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Molecular dating of HIV-1 subtype C from Bangladesh.

Bontell I, Sarker MS, Rahman M, Afrad MH, Sönnerborg A, Azim T - PLoS ONE (2013)

Bottom Line: The phylogenetic analysis included 118 Bangladeshi gag sequences and 128 sequences from other countries and was performed using the BEAST package.Our analysis revealed that the vast majority of Bangladeshi sequences (97/118, 82%) fall into a large regional cluster of samples from Bangladesh, India, China and Myanmar, which dates back to the early 1960's.In addition, there have been multiple (at least ten) introductions of subtype C to Bangladesh from outside this region, but no extensive spread could be detected for any of these.

View Article: PubMed Central - PubMed

Affiliation: Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Solna, Sweden.

ABSTRACT
Bangladesh has an overall low HIV prevalence of <0.1% in the general population and <1% among key affected populations, but it is one of few Asian countries that has yet to reverse the epidemic. In order to do this, it is important to understand the transmission dynamics in this country. The aim of this study was to investigate the phylogenetic relationships of HIV-1 subtype C strains from Bangladesh and related strains from other countries, and thereby clarify when and from where subtype C was introduced in the country and how it subsequently spread within Bangladesh. The phylogenetic analysis included 118 Bangladeshi gag sequences and 128 sequences from other countries and was performed using the BEAST package. Our analysis revealed that the vast majority of Bangladeshi sequences (97/118, 82%) fall into a large regional cluster of samples from Bangladesh, India, China and Myanmar, which dates back to the early 1960's. Following its establishment in the region, this strain has entered Bangladesh multiple times from around 1975 and onwards, but extensive in-country transmission could only be detected among drug users and not through sexual transmission. In addition, there have been multiple (at least ten) introductions of subtype C to Bangladesh from outside this region, but no extensive spread could be detected for any of these. Since many HIV-infections remain undetected while asymptomatic, the true extent of the transmission of each strain remains unknown, especially among hard to reach groups such as clients of sex workers and returning migrants with families.

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Related in: MedlinePlus

Phylogenetic tree of 246 gag-sequences, including 118 Bangladeshi HIV-1 C strains in green.The HIV1-C strains found in Bangladesh do not fall into a country specific clade, instead our results point to repeated introductions with substantial in-country transmission only among PWIDs. Four clades with ≥3 BD strains had a posterior probability of around 0.7 or higher, and are shown in the figure. Clade 1 is a monophyletic clade of 47 BD strains, of which 43 originate from PWIDs in Dhaka. The tMRCA of this clade is around 1975. It is a subset of the large regional Clade 2, which is dominated by strains from Bangladesh, Myanmar, India and China. Over 80% of all BD strains can be found within this clade, which appears to have been introduced to this region around 1962. The intermixing of sequences collected from different countries indicates frequent cross-border transmission in this region. In addition to the 47 strains in Clade 1, the BD strains in Clade 2 includes sequences from returning migrants from Nepal, India and the Middle East as well as some weakly supported clades of strains from sex workers and VCT/STI patients. Clade 3 consists of seven PWID strains from Dhaka, and the short branches in this clade reveal rapid transmission (and detection) within this group. Clade 4 contains five strains from VCT visitors in Dhaka and Chittagong, at least 3 of whom had a history of migrant work in the Middle East. The long branches show that they are not very close genetically and it is possible that they represent separate introductions of related strains. Most of the BD strains found outside these clades appear to represent separate introductions.
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pone-0079193-g001: Phylogenetic tree of 246 gag-sequences, including 118 Bangladeshi HIV-1 C strains in green.The HIV1-C strains found in Bangladesh do not fall into a country specific clade, instead our results point to repeated introductions with substantial in-country transmission only among PWIDs. Four clades with ≥3 BD strains had a posterior probability of around 0.7 or higher, and are shown in the figure. Clade 1 is a monophyletic clade of 47 BD strains, of which 43 originate from PWIDs in Dhaka. The tMRCA of this clade is around 1975. It is a subset of the large regional Clade 2, which is dominated by strains from Bangladesh, Myanmar, India and China. Over 80% of all BD strains can be found within this clade, which appears to have been introduced to this region around 1962. The intermixing of sequences collected from different countries indicates frequent cross-border transmission in this region. In addition to the 47 strains in Clade 1, the BD strains in Clade 2 includes sequences from returning migrants from Nepal, India and the Middle East as well as some weakly supported clades of strains from sex workers and VCT/STI patients. Clade 3 consists of seven PWID strains from Dhaka, and the short branches in this clade reveal rapid transmission (and detection) within this group. Clade 4 contains five strains from VCT visitors in Dhaka and Chittagong, at least 3 of whom had a history of migrant work in the Middle East. The long branches show that they are not very close genetically and it is possible that they represent separate introductions of related strains. Most of the BD strains found outside these clades appear to represent separate introductions.

