To our best knowledge, this is the first report describing the precise mosaic structure of CRF22_01A1. In this study, we characterized five near full-length sequences of HIV-1 isolates 02CMLT72, 02CM1867LE, 02CM3097MN, 01CM001BBY, and 02CM1917LE that are identified in five apparently unlinked individuals from different areas in Cameroon (). They exhibited similar genomic mosaic backbone and were designated as CRF22_01A1 references. A typical CRF22_01A1 mosaic structure was constructed based on two isolates, 02CMLT72 and 02CM1867LE (). The 01CM53122 virus was originally assigned as CRF22_01A1 and phylogenetic analysis showed that the genome closely clustered within the CRF22_01A1 branch (), however, further comparison of these five CRF22_01A1 strains with the 01CM53122 virus demonstrated a moderate difference in mosaic structure. The 01CM53122 virus was reclassified as a URF with 95% of CRF22_01A1 and 5% of CRF01_AE rather than subsubtype A1 sequence in the env region (). We concluded that the 01CM53122 strain is a recombinant of CRF22_01A1 and CRF01_AE, suggesting the existence of a new recombinant of CRF22_01A1 with other subtype/CRFs in Cameroon.
FIG. 10. The mosaic structure of the CRF22_01A1. Breakpoints were determined from two sequences, 02CMLT72 and 02CM1867LE, using the jpHMM program. The schematic structure was created using the Recombinant HIV-1 Drawing Tool. Both programs are available on the (more ...)
CRF22_01A1 is composed of five genomic segments that can be assigned to the subsubtype A1 and CRF01_AE lineages, respectively. Within the subtype A lineages, three CRF22_01A1 segments (I, III, and V) are positioned close to the internal node of CRF01_AE viruses indicating a close relationship between CRF22_01A1 and CRF01_AE. CRF22_01A1 may display some structural features similar to a CRF01_AE sequence. The segment IV is within subtype A radiation, which does not include CRF01_AE. The segment II (nt 2666–5452) is the only one that all three clusters of subsubtype A1, CRF01_AE, and CRF22_01A1 diverge from the same point on the main trunk; their nearest node was found among some of the early subtype A lineages. Further phylogenetic analysis and SUDI distance analysis indicated that segment II is a recombinant of A1 and CRF01_AE, suggesting that different recombination events were involved in the evolution of HIV-1. CRF01_AE was previously reported to be a recombinant of subsubtype A1 and E and consists of at least 10 segments of A1 and E backbone.7,37,38
CRF01_AE is designated as subsubtype A1 in the region of nt 790–5096 and subtype E in the region of nt 5097–5320, respectively.7
The presence of CRF01_AE in segment II suggests that CRF22_01A1 may contain a subtype E sequence in this region. However, it will be difficult to determine the recombinant nature of segment II in CRF22_01A1 due to the lack of pure subtype E sequences.39
Interestingly, CRF22_01A1 showed two of the same recombinant breakpoints as CRF01_AE in the accessory gene (nt 5452) and env
gene (nt 8470) regions. A possible explanation for this is that CRF22_01A1 may share ancestry with CRF01_AE. If so, similar to CRF01_AE, the CRF22_01A1 strain may have existed and circulated in Cameroon or other areas for a long time.37,38
CRF22_01A1 could represent recombination between contemporary strains derived from lineages CRF01_AE or subsubtype A1. Subtype A of HIV-1 has spread in humans for a long time and is one of the parent strains involved in many viral recombinants such as CRF01_AE and CRF02_AG.26,37–40
In this study, we present evidence that CRF22_01A1 was also formed by the recombination of subtype A and CRF01_AE. Five CRF22_01A1 viruses exhibited similar mosaic structure and formed a new CRF, although some minor sequence variations were observed within the different viruses. The genetic diversity of CRF22_01A1 viruses may be due to the duration of infections in the patients,41–43
but further studies are needed to examine this issue.
Identification of CRF22_01A1 from different patients who have no epidemiological links indicates that CRF22_01A1 is apparently another CRF of HIV-1 that is spreading in humans, and may behave like CRF01_AE and CRF02_AG by forming a new recombinant variant of HIV-1 with other subtypes/CRFs capable of geographic spread in Cameroon and perhaps other parts of the world. We have previously reported a novel CRF36_cpx in Cameroon that was assigned as a recombinant of CRF01_AE, CRF02_AG, subtype A and G radiations, however, the pol
genes of CRF36_cpx were found to cluster with CRF22_01A1.21
As described above, the 01CM53122 strain is another example of the recombination of CRF22_01A1 with CRF01_AE. Brennan et al.
reported that 22.4% of HIV-1 URFs contain the genome of CRF22_01A1 in blood donor samples collected between 1996 and 2004 in Cameroon. CRF22_01A1 is the second most frequent CRF found among HIV-1 URFs identified during a 9-year period of HIV surveillance in Cameroon.24
The reported CRF22_01A1 recombinants include CRF22gag
, and CRF22gag
These results suggest that CRF22_01A1 may be a new HIV-1 variant that could potentially have emerged due to a founder effect that resulted in the formation of new HIV-1 recombinant variants in Cameroon.
Recent reports indicate that HIV-1 genetic diversity was relatively stable in Cameroon during the past decade and that some dominant CRFs found in Cameroon are not currently prevalent in the global HIV-1 epidemic.24
However, increasing global travel may contribute to the spread of HIV-1 infection worldwide44
as evidenced from the detection of CRF22_01A1 from HIV-1-infected patients in the United States45
and Saudi Arabia.46
According to a recent report from the Centers for Disease Control and Prevention (CDC), between 2003 and 2006, 5.1% of 3130 HIV-infected individuals in the 11 states in the United States were diagnosed as having HIV-1 non-B infections.47
The prevalence of non-B subtypes in the United States has increased,45
and the majority of non-B subtypes (80.8%) came from recent immigrants from Africa.48
It has been noted previously that strains emerging as dominant variants in Cameroon and West Central Africa have later spread to other regions of the world and emerged as new infections in other geographically distinct countries. It is thus necessary to continuously monitor the evolution of strains in this region as they can be predictive of the phylogenetic nature of future dominating strains in the HIV pandemic. Highly divergent HIV strains could affect HIV pathogenesis, ease of spread in a population, susceptibility to antiretroviral treatment, or vaccine development strategies. Studies of HIV-1 genetic diversity could have a potential impact on the diagnosis of HIV infection and could provide useful reference reagents for standardization of assays. For these reasons it is important to study the evolution of CRF22_01A1 in these regions and characterize its biological characteristics as it may potentially become a major HIV strain, similar to CRF02_AG, globally in the future.