Low prevalence of CCR5-Δ32, CCR2-64I and SDF1-3'A alleles in the Baiga and Gond tribes of Central India

Abstract

Human immunodeficiency virus-1 (HIV-1) which causes acquired immune deficiency syndrome (AIDS), by infecting CD4+ immune cells and hence weakening the host defense mechanism till death, is one of the major factor responsible for human demises worldwide. Both innate (monocytes and macrophages) and adaptive (T cells) immune cells expresses chemokines receptors (2 and 5) and stromal cell derived factor-1 (SDF-1) which play crucial role in HIV-1 virus entry and progression. Allele variants of genes CCR5 (CCR5-Δ32), CCR2 (CCR2-64I) and SDF1 (SDFA-3′A; the ligand of CXCR4) are known to slow down the HIV-1 progression in infected individual. In the present study, the frequency of CCR5-Δ32, CCR2-64I and SDF1-3′A alleles in primitive tribe (Baiga) and a non-primitive tribe (Gond) of central India were investigated. A total 200 seronegative samples for HIV from healthy individuals of tribes were analyzed and observed allele frequencies of CCR5-Δ32, CCR2-64I and SDF1-3′A were (0, 0.035, 0.080) and (0, 0.110, 0.100) in Baiga and Gond respectively. Minor allele frequency of these alleles of Gond and Baiga tribes were compared with different populations of the world for relative hazard (RH), which indicate the risk of progression after infection of HIV1. The RH values were calculated based on genotypic frequency, showed the high RH value (RH1-AIDS1993-0.98, RH2-AIDS1987-0.98 and death/RH3-0.97) in Baiga tribe, indicates the low level of resistance against HIV-1 progression after infection.

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Bharti et al. SpringerPlus (2015) 4:451
DOI 10.1186/s40064-015-1238-6
RESEARCH
Low prevalence ofCCR5-Δ32, CCR2-64I
andSDF1-3′A alleles inthe Baiga andGond
tribes ofCentral India
Deepak Bharti1, Ashish Kumar1, Ranjeet Singh Mahla1, Sushil Kumar1, Harshad Ingle1, Tushar Yadav2,
Anamika Mishra3, Ashwin Ashok Raut3 and Himanshu Kumar1,4*
Abstract
Human immunodeficiency virus-1 (HIV-1) which causes acquired immune deficiency syndrome (AIDS), by infecting
CD4+ immune cells and hence weakening the host defense mechanism till death, is one of the major factor respon-
sible for human demises worldwide. Both innate (monocytes and macrophages) and adaptive (T cells) immune cells
expresses chemokines receptors (2 and 5) and stromal cell derived factor-1 (SDF-1) which play crucial role in HIV-1
virus entry and progression. Allele variants of genes CCR5 (CCR5-Δ32), CCR2 (CCR2-64I) and SDF1 (SDFA-3′A; the ligand
of CXCR4) are known to slow down the HIV-1 progression in infected individual. In the present study, the frequency
of CCR5-Δ32, CCR2-64I and SDF1-3′A alleles in primitive tribe (Baiga) and a non-primitive tribe (Gond) of central India
were investigated. A total 200 seronegative samples for HIV from healthy individuals of tribes were analyzed and
observed allele frequencies of CCR5-Δ32, CCR2-64I and SDF1-3′A were (0, 0.035, 0.080) and (0, 0.110, 0.100) in Baiga
and Gond respectively. Minor allele frequency of these alleles of Gond and Baiga tribes were compared with differ-
ent populations of the world for relative hazard (RH), which indicate the risk of progression after infection of HIV1.
The RH values were calculated based on genotypic frequency, showed the high RH value (RH1-AIDS1993-0.98, RH2-
AIDS1987-0.98 and death/RH3-0.97) in Baiga tribe, indicates the low level of resistance against HIV-1 progression after
infection.
Keywords: Primitive tribes, Non-primitive tribes, Chemokine receptors, HIV-1 resistant polymorphisms, Relative
hazard
© 2015 Bharti et al. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License
(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium,
provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license,
and indicate if changes were made.
Background
It has been nearly three to four decade since the report
of the first acquired immune deficiency syndrome (AIDS)
case which attracted the world’s attention. e AIDS is
caused by the human immunodeficiency virus (HIV)
which targets various types of cells of host immunity
such as dendritic cells, macrophages and T cell subtypes
etc. and slowly weakens the host immune system leading
to severe immunodeficiency. According to recent report,
about 70 million people have been infected by the HIV
which caused 35 million deaths worldwide (Horvath etal.
2012; Ruelas and Greene 2013). HIV-1 and HIV-2 are the
two types of HIV (McCutchan 2006), of which, the for-
mer is found in majority of the AIDS cases and is consid-
ered to be highly pathogenic. Upon infection, progress of
HIV-1 has been shown to be influenced by C–C family
chemokine receptors (CCR) like CCR5, CCR2 and SDF1
(a ligand of CXCR4). ese molecules have been shown
to play an important role in the entry of HIV-1 into
various cell types such as macrophages, monocytes and
T-cells (CD4+) (Herbein and Varin 2010; Doitsh et al.
2014). A 32bp deletion in CCR5 coding sequence is well
known as CCR5-Δ32 polymorphism, was identified in
case of near complete resistance from HIV1 in homozy-
gous state and slower progression of HIV1 in heterozy-
gote state (Dean etal. 1996; Liu etal. 1996; Samson etal.
Open Access
*Correspondence: hkumar@iiserb.ac.in
1 Laboratory of Immunology, Department of Biological Sciences, Indian
Institute of Science Education and Research (IISER), Indore-Bypass Road,
Bhauri, Bhopal 460 066, India
Full list of author information is available at the end of the article

