Review Article - (2014) Volume 5, Issue 5

HIV-1 Diversity in Tanzania and its Implication toward Development of Effective Vaccines: A Review Article

Elichilia R. Shao1,2,3,4*, Emmanuel G. Kifaro1,2,3, James Kimaro3, John G. Mrema2,4, Amos O. Mwasamwaja2,4, Johnstone Kayandabila2,4 and Balthazar M. Nyombi1,2,3
1Kilimanjaro Christian Medical Centre, Moshi, Tanzania, E-mail: [email protected]
2Kilimanjaro Christian Medical University College, Moshi, Tanzania, E-mail: [email protected]
3Molecular Diagnostic Unit, KCMC Clinical Laboratory Moshi, Kilimanjaro, Moshi, Tanzania, E-mail: [email protected]
4Image Doctors Organization, Arusha, Tanzania, E-mail: [email protected]
*Corresponding Author: Elichilia R. Shao, Kilimanjaro Christian Medical Centre, Moshi, Tanzania, Tel: +255784491622 Email:


Background: Human immunodeficiency viruses (HIV) are characterized by extremely high genetic variability. This extensive heterogeneity resulted from high error rate of reverse transcriptase enzyme in combination with fast turnover of virions among HIV-infected individuals. With geographical distribution of subtypes its evolution and unpredictable process and intermixing of HIV-1 variants is inevitable. Recombinant viruses contribute already substantially to the global pandemic especially in sub-Saharan African. East Africa studies has shown more complex mixture of HIV-1 Subtypes and associated recombinant virus especially in Tanzania. Objective: To review past and current literature on HIV-1 diversity and challenges emerging toward effective, safe and cheap HIV-1 Vaccine in Tanzania and gives out some recommendations that could help in tackling these challenges. Methods: A Pub med, HINARI, Springer online archives and Google Scholar literature of publication on HIV-1 Subtypes and Vaccine was performed to identify articles on ‘HIV-1 diversity’, ‘HIV-1 Subtypes’, ‘HIV-1 and vaccine’ , ‘HIV-1 Evolution’, ‘HIV-1 subtypes and vaccine’ and HIV-1 diversity and vaccine in Tanzania. Articles resulting from these searches in the articles were reviewed. Findings: The predominant HIV-1 subtypes across African continent are HIV-1 Subtype C with few cases of Subtypes A in east Africa and recombinant forms in West Africa. In Tanzania the predominant subtype was HIV-1 Subtype A in Northern side compared with HIV-1 subtype C in the western and central part of the country. We also reported few cases of HIV-1 Subtype D and B in the shore of lake Victoria near Uganda border. Conclusion: With regard to HIV infection, we are facing a unique challenge where by a concept of vaccine as a standalone prevention measure to end the epidemic is unlikely. Therefore it is a high time to join global effort to come up with a new paradigm of joining potentially promising ideas toward effective HIV/AIDS vaccine. In area like Tanzania where HIV-1 is very diverse can be taken as an opportunity to harness the possibility of finding broad neutralizing antibodies across all strains for a good candidate of HIV-1 vaccine.

Keywords: HIV-1 subtypes; HIV-evolution; HIV-1; Genetic variability; Recombinant virus; Neutralizing antibodies; Reverse transcriptase and East Africa


The earliest case of HIV-1 infection was identified in 1959 from an adult Bantu male from Kinshasa, the Democratic Republic of the Congo (DRC). It is claimed that this candidate became infected in rural Cameroon and travelled by river to DRC [1]. Furthermore, the evolutionary analyses of phylogenetic data originating from HIV-1 group M in the Congo River basin were linked to the years 1915-1941 [2]. HIV is characterized by a great genetic diversity due to its high mutation rate that occurs during replication. HIV is classified into HIV-1 and HIV-2. HIV-1 is responsible for the AIDS pandemic and HIV-2, a less aggressive virus, is localized in West-Africa. Phylogenetic analysis of the full-length or specific regions of the HIV-1 genome demonstrate a genetic variability which results into classifying the virus into groups M, N, O and P [3]. The pandemic group M is further classified into nine subtypes A, B, C, D, F, G, H, J and K. This diversity has an impact on diagnosis, replication, development of mutations, treatment response as well as the ability to form recombinant viruses during co-infection [4]. Globally, different subtypes of HIV-1 circulate unevenly in different geographical regions. HIV-1 subtype C is predominant in Sub Saharan Africa (SSA), particularly in the southern, central and eastern part of Africa [3].

