NNRTI mutation.

The clinical consequences of infection with MDR virus were unpredictable, Wainberg said.

The physician actually responsible for the care of the superinfected patient was in the audience, and in response to a question added that his patient had failed several regimens and was now on a treatment break with a CD4 count of under 200.

Wainberg added that he personally thought superinfection, at least with resistant viruses, was a relatively rare event, being observed in only one out of 31 patients in six years’ observation of this closely-followed cohort.

Since then instances of superinfection continue to be reported, but it is still unclear how common it is as a phenomenon. Most of the cases reported have only come to light because of adverse clinical consequences such as the sudden appearance of HIV drug resistance. It may be that superinfection is quite common but does not often have adverse effects; equally it may be that some resistance attributed to poor adherence is in fact due to superinfection.

References

Smith D et al. Incidence of HIV Superinfection Following Primary Infection. 11^th CROI, San Francisco, abstract 21, 2004.

Wainberg M. Evolution of transmited wild-type and drug-resistant virus in primary HIV infection. Seventh International Conference on Drug Therapy in HIV Infection, Glasgow. Plenary PL2.3. 2004.