Genetic diversity of Diaphorina citri (Hemiptera: Liviidae) unravels phylogeographic structure and invasion history of eastern African populations

The Asian citrus psyllid (Diaphorina citri Kuwayama) is a key pest of Citrus sp. worldwide, as it acts as a vector for Candidatus Liberibacter asiaticus, the bacterial pathogen that causes citrus Huanglongbing. Diaphorina citri has been reported in Kenya, Tanzania, and more recently in Ethiopia. This study assessed the genetic diversity and phylogeographic structure of the pest to gain insights into the potential sources of its introduction into Africa. Population structure and differentiation of D. citri populations from China, Ethiopia, Kenya, Tanzania, and the USA were assessed using 10 microsatellite loci. Additionally, five new complete mitogenomes of D. citri collected in China, Ethiopia, Kenya, Tanzania, and the USA were analyzed in the context of publicly available sequences. Genotype data grouped the D. citri populations from Kenya and Tanzania in one cluster, and those from Ethiopia formed a separate cluster. The two genetic clusters inferred from genotype data were congruent with mitochondrial sequence data. The mitogenomes from Kenya/Tanzania/China had 99.0% similarity, and the Ethiopia/USA had 99.9% similarity. In conclusion, D. citri populations in eastern Africa have different sources, as the Kenyan and Tanzanian populations probably originated from southeastern Asia, while the Ethiopian population most probably originated from the Americas.     

Speciation of Protopolystoma Bychowsky, 1957 (Monogenea: Polystomatidae) in hosts of the genus shape Xenopus (Anura: Pipidae)

The taxonomy, geographical distribution and hostrange of the polystomatid genus ProtopolystomaBychowsky, 1957 are reviewed. P. xenopodis(Price, 1943) and five new species are recognised,which occur in clawed toads ( Xenopus spp.)throughout subsaharan Africa. Of the two clawed toadsubgenera, Xenopus and Silurana, only theformer is infected. Protopolystoma spp. aredifferentiated by morphological variation of the gut,large hamulus and penis armature. P.xenopodis is found in Xenopus laevis subspeciesin South Africa, Transkei, Zimbabwe, DemocraticRepublic of Congo (D.R.C.), Rwanda, Uganda, Kenya andCameroon ( X. l. poweri and X. l.sudanensis are new host records). It also occurs inintroduced populations of X. l. laevis in theUnited States (southern California) and United Kingdom(South Wales). In subsaharan Africa the speciesdisplays significant, but continuous, geographicalvariation of penis spine size between southernpopulations in X. l. laevis and those in morenortherly host subspecies. Data on the natural hostrange of this parasite were complemented by anexperimental study of host-specificity in the southernform. This can produce patent infections in X.l. victorianus and X. gilli, but not X.wittei nor X. (Silurana) tropicalis. P.simplicis n. sp. is endemic to central and eastAfrican areas, infecting X. laevis subspecies ineastern D.R.C., Rwanda, Uganda and western Kenya, X. wittei-like hosts in eastern D.R.C., westernUganda, Rwanda and Burundi, X. vestitus inwestern Uganda and Xenopus sp. at Nairobi,Kenya. P. ramulosus n. sp. occurs in X.fraseri-like toads in eastern D.R.C. (Gabon andCameroon are also possible literature records), and P. fissilis n. sp. is found in X. fraseri-and X. wittei-like species in Cameroon andeastern D.R.C., and in southern Rwanda, respectively. Two Protopolystoma taxa are found in X.muelleri populations now suspected to representdistinct species: P. occidentalis n. sp. occursin X. muelleri (western form) in Ghana, Togo,Nigeria and Cameroon, while P. orientalis n. sp.is found in X. muelleri (eastern form) in SouthAfrica, Zimbabwe and Tanzania. The allopatricallydistributed species P. ramulosus, P.simplicis, P. occidentalis and P.orientalis form a relatively homogenous grouping withsome interspecific morphological overlap. These taxaare distinguished from P. xenopodis by penisspine morphology and from P. fissilis by hamulusroot form and aspects of gut morphology. Unidentified Protopolystoma sp. have been recorded in X. clivii in Ethiopia, X. fraseri aff. inCameroon and Xenopus sp. in Kenya and Tanzania. At some localities, single host species were infectedby two representatives of Protopolystoma. P. fissilis was recorded in eastern D.R.C. with P. ramulosus, with Protopolystoma sp. inCameroon in X. fraseri-like hosts and with P. simplicis in X. wittei-like hosts in Rwanda. P. xenopodis co-occurred with P. simplicisin X. laevis subspecies through central and eastAfrica.     