Page 2 of 5
Bharti et al. SpringerPlus (2015) 4:451
1996). Many populations studies conducted worldwide
have been shown that genetic variants CCR5-Δ32 (32-
bp deletion), CCR2-64I (V→I) and SDF1-3′A (G-801A)
slower the rate of HIV-1 progression thus leading to
delayed onset and reduced severity of AIDS. e risk of
AIDS onset for populations is calculated through deter-
mination of relative hazard (RH) based on the occurrence
of mutation in these three gene loci (Dean et al. 1996;
Smith etal. 1997; Winkler etal. 1998).
India has the largest portion of the world’s primi-
tive and non-primitive tribal populations, among which
most of the tribal populations distributed mainly in east-
ern and central Indian states followed by Rajasthan and
Gujarat states of India. According to census of 2011, the
total populations of India estimated are 1.29 billion in
which tribal populations contributed 0.1 billion. Tribal
populations are distributed all over India except Punjab
and Haryana, states of India. A significant part (14.7%)
of Indian tribal populations is distributed in the central
Indian state Madhya Pradesh. A tribe is a group of people
who are linguistically, socially and geographically isolated
from modern human populations and for their livelihood,
they are dependent on their land while primitive tribes
are generally considered as those people who are isolated
from tribes in past and are more backward with very low
income, lived in difficult areas in small and scattered hab-
itat therefore their social interaction with main stream
is almost negligible. Baiga tribe is more geographically
and socially isolated than Gond tribe from other caste
populations of India. Consequently, there is less chance
of Baiga tribe to share their gene pool with well devel-
oped human caste populations. Due to the same rea-
son, on the basis of primitive and non primitive, we have
selected Baiga and Gond tribes for present study. Baiga is
a primitive tribe (Population size: approximately 0.5 mil-
lion) mostly found in Mandla and Balaghat districts of a
central Indian state, Madhya Pradesh. ey practice con-
sanguineous marriage and remain poorly informed about
various infectious diseases including HIV/AIDS (Reddy
and Modell 1997; Saha etal. 2013). Women of the tribe
are known to sporting tattoos on their body using nee-
dles. e Gond is the tribal community mostly found in
the forests of the central India. According to census 2011
Gond is a second largest tribe in Madhya Pradesh, a cen-
tral Indian state with a population of 4.36 million. ey
are widely spread in the Chhindwara district of Madhya
Pradesh, Bastar district of neighbouring Indian states of
Chhattisgarh and also in parts of Maharashtra, Andhra
Pradesh and Orissa states. e name by which the Gond
calls themselves is Koi or Koitur which means unclear.
ey are one of the largest tribal groups in the world.
To date, no genetic studies have been conducted on
chemokine marker polymorphism which related with
HIV infection risk in primitive Baiga tribe and non-prim-
itive Gond tribe.
Results
CCR5-Δ32 mutant is well known to provide resistance
from HIV-1 by preventing cell entry through expression
of truncated protein. erefore, individuals harbouring
homozygous mutant allele (Δ32/Δ32) are highly resistant
to HIV-1 infection whereas, heterozygous (Δ32/wt) have
partial protection (Su etal. 2000). In this study, deletion
mutant genotype (Δ32/Δ32) as well as (Δ32/wt) were
not observed in both the tribal populations; (Table1).
CCR2-64I and SDF1-3′A mutant alleles are also shown
to be associated with suppression of HIV-1 progression
to AIDS; however, the suppressive effect is lower in com-
parison to CCR5-Δ32. e suppressive effect exerted by
the SDF1-3′A mutation is recessive i.e., observed only in
homozygote mutant (3′A/3′A) (Su etal. 1999). e fre-
quency of SDF1 genotype (3′A/3′A) was found to be very
less (1%) in Gond and was not found in Baiga tribe. e
CCR2 genotype (64I/64I) was not found in Baiga tribe;
however, it is present in Gond tribe with a very low fre-
quency (1 %) (Table 1). Additionally, the frequency of
heterozygous (64V/64I) was observed less in Baiga (7%)
compared to the Gond tribe (20 %) (Table 1). Further
Table 1 Distribution ofgenotype andallele frequency ofCCR5, CCR2 andSDF-1 genes inprimitive tribe (Baiga) andnon-
primitive tribe (Gond) ofCentral India
Major alleles for CCR5, CCR2 and SDF1 are wild type (wt), “G” and “G” respectively. Minor alleles for CCR5, CCR2 and SDF1 are “Δ32” (CCR5-Δ32), “A” (V→I) and “A” (SDF1-
3′A) respectively
MAF and H.W. represents minor allele frequency and Hardy–Weinberg respectively
Sr. No. Tribe N CCR5 CCR2 SDF1
Genotype MAF χ2
(H.W.) Genotype MAF χ2
(H.W.) Genotype MAF χ2
(H.W.)
CCR5 Δ32 GG AG AA GG AG AA
1. Baiga 100 100 0 0 – 93 7 0 0.035 0.720 84 16 0 0.080 0.390
2. Gond 100 100 0 0 – 79 20 1 0.110 0.830 82 17 1 0.100 0.910

