Intra-species variability in ITS-1 sequences of Haemonchus contortus isolated from goats in West Bengal, India S. Bandyopadhyay*, A.K. Bera, S. Sikdar, S. De, S. Das, T. Rana, D. Pan, S. Bandyopadhyay † and D. Bhattacharya Indian Veterinary Research Institute, Eastern Regional Station, 37 Belgachia Road, Kolkata 37, West Bengal, India (Accepted 24 July 2010; First Published Online 31 August 2010) Abstract This study evaluated the existence of different genotypes of Haemonchus contortus prevailing among goats in West Bengal, India. These parasites were isolated from the abomasum of goat intestine and the molecular characterization was performed by comparing variation of nucleotide sequences of the internal transcribed spacer 1 (ITS-1) gene region. Single-strand conformation poly- morphism (SSCP) analysis of ITS-1 amplified product showed the presence of three distinct conformations both in male and female parasites. The sequence analysis of conformations showed two single nucleotide polymorphisms (SNP) in male parasites at nucleotide positions 106 and 107 and one SNP was detected in female parasites at nucleotide position 157. These nucleotide variations in different isolates did not alter the interior loop structure of the predicted secondary RNA, therefore we believe these variations may not be responsible for any evolutionary changes among conformations. Introduction Haemonchus contortus, a common trichostrongylid parasite of sheep, goats and cattle, is one of the most important blood-sucking parasites. Extensive production losses have been reported in animals in tropical regions due to this parasite (Miller & Horohov, 2006). In the past, morphological features were used for identification of different species of this parasite but currently the mole- cular signature of parasite genes is utilized (Kia et al., 2007). In order to study the genetic variation within a species, a multicopy gene family of ribosomal DNA (rDNA) is the ideal choice due to its ubiquitous nature in all living organisms and its relative easy amplification via polymerase chain reaction (PCR). rDNA is character- ized by multiple tandemly repeated copies of highly conserved genes coding for ribosomal RNA. It is inter- rupted by variable external and internal transcribed ‘spacer’ regions (ETS, ITS-1 and ITS-2). Of these spacer regions, the internal transcribed spacer 1 (ITS-1) located between 18S and 5.8S genes is the most conserved and therefore recognized as a valuable genetic marker at species level (Pontecorvo et al., 2008). Previously it was accepted that the nucleotide sequence homogeneity reported among rDNA multigene families is maintained within individuals and even within species by ‘concerted evolution’ (Dover, 1982; Gandolfi et al., 2001). In contrast to this theory, a certain degree of intra- species variation has been found in the nucleotide sequence of ITS-1 and/or ITS-2 gene regions of different isolates of a species (Harris & Crandall, 2000). In view of the above, the main objective of this study was to ascertain the existence of different isolates of H. contortus prevailing in West Bengal, India, by studying the variation in nucleotide sequences of ITS-1. Primers for amplification of ITS-1 were designed from the published ITS-1 sequence of H. contortus (accession #AF044927). The amplified product was further analysed through single-strand conformation polymorphism (SSCP). Different SSCP conformations were sequenced and their variation among isolates of H. contortus was determined. *E-mail: subuicar@rediffmail.com † Scientist, NRC on Yak, Dirang, Arunachal Pradesh, India. Journal of Helminthology (2011) 85, 204–209 doi:10.1017/S0022149X10000465 q Cambridge University Press 2010