Mentions: Our analysis of 118 HIV subtype C strains from Bangladesh reveal that the vast majority of Bangladeshi strains (97/118, 82%) fall into a large cluster of HIV strains sampled mainly from Bangladesh (BD), India (IN), China (CN) and Myanmar (MM), (Figure 1). There has been repeated transmission between Bangladesh and these three nearby countries, and many BD strains are intermixed with strains from IN, CN and MM. The combined calculated tMRCA of this clade for the two BEAST runs was the year 1962 (95% CI: 1951-1969). However, the first introductions into Bangladesh occurred around 1975, which is 14 years before the first known HIV-case in the country and over two decades prior to the first identification of subtype C in Bangladesh in 1997 [14]. The ancestral strain for this south Asian cluster appears to originate from southern Africa, but the exact country could not be determined. Six of the BD strains located outside the main clade were also genetically related to strains from southern Africa (especially Zambia), while twelve BD strains were more closely related to strains from Israel and Ethiopia. Furthermore, three strains from Bangladesh could be classified as sub-subtype C’, which is common in Ethiopia. These three strains were not closely related and originated from seemingly unrelated male VCT visitors who were all returning migrant workers (one from Malaysia and two from Saudi Arabia) and most likely represent separate introductions.


Molecular dating of HIV-1 subtype C from Bangladesh.

Bontell I, Sarker MS, Rahman M, Afrad MH, Sönnerborg A, Azim T - PLoS ONE (2013)

Phylogenetic tree of 246 gag-sequences, including 118 Bangladeshi HIV-1 C strains in green.The HIV1-C strains found in Bangladesh do not fall into a country specific clade, instead our results point to repeated introductions with substantial in-country transmission only among PWIDs. Four clades with ≥3 BD strains had a posterior probability of around 0.7 or higher, and are shown in the figure. Clade 1 is a monophyletic clade of 47 BD strains, of which 43 originate from PWIDs in Dhaka. The tMRCA of this clade is around 1975. It is a subset of the large regional Clade 2, which is dominated by strains from Bangladesh, Myanmar, India and China. Over 80% of all BD strains can be found within this clade, which appears to have been introduced to this region around 1962. The intermixing of sequences collected from different countries indicates frequent cross-border transmission in this region. In addition to the 47 strains in Clade 1, the BD strains in Clade 2 includes sequences from returning migrants from Nepal, India and the Middle East as well as some weakly supported clades of strains from sex workers and VCT/STI patients. Clade 3 consists of seven PWID strains from Dhaka, and the short branches in this clade reveal rapid transmission (and detection) within this group. Clade 4 contains five strains from VCT visitors in Dhaka and Chittagong, at least 3 of whom had a history of migrant work in the Middle East. The long branches show that they are not very close genetically and it is possible that they represent separate introductions of related strains. Most of the BD strains found outside these clades appear to represent separate introductions.
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815104&req=5