Drug resistance against viral infection emerge when one or more drug levels concentration which previously was enough to control viral replication is unable to perform the same function. This is the consequences of mutations that occur in the viral proteins targeted by antiviral agents. The following mechanism must be employed for this phenomenon to develop; HIV is characterized with high levels of viral replication which is accompanied by absence of proof reading of reverse transcriptase enzyme hence diversity of viral strains from single ancestor. Introduction of one mutation for each viral genome transcribed with the very short half-life of the virus been one or two days, hence lots of viral particles must be produced to maintain the infection [5]. These errors lead to base substitutions, duplication, insertion and recombinant quasi species among newly formed virus. Therefore emergency of resistance strains may occur in the matter of weeks and keeps on accumulating over the time. In other scenario substitution of single amino acids can produce high level resistance because minority viral quasi species carrying single mutations may exist even before commencement of treatment [6]. Recombination is the process similar to sexual replication in higher organisms where contents of distinct viral genomes are mixed up and form a new hybrid virus. HIV recombination introduces large genetic alteration very rapidly and in uncontrolled manner. This phenomenon is a driving force in HIV evolution which occurs at the speed of 2.8 crossovers per genome per cycle [5]. This may affect drug susceptibility because within a single host, recombinant may produce variants resistant to HIV-1 specific regimens and immune pressure. Recombinant can be circulating recombinant form (CRFs) or unique recombinant forms (URFs) means recombinant that are transmitted in the population and those in one individual respectively. This phenomenon complicates effort towards development of effective vaccines due to existing diversity [7].

This diversity of HIV-1 has a significant role on its epidemiology and preventive strategies. Among the impact of diversity is sensitivity to antiretrovirals especially for HIV-1 Subtypes with natural occurring mutations in the absence of drugs [8]. This polymorphism has been seen commonly on reverse transcriptase (RT) and protease regions which are responsible for drug susceptibility [9]. With high diversity of virus in West and Central Africa, very few strain have spread with only four principle subtype and at least two Circulating recombinant Forms (CRFs) been responsible to more than 90% of global epidemic [10]. More than 50% of global infection is due HIV-1 Subtype C, where about 15% Subtype A, 12% Subtype B, 5% Subtype G, 2% Subtype D and about 20% being recombinant forms [10,11]. The diversity of Subtypes is very distinctive in such a way that strains belonging to the same subtypes like HIV-1 C from Kenya and HIV-1 from Tanzania can differ by up 20% in their env gene while the different between HIV-1 A and HIV-1 C env differ by 35% [12]. Basing on the different presented and HIV virus is continuously evolving with the possibility of super-infection or co-infection means there is increasing genetic distance between strains and formation of intra-subtypes recombinant forms [11] (Table 1).

Region Authors/Year of publication Subtypes/inter-subtypes Dominant Subtype
Northern Africa Karray-Hakim M, et al.(2003)
El Sayed N, et al.(2000)
Elharti E, et al.(1997)
B, C, A, CRF01_AE, CRF11-cpx and D B and C
Central Africa Ndembi N, et al.(2004)
Punzi G, et al.(2005)
Marechal V, et al.(2005)
Anderson J, et al.(2000)
A, B, C, D, CRF06-cpx, CRF11_cpx, CRF06_cpx and F CRF_cpx
Western Africa Monlean M, et al.(2011)
Tebid DM, et al.((2009)
Takehisa J, et al.(1998)
Chaillet P, et al.(2010)
Toni T, et al.(2003)
Jallow S, et al.(2009)
CRF02-AG, G,A, URF,B, C, D, CRF01-AE and F CRF02-AG
Eastern Africa Somi G, et al.(2008)
Mosha F, et al.(2011)
Nyombi B, et al.(2008)
Kiwelu I, et al.(2012)
Yirrell D, et al.(2004)
Gale Y, et al.(2006)
Herbeck J, et al.(2007)
Harmers R, et al.(2011)
Ssemwanga D, et al.(2011)
Arroyo M, et al.(2009)
Lihana R, et al.(2009)
Kageha S, et al.(2011)
Nyageka B, et al.(2011)
Elichilia R, et al.(2014)
A, C, D, AD, B, CRF, URF, CD and AG A and C
Southern Africa Bussmann H, et al. 2005)
Bredell H, et al. 2002)
Deho L, et al. 2008)
Maldonaldo F, et al. 2009)
Scriba T, et al.(2001)
Gordon M, et al.(2003)
C, B, G and CFR02-AG C

Table 1: The degree of HIV-1 Subtypes and inter-subtypes diversity and its diversity in Africa is summarised [8].