Genetic diversity and geographic distribution of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) genotypes associated with cassava in East Africa

The genetic variability of whitefly (Bemisia tabaci) species, the vectors of cassava mosaic begomoviruses (CMBs) in cassava growing areas of Kenya, Tanzania, and Uganda, was investigated through comparison of partial sequences of the mitochondria cytochrome oxidase I (mtCOI) DNA in 2010/11. Two distinct species were obtained including sub‐Saharan Africa 1 (SSA1), comprising of two sub‐clades (I and II), and a South West Indian Ocean Islands (SWIO) species. Among the SSA1, sub‐clade I sequences shared a similarity of 97.8–99.7% with the published Uganda 1 genotypes, and diverged by 0.3–2.2%. A pairwise comparison of SSA1 sub‐clade II sequences revealed a similarity of 97.2–99.5% with reference southern Africa genotypes, and diverged by 0.5–2.8%. The SSA1 sub‐clade I whiteflies were widely distributed in East Africa (EA). In comparison, the SSA1 sub‐clade II whiteflies were detected for the first time in the EA region, and occurred predominantly in the coast regions of Kenya, southern and coast Tanzania. They occurred in low abundance in the Lake Victoria Basin of Tanzania and were widespread in all four regions in Uganda. The SWIO species had a sequence similarity of 97.2–97.7% with the published Reunion sequence and diverged by 2.3–2.8%. The SWIO whiteflies occurred in coast Kenya only. The sub‐Saharan Africa 2 whitefly species (Ug2) that was associated with the severe CMD pandemic in Uganda was not detected in our study.     

Loop-mediated isothermal amplification (LAMP) assays for detection of Theileria parva infections targeting the PIM and p150 genes

We have developed two loop-mediated isothermal amplification (LAMP) assays for the detection of Theileria parva, the causative agent of East Coast fever (ECF), an economically important cattle disease in eastern, central and southern Africa. These assays target the polymorphic immunodominant molecule (PIM) and p150 LAMP genes. The primer set for each gene target consists of six primers, and each set recognises eight distinct regions on the target gene to give highly specific detection of T. parva. The detection limit of each primer set is 1 fg, which is equivalent to one copy of the PIM and p150 T. parva genes. These PIM and p150 LAMP primer sets amplify DNA of T. parva isolates from cattle and buffalo from different countries including Kenya, South Africa, Tanzania, Rwanda, Uganda and Burundi, indicating their ability to detect T. parva from different countries. With the advantages of simplicity, rapidity and cost effectiveness, these LAMP assays are good candidates for molecular epidemiology studies and for monitoring control programs in ECF-endemic, resource poor countries.     

Genetic and morphological characterisation of the Ankole Longhorn cattle in the African Great Lakes region

The study investigated the population structure, diversity and differentiation of almost all of the ecotypes representing the African Ankole Longhorn cattle breed on the basis of morphometric (shape and size), genotypic and spatial distance data. Twentyone morphometric measurements were used to describe the morphology of 439 individuals from 11 sub-populations located in five countries around the Great Lakes region of central and eastern Africa. Additionally, 472 individuals were genotyped using 15 DNA microsatellites. Femoral length, horn length, horn circumference, rump height, body length and fore-limb circumference showed the largest differences between regions. An overall F_ST index indicated that 2.7% of the total genetic variation was present among sub-populations. The least differentiation was observed between the two sub-populations of Mbarara south and Luwero in Uganda, while the highest level of differentiation was observed between the Mugamba in Burundi and Malagarasi in Tanzania. An estimated membership of four for the inferred clusters from a model-based Bayesian approach was obtained. Both analyses on distance-based and model-based methods consistently isolated the Mugamba sub-population in Burundi from the others.     

The genus Urera (Urticaceae) in eastern tropical Africa

The species of Urera Gaud. occurring in eastern tropical Africa are revised. Three species are recognized: U. cameroonensis Wedd., occurring from Uganda to the South African Republic (Natal), U. sansibarica Engl., restricted to the coastal zone of Kenya and Tanzania, and U. hypselodendron (Hochst. ex A. Rich.) Wedd., occurring in montane forest from Ethiopia to Malawi. The original material of U. hypselodendron var. flamigniana Hauman (nom. inval.) and var. platyrrhachis Hauman (nom. inval.) is excluded from U. hypselodendron; the same applies to the other material of U. hypselodendron cited from central Zaire in Flore du Congo belge. Distribution maps of the eastern African species are provided. Also included is a preliminary study and discussion of the generic subdivision of Urera , with special reference to the species of this revision.     

