Identification of subtype C human immunodeficiency virus type 1 by subtype-specific PCR and its use in the characterization of viruses circulating in the southern parts of India

Nagadenahalli B. Siddappa, Prashanta K. Dash, Anita Mahadevan, Narayana Jayasuryan, Fen Hu, Bethany Dice, Randy Keefe, Kadappa S. Satish, Bhuthiah Satish, Kuttan Sreekanthan, Ramdas Chatterjee, Kandala Venu, Parthasarathy Satishchandra, Vasanthapuram Ravi, Susarla K. Shankar, Raj Shankarappa, Udaykumar Ranga

Research output: Contribution to journalArticle

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Abstract

Human immunodeficiency virus type 1 (HIV-1) subtype C viruses are associated with nearly half of worldwide HIV-1 infections and are most predominant in India and the southern and eastern parts of Africa. Earlier reports from India identified the preponderance of subtype C and a small proportion of subtype A viruses. Subsequent reports identifying multiple subtypes suggest new introductions and/or their detection due to extended screening. The southern parts of India constitute emerging areas of the epidemic, but it is not known whether HIV-1 infection in these areas is associated with subtype C viruses or is due to the potential new introduction of non-subtype C viruses. Here, we describe the development of a specific and sensitive PCR-based strategy to identify subtype C-viruses (C-PCR). The strategy is based on amplifying a region encompassing a long terminal repeat and gag in the first round, followed by two sets of nested primers; one amplifies multiple subtypes, while the other is specific to subtype C. The common HIV and subtype C-specific fragments are distinguishable by length differences in agarose gels and by the difference in the numbers of NF-κB sites encoded in the subtype C-specific fragment. We implemented this method to screen 256 HIV-1-infected individuals from 35 towns and cities in four states in the south and a city in the east. With the exception of single samples of subtypes A and B and a B/C recombinant, we found all to be infected with subtype C viruses, and the subtype assignments were confirmed in a subset by using heteroduplex mobility assays and phylogenetic analysis of sequences. We propose the use of C-PCR to facilitate rapid molecular epidemiologic characterization to aid vaccine and therapeutic strategies.

Original languageEnglish (US)
Pages (from-to)2742-2751
Number of pages10
JournalJournal of clinical microbiology
Volume42
Issue number6
DOIs
StatePublished - Jun 1 2004

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HIV-1
India
Viruses
Polymerase Chain Reaction
Virus Diseases
Eastern Africa
Terminal Repeat Sequences
Sepharose
Sequence Analysis
Vaccines
Gels
HIV
Therapeutics

ASJC Scopus subject areas

  • Microbiology (medical)

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Identification of subtype C human immunodeficiency virus type 1 by subtype-specific PCR and its use in the characterization of viruses circulating in the southern parts of India. / Siddappa, Nagadenahalli B.; Dash, Prashanta K.; Mahadevan, Anita; Jayasuryan, Narayana; Hu, Fen; Dice, Bethany; Keefe, Randy; Satish, Kadappa S.; Satish, Bhuthiah; Sreekanthan, Kuttan; Chatterjee, Ramdas; Venu, Kandala; Satishchandra, Parthasarathy; Ravi, Vasanthapuram; Shankar, Susarla K.; Shankarappa, Raj; Ranga, Udaykumar.

In: Journal of clinical microbiology, Vol. 42, No. 6, 01.06.2004, p. 2742-2751.

Research output: Contribution to journalArticle

Siddappa, NB, Dash, PK, Mahadevan, A, Jayasuryan, N, Hu, F, Dice, B, Keefe, R, Satish, KS, Satish, B, Sreekanthan, K, Chatterjee, R, Venu, K, Satishchandra, P, Ravi, V, Shankar, SK, Shankarappa, R & Ranga, U 2004, 'Identification of subtype C human immunodeficiency virus type 1 by subtype-specific PCR and its use in the characterization of viruses circulating in the southern parts of India', Journal of clinical microbiology, vol. 42, no. 6, pp. 2742-2751. https://doi.org/10.1128/JCM.42.6.2742-2751.2004
Siddappa, Nagadenahalli B. ; Dash, Prashanta K. ; Mahadevan, Anita ; Jayasuryan, Narayana ; Hu, Fen ; Dice, Bethany ; Keefe, Randy ; Satish, Kadappa S. ; Satish, Bhuthiah ; Sreekanthan, Kuttan ; Chatterjee, Ramdas ; Venu, Kandala ; Satishchandra, Parthasarathy ; Ravi, Vasanthapuram ; Shankar, Susarla K. ; Shankarappa, Raj ; Ranga, Udaykumar. / Identification of subtype C human immunodeficiency virus type 1 by subtype-specific PCR and its use in the characterization of viruses circulating in the southern parts of India. In: Journal of clinical microbiology. 2004 ; Vol. 42, No. 6. pp. 2742-2751.
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AU - Siddappa, Nagadenahalli B.

AU - Dash, Prashanta K.

AU - Mahadevan, Anita

AU - Jayasuryan, Narayana

AU - Hu, Fen

AU - Dice, Bethany

AU - Keefe, Randy

AU - Satish, Kadappa S.

AU - Satish, Bhuthiah

AU - Sreekanthan, Kuttan

AU - Chatterjee, Ramdas

AU - Venu, Kandala

AU - Satishchandra, Parthasarathy

AU - Ravi, Vasanthapuram

AU - Shankar, Susarla K.

AU - Shankarappa, Raj

AU - Ranga, Udaykumar

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N2 - Human immunodeficiency virus type 1 (HIV-1) subtype C viruses are associated with nearly half of worldwide HIV-1 infections and are most predominant in India and the southern and eastern parts of Africa. Earlier reports from India identified the preponderance of subtype C and a small proportion of subtype A viruses. Subsequent reports identifying multiple subtypes suggest new introductions and/or their detection due to extended screening. The southern parts of India constitute emerging areas of the epidemic, but it is not known whether HIV-1 infection in these areas is associated with subtype C viruses or is due to the potential new introduction of non-subtype C viruses. Here, we describe the development of a specific and sensitive PCR-based strategy to identify subtype C-viruses (C-PCR). The strategy is based on amplifying a region encompassing a long terminal repeat and gag in the first round, followed by two sets of nested primers; one amplifies multiple subtypes, while the other is specific to subtype C. The common HIV and subtype C-specific fragments are distinguishable by length differences in agarose gels and by the difference in the numbers of NF-κB sites encoded in the subtype C-specific fragment. We implemented this method to screen 256 HIV-1-infected individuals from 35 towns and cities in four states in the south and a city in the east. With the exception of single samples of subtypes A and B and a B/C recombinant, we found all to be infected with subtype C viruses, and the subtype assignments were confirmed in a subset by using heteroduplex mobility assays and phylogenetic analysis of sequences. We propose the use of C-PCR to facilitate rapid molecular epidemiologic characterization to aid vaccine and therapeutic strategies.

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