HIV-1 Diversity and Vaccine

Literature revealed that HIV-1 diversity is heterogeneous distributed within different geographical locations with different genetic subtypes. This diversity has big impact on transmissibility, pathogenesis, diagnostic methodologies, treatment outcomes, mutations development and the most important is vaccine development [9,13]. The knowledge about effective vaccine to be developed which will be able to elicit cross-protection across subtypes is poorly understood. This knowledge is very crucial for appropriate planning of HIV vaccine trials so for the future vaccine. For the past three decades no one know if an effective vaccine will depend on specific epitopes or protein conformational changes [14]. Although HIV-1 infected individuals can mount new response, there are upcoming insight that mutations escape by virus from CD8+ Cytotoxic T-Cells and neutralizing over time [15]. Furthermore peptides from highly conserved HIV-1 regions among group M sequences which are close related phylogenetically among strains can be a good model for effective vaccine development [16]. In area of HIV-1 Subtype diversity like Tanzania, we can use this opportunity to study different neutralizing antibodies produced from infected individuals to plan a good vaccine which will work out across the Subtypes.

Tanzania among other East African countries has peculiar diversity of HIV-1 including subtype A, C, D and other recombinant strains such as CRF10_CD which was first documented in Moshi Tanzania [17]. Since envelope gene at V3 loop is the most conserved region is there need for a vaccine which is specific for each HIV subtype. Glycoprotein 120 is responsible for inducing neutralizing antibodies which will cut across the subtypes. The ability of Glycoprotein 120 to induce production of Cytotoxic T lymphocytes against other conserved HIV-1 proteins will be able to cross react and offer a new hope for vaccines [18]. T lymphocytes (CTLs) against gag gene products and other relatively conserved HIV-1 proteins are usually assumed to be more cross-reactive, offering a hope for the development of broadly protective vaccines [18]. The new challenges arriving from HIV-1 strains capable of using both chemokine receptor (CCR5) and Chemokine receptor (CXCR4), therefore there will be a need to develop antibodies capable of neutralizing both X5 and X4 strains [19]. To solve this puzzle we might think of using cocktail vaccines with different antigens from different subtypes to design candidate vaccines which will target specific HIV epitopes.

HIV-1 Diversity in East Africa

Global HIV diversity complexity has profound implication for many aspects of the pandemic. This diversity of strains possesses threats toward HIV diagnosis as well as viral load measurements assays. Finding Ashwin Vasan s from east Africa evidenced on how different strains has different disease progression and even transmission capacity [20]. Basing on current phylogenetic analysis HIV-1 has been classified into four groups: main group (M), outlier group (O), non-M-non-O (N) group and newly group P [20]. Group M is responsible for the majority of HIV-1 infections globally and is divided into nine genetic subtypes (A, B, C, D, F, G, H, J, and K) [21]. To date HIV-1 subtypes A and C are the most prevalent in the worldwide epidemic. Furthermore HIV-1 subtypes A and F are further subdivided into sub-types A1-A4 and F1-F2 [22]. Of more interest viruses from different lineages within group M are able to recombine during infection and form recombinant viruses [23,24]. Currently more 60 circulating recombinant forms (CRFs) and a large number of unique recombinant forms (URFs) have been described [25], providing evidence for ongoing evolution of HIV-1 in the global epidemic [11]. Furthermore, individuals infected with multiple HIV-1is well as individuals infected with multiple strains of the same HIV-1 subtype have been reported [26]. Increasing national HIV-diversity has brought in profound implication for many aspects of HIV pandemic and possess great challenges for global HIV prevention efforts. In order to define a new subtype, sub-subtype or CRF, representative strains must be identified in at least three individuals with no direct epidemiological linkage [27]. Three near full-length genomic sequences are preferred, but two complete genomes in conjunction with partial sequences of a third strain are sufficient to designate a new subtype, sub-subtype or CRF (to define a CRF, the partial sequence(s) must also confirm the CRFs mosaic structure [28].