Two new species of Justicia sect. Ansellia (Acanthaceae) from E and NE tropical Africa

The new species Justicia ornatopila from Sudan, Ethiopia, Somalia, Uganda, Kenya and Tanzania, and J. lorata from Kenya are described and illustrated. Information on pollen morphology is also provided     

Ten years experience with 497 cases of neuroinfections in tropic: in limited laboratory infrastructure initially treat both, cerebral malaria and meningitis

Review of 497 cases of neuroinfections in 7 tropical clinics in Ethiopia, Uganda, Burundi, Kenya, Sudan within 2000-2007 was performed. 97.5% of all cases was cerebral malaria (40.1%) and bacterial meningitis (56.4%). TB meningitis, cerebral cryptococcosis and sleeping sickness were very rare.     

Onset and spread of an African army worm upsurge

Abstract. 1. Onset and spread of the severe outbreaks of African armyworm, Spodoptera exempta (Walk.), over Ethiopa, Kenya, Tanzania and Burundi in late 1984 have been analysed in relation to trap and weather records.
2. Although first outbreaks in each country appeared progressively further south, winds on the best estimated dates of moth concentration and egg laying blew from directions precluding moth movements between them.
3. Such independently developing outbreaks are called 'primary' to distinguish them from any 'secondary' outbreaks that may develop from them.
4. Parent moths giving rise to all seven areas of primary outbreaks were derived from low-density populations that had persisted through the dry season, probably near the coast of East Africa.
5. Primary outbreaks developed on the south-eastern sides of individual rainstorms over the highlands, most likely because windborne moths were concentrated there by convergent winds.
6. Of the secondary outbreaks within Kenya, Tanzania and Burundi, most were derived from only one area of primary outbreaks in Kenya, which were therefore critical for effective control of spread; the paucity of other secondaries was presumably due to a lack of timely rainstorms or other concentrating mechanisms.     

Molecular and Phylogeographic Analysis of Human Immuno-deficiency Virus Type 1 Strains Infecting Treatment-naive Patients from Kigali, Rwanda

This study aimed at describing the genetic subtype distribution of HIV-1 strains circulating in Kigali and their epidemiological link with the HIV-1 strains from the five countries surrounding Rwanda. One hundred and thirty eight pol (RT and PR) sequences from 116 chronically- and 22 recently-infected antiretroviral therapy (ART)-naïve patients from Kigali were generated and subjected to HIV drug resistance (HIV-DR), phylogenetic and recombinant analyses in connection with 366 reference pol sequences from Rwanda, Burundi, Kenya, Democratic Republic of Congo, Tanzania and Uganda (Los Alamos database). Among the Rwandan samples, subtype A1 predominated (71.7%), followed by A1/C recombinants (18.1%), subtype C (5.8%), subtype D (2.9%), one A1/D recombinant (0.7%) and one unknown subtype (0.7%). Thirteen unique and three multiple A1/C recombinant forms were identified. No evidence for direct transmission events was found within the Rwandan strains. Molecular characteristics of HIV-1 were similar between chronically and recently-infected individuals and were not significantly associated with demographic or social factors. Our report suggests that the HIV-1 epidemic in Kigali is characterized by the emergence of A1/C recombinants and is not phylogenetically connected with the HIV-1 epidemic in the five neighboring countries. The relatively low level of transmitted HIV-DR mutations (2.9%) reported here indicates the good performance of the ART programme in Rwanda. However, the importance of promoting couples'' counseling, testing and disclosure during HIV prevention strategies is highlighted.     