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Bharti et al. SpringerPlus (2015) 4:451
analysis of genotype data did not show significant devia-
tion from the Hardy–Weinberg expected frequency, indi-
cating that the alleles are in genetic equilibrium (Table1).
Furthermore, we estimated the RH indices by using the
three locus genotype data. RH values were calculated
for all the three definitions, AIDS-1993, AIDS-1987 and
Death by using formula RH=∑(Wi*Pi); where Wi and Pi
denotes the genotype specific RH and frequencies respec-
tively. RH value vary from population to population, how-
ever geographically or ethically related populations tend
to have similar RH values as they have comparable minor
allele frequency (MAF) for three genes. Out of 27 possi-
ble three locus genotypes, we found only 4 in Baiga and
6 in Gond tribe (Additional file 1: TableS1). Detection
of only 4 and 6 different genotypes is due to the fact that
the CCR5-wt allele is fixed in these populations and also
the homozygous genotypes of CCR2 genotype (64I/64I)
and SDF1 (3′A/3′A) are not found in the Baiga popula-
tion. Baiga tribe showed a high RH value [AIDS1993-0.98
(RH1), AIDS1987-0.98 (RH2) and Death-0.97 (RH3)]
(Table2).
Discussion
HIV-1 is highly pathogenic and relatively modern virus
compared to the several other pathogens. Progression
of HIV-1 after infection in slow in those individuals who
carries the mutant form of genes such as CCR5, CCR2
and SDF1. ese mutational changes have originated
outside India, however, due to social interaction among
various world populations, the frequency of mutant
alleles were raised in several populations. Earlier study on
ethnic populations of India have shown that CCR5-Δ32
allele is completely absent in tribes, however it can be
found very low in Caste populations (Majumder and Dey
2001). It can be predicted that endogamy practices, geo-
graphical isolation might be the factors for the low fre-
quencies of CCR5-Δ32, CCR2-64I and SDF1-3′A. Due to
the absence of social interactions with modern popula-
tions, primitive tribes have not acquired the alleles that
reduce the progression of HIV-1 infection making them
highly susceptible. In this study all the individuals were
expressing homozygous wild type allele (wt/wt) for the
CCR5 gene (Table1), indicating that the allele CCR5-Δ32
is completely absent in both the tribal groups and very
low allele frequency of mutant alleles of CCR2 and SDF1
were recorded in Gond and Baiga tribes. All together
our study indicates that the frequency of the alleles,
CCR5-Δ32, CCR2-64I and SDF1-3′A are significantly low
in both the tribal populations (Table1). e comparison
of RH values of present studied tribe with earlier studied
populations of India and the different populations (Su
etal. 2000; Xiao etal. 2000; Ramana etal. 2001 and Salem
etal. 2009) of the world showing the highest RH value in
primitive tribe “Baiga” (Fig.1; Additional file1: TableS2).
Conclusion
e frequency of CCR5-Δ32, CCR2-64I and SDF1-3′A
are recorded low in Gond and very low in the Baiga tribe.
It can be predicted that endogamy practices, geographi-
cal isolation might be the factors for low frequencies of
CCR5-Δ32, CCR2-64I and SDF1-3′A. Due to absence of
social interaction with modern populations, primitive
tribes have not acquired the alleles that reduce the pro-
gression of HIV-1 infection making them highly suscep-
tible to the same. e high RH of AIDS onset indicates
very low resistance in Baiga against HIV-1 progression
after infection. erefore, present study showed that
there are not enough protective shields against HIV-1 for
central Indian tribes.
Methods
e 200 samples were obtained from unrelated healthy
individuals of Baiga and Gond tribes of central India. All
the samples were seronegative for HIV. is study was
carried out according to the ethical guidelines of Institu-
tional Ethical Committee (IEC), IISER Bhopal and with
the written consent of all the participants. Blood sam-
ples from the individuals were spotted on Whatman FTA
classic Cards (GE healthcare) and processed for PCR as
per manufacturer instructions. e region containing
the CCR5-Δ32, CCR2-64I and SDF1-3′A were amplified
using Phusion Blood Direct PCR Kit (ermo scientific)
as per manufacturer protocol with corresponding Prim-
ers (CCR5-Fw: 5′-GCTGTCGTCCATGCTGTGTTT-3′,
Rv:5′-CAACCTGTTAGAGCTACTGCAATT-3′);
(CCR2-Fw:5′ATCAGAAATACCAACGAGAGCGG-3′,
Rv:5′-ACACCGAAGCAGGGTTTTCAGG-3′) and (SDF1-
Fw:5′-CAGTCAACCTGGGCAAAGCC-3′, Rv:5′-AGCT
TTGGTCCTGAGAGTCC-3′) (Struyfa etal. 2000; Jun-
hua etal. 2000; Bhatnagar etal. 2009). e sequencing of
PCR products were performed using 3730 DNA Analyzer
(Applied Bio systems) sequencer using the Fw primer
used in the PCR amplification. e SNPs were then ana-
lysed using Sequencing Analysis software v5.4. Allele
frequencies were calculated using the formula, Allele
Frequency={(2×Number of individuals having geno-
type homozygous for that particular allele) +(Number
Table 2 The RH values inBaiga andGond tribes ofCentral
India
The RH values were calculated based on three AIDS denitions, AIDS-1993 (RH1),
AIDS-1987 (RH2), and Death (RH3)
Population N RH1 RH2 RH3
Baiga 100 0.98 0.98 0.97
Gond 100 0.92 0.92 0.90