In our neighbour country Kenya, HIV-1 Subtype A is the most prevalent strain especially in Southern part of the country. Other subtypes are C, D and G with other recombinant which account for about 30% [29]. The origin of HIV-1 Subtype G is believed to be introduced into Kenya from West Africa through Lake Victoria shore near Uganda. There are two different epidemic of HIV-1 subtype C, there is Subtype C of Indian origin introduced to Kenya through Ethiopia while the second epidemic is Subtype C of South African origin introduced through Tanzania [30]. Other strains seems to be from West Africa where by evidence of HIV-1 patients at Kilifi basing on Phylogenetic analyses of more than 153 pol sequences showed resembling sequences from other part of West Africa, with evidence of one ancestral founder virus. In Rwanda there are very limited information on HIV-1 diversity which might be due to civil war and 1994 genocide. The available few studies among pregnant women attending antenatal clinics showed the dominant Subtypes were A and C. Likewise Burundi, there are very few data on HIV-1 Subtype distribution in the country. Study which was done among infected children at Bujumbura showed that the dominant Subtypes is HIV-1 Subtype C which seems to be introduced from Democratic Republic of Congo (DRC) [8].

Uganda has special interest on HIV-1 Subtypes in East Africa because the fact that first HIV/AIDS case in the region was identified in Kasensero and Lukunyu fishing villages in Rakai, Uganda [8]. Since then intensive studies and preventive measures toward control of the epidemic has been long time started in the country. Those efforts showed significant decrease of epidemic from 14% in 1990 to 8% in 1999, but in the past two years the epidemic started to rise again. Phylogenetic data from those studies showed that Subtype A and D are dominant among others. Subtype D is believed to be originated from central Africa. The prevalence of HIV-1 Subtype D started to decrease around 1990 which might be explained by fast disease progression, this was replaced with increase of A/D recombinant which is less virulence when compared to pure Subtype D [31]. In Tanzania the most dominant Subtypes are A and C where Subtype C is believed to be originated from South Africa through Lubumbashi in DRC. This also explains why most of western part of Tanzania, Mbeya among other region is dominated by HIV-1 Subtype C compared with Northern Tanzania where A seems to dominate. In East Africa, Tanzania is leading for the presence of different recombinant viruses; it is the place where CRF10_CD was reported for the first time among HIV-1 infected infants in Dar es Salaam [32].

HIV-1 Diversity in Tanzania

Studies from Tanzania evidenced on how different strains has different disease progression and even transmission capacity [3]. It is one of the countries in SSA that has been severely affected by the HIV epidemic. Molecular epidemiological studies have reported that HIV-1 subtypes A1, A2, C, D, G, CRF10_CD and other inter-subtype recombinant viruses are circulating in Tanzania [13,23,33]. HIV-1 subtypes A1, A2, C, D, CRF10_CD and other inter-subtype recombinant viruses were reported among bar and hotel workers in Moshi town at Kilimanjaro region [24]. The HIV-1 subtype profile was almost similar with Mbeya region except HIV-1 subtype A2 and CRF10_CD which have not been found in the region [13] (Table 2). Furthermore, HIV-1multiple variants were reported in almost quarter of a high-risk population of female bar and hotel workers with acute HIV-1 infection in the Mbeya region of Tanzania. It is possible that female commercial sex workers and their male clients, as well as female bar and hotel workers, contribute substantially to the rapid expansion of the HIV-1 epidemic in developing countries like Tanzania [11]. These populations may play an important role in evolution facilitating multiple infections and recombination events [13]. The current work which was done in Mwanza Tanzania showed low prevalent of recombinant comparing to the previous studies [33]. This study pointed out the predominant HIV-1 subtypes was A and C which is similar to the previous work from Kilimanjaro by Ireen and Nyombi [11,23]. When we combine all information from these studies in different part of Tanzania we are getting groundwork for the future HIV-1 vaccine in the region. Diversity of studied population from this region provides future perspectives toward exploration of the efficiency set up for the specific HIV vaccine candidate which will be cut across the diversity of HIV-1 strains at large. Apart from challenges posed from published work on the difficulties to come out with Vaccine which will cover across the diversity of viruses, the other way it may increase the chance of using different HIV-1 strains to come up with the broad neutralizing antibodies.