Release and establishment of Cotesia flavipes Cameron (Hymenoptera: Braconidae) an exotic parasitoid of Chilo partellus (Swinhoe) (Lepidoptera: Crambidae) in East and Southern Africa

Cotesia flavipes Cameron (Hymenoptera: Braconidae) was first imported into Kenya in 1991 from Pakistan for control of Chilo partellus (Swinhoe) (Lepidoptera: Crambidae). First releases were made at the Kenya coast in 1993 and a few recoveries of the parasitoid were made the following year. Additional foreign exploration for C. flavipes was conducted in central India in 1996 and 1998, which resulted in additional importation of the parasitoid for subsequent releases in eastern and southern Africa. Region-wide releases commenced with releases in Mozambique in 1996, Somalia in 1997 and Uganda in 1998. By 2005, many releases had been made in 10 countries in East and Southern Africa with establishment being reported in all of them except Eritrea but including Ethiopia where releases had never been made. This paper describes the progress made in the release and establishment of C. flavipes in East and Southern Africa and quantifies the rate of spread from the initial release sites in Kenya.     

African 2, a clonal complex of Mycobacterium bovis epidemiologically important in East Africa

We have identified a clonal complex of Mycobacterium bovis isolated at high frequency from cattle in Uganda, Burundi, Tanzania, and Ethiopia. We have named this related group of M. bovis strains the African 2 (Af2) clonal complex of M. bovis. Af2 strains are defined by a specific chromosomal deletion (RDAf2) and can be identified by the absence of spacers 3 to 7 in their spoligotype patterns. Deletion analysis of M. bovis isolates from Algeria, Mali, Chad, Nigeria, Cameroon, South Africa, and Mozambique did not identify any strains of the Af2 clonal complex, suggesting that this clonal complex of M. bovis is localized in East Africa. The specific spoligotype pattern of the Af2 clonal complex was rarely identified among isolates from outside Africa, and the few isolates that were found and tested were intact at the RDAf2 locus. We conclude that the Af2 clonal complex is localized to cattle in East Africa. We found that strains of the Af2 clonal complex of M. bovis have, in general, four or more copies of the insertion sequence IS6110, in contrast to the majority of M. bovis strains isolated from cattle, which are thought to carry only one or a few copies.     

Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers

Unravelling the genetic history of any livestock species is central to understanding the origin, development and expansion of agricultural societies and economies. Domestic village chickens are widespread in Africa. Their close association with, and reliance on, humans for long‐range dispersal makes the species an important biological marker in tracking cultural and trading contacts between human societies and civilizations across time. Archaezoological and linguistic evidence suggest a complex history of arrival and dispersion of the species on the continent, with mitochondrial DNA (mtDNA) D‐loop analysis revealing the presence of five distinct haplogroups in East African village chickens. It supports the importance of the region in understanding the history of the species and indirectly of human interactions. Here, through a detailed analysis of 30 autosomal microsatellite markers genotyped in 657 village chickens from four East African countries (Kenya, Uganda, Ethiopia and Sudan), we identify three distinct autosomal gene pools (I, II and III). Gene pool I is predominantly found in Ethiopia and Sudan, while II and III occur in both Kenya and Uganda. A gradient of admixture for gene pools II and III between the Kenyan coast and Uganda's hinterland (P = 0.001) is observed, while gene pool I is clearly separated from the other two. We propose that these three gene pools represent genetic signatures of separate events in the history of the continent that relate to the arrival and dispersal of village chickens and humans across the region. Our results provide new insights on the history of chicken husbandry which has been shaped by terrestrial and maritime contacts between ancient and modern civilizations in Asia and East Africa.     

<Emphasis Type="Italic">Chromolaena odorata</Emphasis> (Siam weed) in eastern Africa: distribution and socio-ecological impacts

Invasive alien plant species such as Chromolaena odorata have negative impacts on biodiversity, ecosystem services and human well-being. Ecological impacts of this shrub are relatively well understood, but its impacts on local livelihoods and perceptions are poorly documented. We mapped C. odorata distribution in eastern Africa (Ethiopia, Kenya, Rwanda, Tanzania and Uganda) and compared perceptions and quantified the impacts of this species across Tanzanian villages with varying degrees of invasion density. Data were collected through 240 household questionnaires. Results indicate that C. odorata is a relatively new invader that already has severe negative impacts and is threatening livelihoods and the environment. Impacts include reductions in native biodiversity and the amount of available forage for livestock, reduced crop and water yields, and impaired mobility. Continued spread will cause additional negative impacts on poor rural communities. Implementation of a biological control programme targeting C. odorata is needed as a cost effective management approach along with other control and restoration measures.     