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Bharti et al. SpringerPlus (2015) 4:451
Fig. 1 Comparison of relative hazard (RH) in Baiga tribe with Gond tribe and rest of world populations (Ramana et al. 2001; Salem et al. 2009; Su
et al. 2000; Xiao et al. 2000). RH1, RH2 and RH3 refer to AIDS-1993, AIDS-1987 and Death respectively

Page 5 of 5
Bharti et al. SpringerPlus (2015) 4:451
of individuals having heterozygous genotype)}/(2×Total
Number of individuals). RH values is estimated on based
on genotype frequency and calculated for all the three
definitions, AIDS-1993, AIDS-1987 and Death by using
formula RH =∑(Wi*Pi); where Wi and Pi denote the
genotype specific RH and frequencies respectively. 
Authors’ contributions
HK and DB conceived the study. DB, RSM, SK, HI, TY, AM, AAR, collected
tribal blood samples, extracted DNA and performed sequencing. DB and AK
analysed the data. HK and AK wrote the manuscript. HK supervised the overall
study. All authors read and approved the final manuscript.
Author details
1 Laboratory of Immunology, Department of Biological Sciences, Indian Insti-
tute of Science Education and Research (IISER), Indore-Bypass Road, Bhauri,
Bhopal 460066, India. 2 Chemical Engineering Department, Sardar Vallabhb-
hai National Institute of Technology, Surat 395007, India. 3 Pathogenomics
Lab, ICAR-National Institute of High Security Animal Diseases, Anand Nagar,
Bhopal 462022, India. 4 Laboratory of Host Defense, WPI Immunology Frontier
Research Center, Osaka University, Osaka, Japan.
Acknowledgements
This work is supported by research grants number SR/S2/RJN-55/2009 and
BT/PR6009/GBD/27/382/2012 from Department of Science and technology
(DST) and Department of Biotechnology (DBT), Government of India (H.K.);
MPCST3657/CST/BTA (D.B.) and Intramural Research Grant of IISER, Bhopal,
India, Authors would like to thank the sequencing facility of Department of
Biological Sciences, IISER Bhopal. D.B. would like to thank the PDF support
from IISER Bhopal.
Compliance with ethical guidelines
Competing interests
The authors declare that they have no competing interests.
Received: 10 April 2015 Accepted: 12 August 2015
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