Region Authors/Year of publication Subtypes/inter-subtypes Dominant Subtype
Lake(Kagera, Mwanza, Geita, Singida and Shinyanga) Kasang C, et al.(2012)
Kapiga S, et al.(2002)
Nyombi B, et al.(2008)
A, B, D, CRF10-CD and recombinant A/D A
Southern Highlands(Katavi, Rukwa and Mbeya) Arroyo M, et al.(2004)
Arroyo M, et al.(2005)
Herbinger K, et al.(2006)
A, C, D, AC, CD, B and CRF10-CD C and AC
Central (Manyara, Singida and Dodoma) Johannessen A (2009)
Johannessen A (2010)
Clara B, et al.(2010)
A, C, D and CRF01-AE A
Northern (Arusha, Kilimanjaro and Tanga) Kiwelu I, et al.(2005)
Kiwelu I, et al.(2012)
Nyombi B, et al.(2008)
Elichilia S, et al.(2014)
  A, C, AD, D andCRF10-CD A
Eastern (Pwani, Morogoro and Dar es salaam) Somi G, et al.(2008)
McCutchen F, et al.(2005)
Mosha F, et al.(2011)
A, C, D, C/A, CRF08-BC/C, D/CRF10-CD, A/D, CRF15-01B/A and C/D A and C
Southern (Lindi and Mtwara)     No data
Southern Highlands (Ruvuma, Njombe and Iringa)     No data
Western (Kigoma and Tabora)     No data

Table 2: Summary of different studies on HIV-1 diversity in Tanzania (1985-2014) [13,23,24,33-45].

Scientific Challenges toward HIV Vaccine

The forefront reasons for the difficulties towards HIV vaccine development can be summarized below. First, nobody has ever recovered from HIV infection except Timothy Ray Brown ‘Berlin patient’ therefore natural mechanism to imitate and produce vaccine which will be potent across subtypes and all recombinant forms. Secondly no good animal models to use in experiments, because monkeys are mostly similar but not identical to human beings. Thirdly, HIV integrate its genetic materials into human host cells and destroys the immune system cells that are responsible to fight against it without being noticed by immune surveillance cells. Fourthly, HIV is highly variable; constantly changing therefore it is difficult to find a vaccine which will have the same effects across changing strains. Fifthly, scientific community miss the link or understanding of immune response responsible to protect people against HIV/AIDS.


In this review, we explored HIV-1 diversity and its challenges towards effective vaccine across the available viral strains in Tanzania. For the past three decades new ideas, new minds and its implication with use of automated high technology has made it possible to study HIV molecular diversity, mutations and new drugs towards its eradication. With some promising vaccine trial findings such asRV144 among others, means there are chance to achieve up to 50% protection. For example RV144 trial which involved boosting immunity with an avipox vector (ALVAC) together with gp 120 protein domain which showed that volunteers in vaccine arm acquired 31% fewer HIV-1 infections than individuals in the placebo arm.We are not yet about to celebrate the victory on HIV epidemic eradication due to more challenges toward effective vaccine. With regard to HIV infection, we are facing a unique challenge where by a concept of vaccine as a standalone prevention measure to end the epidemic is unlikely. Envelope gene has an advantage of evading host immune recognition through its sequence diversity which gives it protein conformational flexibility. With its diversity HIV-1 has been difficult to classify by traditional serotyping which means the ordinary approaches to good vaccine candidate in unlikely so far. But the approach of looking for broad neutralizing antibodies among individuals who have controlled infection should not be ignored.

Therefore it is a high time to join global effort to come up with a new paradigm of joining potentially promising ideas toward effective HIV/AIDS vaccine. In area like Tanzania where HIV-1 is very diverse can be taken as an opportunity to harness the possibility of finding broad neutralizing antibodies across all strains.


This work was supported by Training Health Researchers into Vocational Excellence in East Africa (THRiVE), grant number 087540 funded by the Wellcome Trust. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the supporting office.


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Citation: Shao ER, Kifaro EG, Kimaro J, Mrema JG, Mwasamwaja AO, et al. (2014) HIV-1 Diversity in Tanzania and its Implication toward Development of Effective Vaccines: A Review Article. J Vaccines Vaccin 5:249.

Copyright: © 2014 Shao ER, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.