pone-0079193-g001: Phylogenetic tree of 246 gag-sequences, including 118 Bangladeshi HIV-1 C strains in green.The HIV1-C strains found in Bangladesh do not fall into a country specific clade, instead our results point to repeated introductions with substantial in-country transmission only among PWIDs. Four clades with ≥3 BD strains had a posterior probability of around 0.7 or higher, and are shown in the figure. Clade 1 is a monophyletic clade of 47 BD strains, of which 43 originate from PWIDs in Dhaka. The tMRCA of this clade is around 1975. It is a subset of the large regional Clade 2, which is dominated by strains from Bangladesh, Myanmar, India and China. Over 80% of all BD strains can be found within this clade, which appears to have been introduced to this region around 1962. The intermixing of sequences collected from different countries indicates frequent cross-border transmission in this region. In addition to the 47 strains in Clade 1, the BD strains in Clade 2 includes sequences from returning migrants from Nepal, India and the Middle East as well as some weakly supported clades of strains from sex workers and VCT/STI patients. Clade 3 consists of seven PWID strains from Dhaka, and the short branches in this clade reveal rapid transmission (and detection) within this group. Clade 4 contains five strains from VCT visitors in Dhaka and Chittagong, at least 3 of whom had a history of migrant work in the Middle East. The long branches show that they are not very close genetically and it is possible that they represent separate introductions of related strains. Most of the BD strains found outside these clades appear to represent separate introductions.
Mentions: Our analysis of 118 HIV subtype C strains from Bangladesh reveal that the vast majority of Bangladeshi strains (97/118, 82%) fall into a large cluster of HIV strains sampled mainly from Bangladesh (BD), India (IN), China (CN) and Myanmar (MM), (Figure 1). There has been repeated transmission between Bangladesh and these three nearby countries, and many BD strains are intermixed with strains from IN, CN and MM. The combined calculated tMRCA of this clade for the two BEAST runs was the year 1962 (95% CI: 1951-1969). However, the first introductions into Bangladesh occurred around 1975, which is 14 years before the first known HIV-case in the country and over two decades prior to the first identification of subtype C in Bangladesh in 1997 [14]. The ancestral strain for this south Asian cluster appears to originate from southern Africa, but the exact country could not be determined. Six of the BD strains located outside the main clade were also genetically related to strains from southern Africa (especially Zambia), while twelve BD strains were more closely related to strains from Israel and Ethiopia. Furthermore, three strains from Bangladesh could be classified as sub-subtype C’, which is common in Ethiopia. These three strains were not closely related and originated from seemingly unrelated male VCT visitors who were all returning migrant workers (one from Malaysia and two from Saudi Arabia) and most likely represent separate introductions.

Bottom Line: The phylogenetic analysis included 118 Bangladeshi gag sequences and 128 sequences from other countries and was performed using the BEAST package.Our analysis revealed that the vast majority of Bangladeshi sequences (97/118, 82%) fall into a large regional cluster of samples from Bangladesh, India, China and Myanmar, which dates back to the early 1960's.In addition, there have been multiple (at least ten) introductions of subtype C to Bangladesh from outside this region, but no extensive spread could be detected for any of these.

View Article: PubMed Central - PubMed

Affiliation: Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Solna, Sweden.

ABSTRACT
Bangladesh has an overall low HIV prevalence of <0.1% in the general population and <1% among key affected populations, but it is one of few Asian countries that has yet to reverse the epidemic. In order to do this, it is important to understand the transmission dynamics in this country. The aim of this study was to investigate the phylogenetic relationships of HIV-1 subtype C strains from Bangladesh and related strains from other countries, and thereby clarify when and from where subtype C was introduced in the country and how it subsequently spread within Bangladesh. The phylogenetic analysis included 118 Bangladeshi gag sequences and 128 sequences from other countries and was performed using the BEAST package. Our analysis revealed that the vast majority of Bangladeshi sequences (97/118, 82%) fall into a large regional cluster of samples from Bangladesh, India, China and Myanmar, which dates back to the early 1960's. Following its establishment in the region, this strain has entered Bangladesh multiple times from around 1975 and onwards, but extensive in-country transmission could only be detected among drug users and not through sexual transmission. In addition, there have been multiple (at least ten) introductions of subtype C to Bangladesh from outside this region, but no extensive spread could be detected for any of these. Since many HIV-infections remain undetected while asymptomatic, the true extent of the transmission of each strain remains unknown, especially among hard to reach groups such as clients of sex workers and returning migrants with families.

Show MeSH
Related in: MedlinePlus