Population genetics of the potentially invasive African fruit fly species, Ceratitis rosa and Ceratitis fasciventris (Diptera: Tephritidae)

A set of 10 microsatellite markers was used to survey the levels of genetic variability and to analyse the genetic aspects of the population dynamics of two potentially invasive pest fruit fly species, Ceratitis rosa and C. fasciventris, in Africa. The loci were derived from the closely related species, C. capitata. The degree of microsatellite polymorphism in C. rosa and C. fasciventris was extensive and comparable to that of C. capitata. In C. rosa, the evolution of microsatellite polymorphism in its distribution area reflects the colonization history of this species. The mainland populations are more polymorphic than the island populations. Low levels of differentiation were found within the Africa mainland area, while greater levels of differentiation affect the islands. Ceratitis fasciventris is a central-east African species. The microsatellite data over the Uganda/Kenya spatial scale suggest a recent expansion and possibly continuing gene flow within this area. The microsatellite variability data from C. rosa and C. fasciventris, together with those of C. capitata, support the hypothesis of an east African origin of the Ceratitis spp.     

The origin and evolutionary history of HIV-1 subtype C in Senegal

Background

The classification of HIV-1 strains in subtypes and Circulating Recombinant Forms (CRFs) has helped in tracking the course of the HIV pandemic. In Senegal, which is located at the tip of West Africa, CRF02_AG predominates in the general population and Female Sex Workers (FSWs). In contrast, 40% of Men having Sex with Men (MSM) in Senegal are infected with subtype C. In this study we analyzed the geographical origins and introduction dates of HIV-1 C in Senegal in order to better understand the evolutionary history of this subtype, which predominates today in the MSM population

Methodology/Principal Findings

We used a combination of phylogenetic analyses and a Bayesian coalescent-based approach, to study the phylogenetic relationships in pol of 56 subtype C isolates from Senegal with 3,025 subtype C strains that were sampled worldwide. Our analysis shows a significantly well supported cluster which contains all subtype C strains that circulate among MSM in Senegal. The MSM cluster and other strains from Senegal are widely dispersed among the different subclusters of African HIV-1 C strains, suggesting multiple introductions of subtype C in Senegal from many different southern and east African countries. More detailed analyses show that HIV-1 C strains from MSM are more closely related to those from southern Africa. The estimated date of the MRCA of subtype C in the MSM population in Senegal is estimated to be in the early 80''s.

Conclusions/Significance

Our evolutionary reconstructions suggest that multiple subtype C viruses with a common ancestor originating in the early 1970s entered Senegal. There was only one efficient spread in the MSM population, which most likely resulted from a single introduction, underlining the importance of high-risk behavior in spread of viruses.     

Establishment of Cotesia flavipes (Hymenoptera: Braconidae) in sugarcane fields of Ethiopia and origin of founding population

Cotesia flavipes (Cameron) (Hymenoptera: Braconidae) is used as a classical biological control agent against Chilo partellus (Swinhoe) (Lepidoptera: Crambidae), a serious exotic pest of cereal crops in eastern and southern Africa. This parasitoid has been introduced into several African countries for the control of C. partellus in maize, Zea mays L., and sorghum, Sorghum bicolor (L.), but it has never been released in Ethiopia. It is hypothesized that it spread into Ethiopia from populations released in Kenya and Somalia to become the predominant parasitoid of C. partellus in maize and sorghum fields of the country. In recent surveys conducted in Ethiopia, C. flavipes was recovered from C. partellus in sugarcane, Saccharum L. spp. hybrids, at a site >2,000 km from the nearest known release sites in Kenya and Somalia. These findings question published hypotheses that estimate the dispersal rate of C. flavipes to be 60 km per year in Africa, and they suggest that since its release in Africa this parasitoid has developed strains adapted to searching particular host plants infested by particular stem borers. The anomalies between our results and previous reports evoked the hypothesis that C. flavipes in Ethiopian sugarcane might be a different strain. To test this hypothesis, we compared partial COI gene sequences of C. flavipes collected from sugarcane in Ethiopia and those of specimens from other African countries to determine the origin of the Ethiopian population. In addition, COI sequences were obtained for C. flavipes from other continents. The C. flavipes population established in Ethiopian sugarcane is most closely related to the populations released against C. partellus in maize in other parts of Africa, which were derived from the original population imported from Pakistan. The dispersal rate of the parasitoid was estimated to be >200 km per year.     

Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa

Chicken were possibly domesticated in South and Southeast Asia. They occur ubiquitously in East Africa where they show extensive phenotypic diversity. They appeared in the region relatively late, with the first undisputed evidence of domestic chicken in Sudan, around ~ 700 BC. We reveal through a detailed analysis of mitochondrial DNA D-loop sequence diversity of 512 domestic village chickens, from four East African countries (Kenya, Ethiopia, Sudan, Uganda), the presence of at least five distinct mitochondrial DNA haplogroups. Phylogeographic analyses and inclusion of reference sequences from Asia allow us to address the origin, ways of introduction and dispersion of each haplogroup. The results indicate a likely Indian subcontinent origin for the commonest haplogroup (D) and a maritime introduction for the next commonest one (A) from Southeast and/or East Asia. Recent introgression of commercial haplotypes into the gene pool of village chickens might explain the rare presence of two haplogroups (B and C) while the origin of the last haplogroup (E) remains unclear being currently observed only outside the African continent in the inland Yunnan Province of China. Our findings not only support ancient historical maritime and terrestrial contacts between Asia and East Africa, but also indicate the presence of large maternal genetic diversity in the region which could potentially support genetic improvement programmes.     

Genetic Diversity and Population Structure of Trypanosoma brucei in Uganda: Implications for the Epidemiology of Sleeping Sickness and Nagana

Background

While Human African Trypanosomiasis (HAT) is in decline on the continent of Africa, the disease still remains a major health problem in Uganda. There are recurrent sporadic outbreaks in the traditionally endemic areas in south-east Uganda, and continued spread to new unaffected areas in central Uganda. We evaluated the evolutionary dynamics underpinning the origin of new foci and the impact of host species on parasite genetic diversity in Uganda. We genotyped 269 Trypanosoma brucei isolates collected from different regions in Uganda and southwestern Kenya at 17 microsatellite loci, and checked for the presence of the SRA gene that confers human infectivity to T. b. rhodesiense.

Results

Both Bayesian clustering methods and Discriminant Analysis of Principal Components partition Trypanosoma brucei isolates obtained from Uganda and southwestern Kenya into three distinct genetic clusters. Clusters 1 and 3 include isolates from central and southern Uganda, while cluster 2 contains mostly isolates from southwestern Kenya. These three clusters are not sorted by subspecies designation (T. b. brucei vs T. b. rhodesiense), host or date of collection. The analyses also show evidence of genetic admixture among the three genetic clusters and long-range dispersal, suggesting recent and possibly on-going gene flow between them.

Conclusions

Our results show that the expansion of the disease to the new foci in central Uganda occurred from the northward spread of T. b. rhodesiense (Tbr). They also confirm the emergence of the human infective strains (Tbr) from non-infective T. b. brucei (Tbb) strains of different genetic backgrounds, and the importance of cattle as Tbr reservoir, as confounders that shape the epidemiology of sleeping sickness in the region.     

Origin and dynamics of HIV-1 subtype C infection in India

Objective

To investigate the geographical origin and evolution dynamics of HIV-1 subtype C infection in India.

Design

Ninety HIV-1 subtype C env gp120 subtype C sequences from India were compared with 312 env gp120 reference subtype C sequences from 27 different countries obtained from Los Alamos HIV database. All the HIV-1 subtype C env gp120 sequences from India were used for the geographical origin analysis and 61 subtype C env gp120 sequences with known sampling year (from 1991 to 2008) were employed to determine the origin of HIV infection in India.

Methods

Phylogenetic analysis of HIV-1 env sequences was used to investigate the geographical origin and tMRCA of Indian HIV-1 subtype C. Evolutionary parameters including origin date and demographic growth patterns of Indian subtype C were estimated using a Bayesian coalescent-based approach under relaxed molecular clock models.

Findings

The majority of the analyzed Indian and South African HIV-1 subtype C sequences formed a single monophyletic cluster. The most recent common ancestor date was calculated to be 1975.56 (95% HPD, 1968.78–1981.52). Reconstruction of the effective population size revealed three phases of epidemic growth: an initial slow growth, followed by exponential growth, and then a plateau phase approaching present time. Stabilization of the epidemic growth phase correlated with the foundation of National AIDS Control Organization in India.

Interpretation

Indian subtype C originated from a single South African lineage in the middle of 1970s. The current study emphasizes not only the utility of HIV-1 sequence data for epidemiological studies but more notably highlights the effectiveness of community or government intervention strategies in controlling the trend of the epidemic.