REVEALING NEW MEASLES VIRUS TRANSMISSION ROUTES BY USE OF SEQUENCE ANALYSIS OF PHOSPHOPROTEIN AND HEMAGGLUTININ GENES

Friday, 7th of August 2015

 

REVEALING NEW MEASLES VIRUS TRANSMISSION ROUTES BY USE OF SEQUENCE ANALYSIS OF PHOSPHOPROTEIN AND HEMAGGLUTININ GENES

1. Julia R. Kessler¹,
2. Jacques R. Kremer¹,
3. Sergey V. Shulga²,
4. Nina T. Tikhonova²,
5. Sabine Santibanez³,
6. Annette Mankertz³,
7. Galina V. Semeiko⁴,
8. Elena O. Samoilovich⁴,
9. Jean-Jacques Muyembe Tamfum⁵,
10. Elisabeth Pukuta⁵ and
11. Claude P. Muller¹,*

+ Author Affiliations

1.      ¹Institute of Immunology, Centre de Recherche Public-Santé/Laboratoire National de Santé, WHO Regional Reference Laboratory for Measles and Rubella and WHO Collaboration Centre for Measles Research, Luxembourg, Luxembourg

2.      ²WHO Regional Reference Laboratory for Measles and Rubella, Moscow, Russian Federation

3.      ³WHO Regional Reference Laboratory for Measles and Rubella, Berlin, Germany

4.      ⁴The Republican Research and Practical Centre for Epidemiology and Microbiology, WHO National Measles and Rubella Laboratory, Minsk, Belarus

5.      ⁵Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo

 

Excerpts below; full text, with tables, is at http://jcm.asm.org/content/49/2/677.full

ABSTRACT

With improved measles virus (MV) control, the genetic variability of the MV-nucleoprotein hypervariable region (NP-HVR) decreases. Thus, it becomes increasingly difficult to determine the origin of a virus using only this part of the genome. During outbreaks in Europe and Africa, we found MV strains with identical NP-HVR sequences. However, these strains showed considerable diversity within a larger sequencing window based on concatenated MV phosphoprotein and hemagglutinin genes (P/H pseudogenes). In Belarus, Germany, Russia, and the Democratic Republic of Congo, the P/H pseudogenes provided insights into chains of transmission, whereas identical NP-HVR provided none. In Russia, for instance, the P/H pseudogene identified temporal clusters rather than geographical clusters, demonstrating the circulation and importation of independent variants rather than large local outbreaks lasting for several years, as suggested by NP-HVR. Thus, by extending the sequencing window for molecular epidemiology, a more refined picture of MV circulation was obtained with more clearly defined links between outbreaks and transmission chains. Our results also suggested that in contrast to the P gene, the H gene acquired fixed substitutions that continued to be found in subsequent outbreaks, possibly with consequences for its antigenicity. Thus, a longer sequencing window has true benefits both for the epidemiological surveillance of measles and for the better monitoring of viral evolution.

INTRODUCTION

Since the introduction of measles vaccination, the global burden of measles disease has continuously decreased (13). Significant progress has been made during the last decade, with the elimination of measles from the Americas and the dramatic reduction in measles mortality worldwide (8). However, measles continues to be endemic in many developing countries and some industrialized countries (6). The molecular epidemiology of measles virus (MV) has proven to be a very useful tool for monitoring the progress in measles control (7). The negative-sense RNA genome (15,894 nucleotides [nt]) contains six genes, encoding the nucleoprotein (NP), the phosphoprotein (P), and the matrix (M), fusion (F), hemagglutinin (H), and large (L) proteins (5). Although MV is serologically a monotypic virus, genetic characterization so far has identified eight clades (A to H), subdivided into 24 genotypes (A, B1 to B3, C1 and C2, D1 to D11, E, F, G1 to G3, and H1 and H2) (8, 16). Since 1998, the World Health Organization (WHO) recommends the sequencing of the hypervariable region of 450 nt encoding the C-terminal 150 amino acids of the NP (NP-HVR) and the use of it as the minimal data for MV genotyping (12). Additionally, the complete H sequence should be obtained if a new genotype is suspected (8). However, only the sequences of the NP-HVR are available for most strains obtained from clinical cases.

MV genotyping is an important tool of measles surveillance to document chains of transmission, discriminate between imported or indigenous viruses, and monitor elimination programs. However, identical NP-HVR sequences have been found for several years in Europe and beyond (8). For instance, two main variants of genotype D6, differing by a single nucleotide in their NP-HVR, were widely distributed in the WHO European region in 2005 and 2006 (3). Thus, it is difficult to determine the origin of a virus using molecular tools based on the NP-HVR alone.

In this study, the sequence variability of P and H genes of strains with identical or very similar NP-HVR sequences was investigated. We showed for four different outbreaks in Europe and Africa that the phylogenetic analysis of the P/H pseudogene sequences provides a more refined picture of MV circulation.