Available online at www.sciencedirect.com Virus Research 130 (2007) 310–314 Short communication Detection of intersubtype recombinants with respect to env and nef genes of HIV-1 among female sex workers in Calcutta, India Payel Bhanja a , Satarupa Sengupta a , Debjani Banerjee b , Kamalesh Sarkar a , Smarajit Jana b , Sekhar Chakrabarti a,∗ a HIV/AIDS Laboratory, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Calcutta, India b STD/HIV Intervention Program, Calcutta, India Received 17 April 2007; received in revised form 14 June 2007; accepted 17 June 2007 Available online 7 August 2007 Abstract HIV-1 detected among female sex workers in Calcutta, India was characterized in respect to env and nef genes. A total of 39 HIV-1 seropositive samples were used in the study. Phylogenetic analysis of the nucleotide sequences of respective regions showed that 22 out of 39 samples (56.4%) were infected with subtype C with respect to both env and nef genes; however, 17 samples (43.6%) showed distinct subtype discordance. Simplot analysis of these samples showed the presence of intersubtype recombination between subtypes C and B. Both env C/nef B and env B/nef C recombinants were found to be present; 16 samples were found to be env C/nef B and 1 sample was detected as env B/nef C. This result indicates the emergence of intersubtype recombinants of HIV-1 for the first time in this eastern part of India. © 2007 Elsevier B.V. All rights reserved. Keywords: Phylogenetic tree; Sequence analysis; Intersubtype recombinants Since the first case in 1986, HIV infection is spreading rapidly in India mainly through heterosexual transmission. The nature of HIV-1 circulating in different parts of India has been reported so far in the context of specific regions within envelope and gag gene (Sahni et al., 2002; Mandal et al., 2002; Shankarappa et al., 2001; Jameel et al., 1995; Sengupta et al., 2005a, 2005b). These studies revealed HIV-1 subtype C to be the most prevalent all over India while ThaiB being the second major subtype in north- eastern regions of India. The recombinants reported so far from India were—the A/C recombinant among early seroconverters of Pune (Lole et al., 1999), C/ThaiB intersubtype recombinant among injecting drug users (IDUs) from Manipur (Bhanja et al., 2005) and unique B/C recombinant from southern state of Karnataka. (Siddappa et al., 2005). Besides the env (C2–V3–C3 fragment) and gag (p24–p7 fragment), nef gene of HIV-1 has always been a useful marker for genetic subtype determina- tion and molecular epidemiological studies with reports from Portugal, Africa and India (Parreira et al., 2005; Chakraborty et al., 2006; Jere et al., 2004). In the present communication, ∗ Corresponding author. Tel.: +91 33 2370 1176; fax: +91 33 2370 5066. E-mail address: drsekharchakrabarti@yahoo.co.in (S. Chakrabarti). we report the presence of intersubtype recombinants of HIV-1 detected from female sex workers (FSWs) in Calcutta based on env (C2–V3) and nef genomic regions. The study population was 20–30 years old female sex workers (FSWs) in Calcutta during the year 2005–2006. Blood sam- ples were collected in EDTA vacutainers (Becton Dickinson) after obtaining the informed consent following pre- and post- test counseling as approved by institutional ethical committee. Out of 250 blood samples screened for the presence of anti- bodies for HIV-1, 42 samples (16.8%) were positive and used for further study. Majority (28 among 42) of them were clin- ically asymptomatic while others showed some features like fever, diarrhoea, tuberculosis, skin rash, genital ulcer, etc. HIV-1 seropositive individuals were na¨ ıve in respect to antiretroviral therapy. Peripheral blood mononuclear cells (PBMCs) were sepa- rated from whole blood (Boyum, 1968) and the DNA was extracted by using the QIAamp DNA Blood Mini Kit 250 (QIAGEN, Germany). Thirty-nine out of 42 samples (93%) could be amplified, for both env C2–V3 and nef genomic regions. C2–V3 region of env gene (550 bp) was amplified from PBMC DNA by nested polymerase chain reaction (PCR), using the primer pairs ED3 and ED14 in round I and ED31 0168-1702/$ – see front matter © 2007 Elsevier B.V. All rights reserved. doi:10.1016/j.virusres.2007.06.013