Identification of measles virus genotypes from recent outbreaks in countries from the Eastern Mediterranean Region

Abstract

Background:

Molecular characterization of measles viruses (MV) helps to identify transmission pathways of the virus and to document persistence or interruption of endemic virus circulation. In the Eastern Mediterranean Region, measles genotypes from only few countries have been documented.

Objectives:

This study reports the genetic characteristics of virus strains from recent measles outbreaks in Tunisia, Libya, Syria and Iran in 2002–2003.

Study design:

Virus sequences in the nucleoprotein gene were obtained by PCR amplification of virus isolates or serum samples. The sequences were compared to the reference ones for genotype identification and to other published sequences within the same genotype.

Results and conclusions:

The Tunisian and Libyan epidemic strains belonged to genotype B3, they were closely related to each other and to isolates from Western Africa. The Syrian and Iranian viruses belonged to genotype D4, and differed from each other and from the other published sequences within this genotype. Our results provide valuable baseline and new tools for improved virological measles surveillance in the future, at country, regional and global levels.

Introduction

Genetic variation among wild-type measles isolates has been largely demonstrated (Giraudon et al., 1988, Taylor et al., 1991, Baczko et al., 1992, Schulz et al., 1992, Rota et al., 1992, Rota et al., 1994, Tamin et al., 1994, Rima et al., 1995). The 450 nucleotides coding for the COOH-terminus of the nucleoprotein is the most variable region in the measles genome (Xu et al., 1998); standard protocols recommend its use to genotype wild-type isolates. Complete H gene sequence is required for some viruses of interest such as newly identified genotypes (WHO, 1998, WHO, 2001, WHO, 2003a). In addition to serum samples collected for serological confirmation of suspected measles cases, it is recommended to collect, from selected cases, a urine and/or nasopharyngeal sample for virus isolation and genotyping (WHO, 1999). Currently, there are 23 recognized genotypes: A, B1-B3, C1, C2, D1-D10, E, F, G1-G3, H1 and H2 (WHO, 2003a). Most of them are actively circulating but geographically restricted with possible long distance importations (Bellini and Rota, 1998, Rota and Bellini, 2003, WHO, 2003a). In a given geographic region, a genotype is considered endemic if it is consistently associated with outbreaks in that area over an extended time period. The identification of different genotypes in limited outbreaks and/or sporadic cases is more consistent with multiple virus importation than with endemic virus circulation. Thus, the high diversity of genotypes detected during the last 10 years in the USA, Australia, Canada and the United Kingdom suggests lack of endemic circulation (Rota et al., 1995, Rota et al., 1996, Rota et al., 1998, Rota et al., 2002, Tipples et al., 2004, Chibo et al., 2003, Alla et al., 2002). In the Eastern Mediterranean Region (EMR), circulating measles virus (MV) genotypes from only Morocco and Sudan, have been reported (Bellini and Rota, 1998, El Mubarak et al., 2002, Gaafar et al., 2003) and suspected in Afghanistan, Pakistan, Oman and Iran (Jin et al., 1997; Rota et al., 1998, Rota et al., 2002, Rota and Bellini, 2003) mainly after importation of measles cases into the USA and UK directly from these countries. In this study, we identified wild-type measles genotypes associated with outbreaks in Tunisia, Syria, Libya and Iran during 2002–2003, using partial sequencing of the N gene. To obtain the sequences of interest, we used PCR amplification of viral strains isolated from urine and/or nasopharyngeal samples and a modified PCR technique to amplify the viral genome from serum samples collected for IgM testing.