Genetic analysis of measles virus nucleocapsid gene identifies measles virus isolate of close similarity to Clade A viruses from Nigeria

Introduction

Measles is an acute viral illness characterised by a prodromal illness of fever, coryza, cough, conjunctivitis and presence of Koplik spots followed by the appearance of a generalised maculopapular rash. The illness is either mild or severe depending on the immune and nutritional status of the infected person. It is caused by measles virus (MV), which is a negative sense single stranded RNA virus of the family Paramyxoviridae, genus Morbillivirus¹. The virus is relatively antigenically stable and monotypic but has genetic variation in the hemagglutinin (H) and nucleoprotein (N) genes². Measles is one of the leading causes of death among young children despite the availability of a safe and cost effective vaccine for over 40 years³. It accounted for over 145700 deaths in 2013 globally, 51% of which are from World Health Organization (WHO) defined African region⁴. Nigeria still ranks high among countries reporting measles infection yearly, with over 7000 suspected and over 3000 confirmed cases reported in 2014⁴.

The 450 nucleotides that code for the COOH-terminus of the N protein is the single most variable part of the measles genome and analysis of this part of MV isolates or clinical specimens has helped to classify measles into eight clades (Clades A-H) and 23 genotypes⁵. Different measles genotypes and strains circulate in specific geographical regions^5,6. Measles virus clades B3, D4, D5, D8 and H1 were isolated in the WHO Americas region between 2007 and 2009, genotypes D6 and D9, in addition to those found in the Americas, are also found in the European region, and genotype B3 is the major circulating strain in the Africa region in this period⁶.

Previous reports on circulating measles strains from Nigeria have indicated the circulation of only genotypes B3 cluster 1 and 2. However, due to the absence of integrated molecular surveillance in measles’ elimination programs, there has been only a few sequence data of Nigerian measles isolates, especially in recent times^7,8. Molecular surveillance is essential in order to observe the changes in viral genotypes over time in a particular region. It is also an important tool in assessing the effectiveness of vaccination programs⁹. This study reports the molecular characterization of a previously unreported genotype of measles virus from Nigeria.

Methods

Results and discussion

Both the swab and tissue culture sample showed the expected 560 base pairs after nested RT-PCR. Phylogenetic analysis of the measles sample MViIbadan/NIE/11.10 sequence (ccession no LN876569.1) gave a distinct BLAST search result (Supplementary File 1). From the search it was observed that the sequence with ascension no JF727650.1 Leningrad is the most closely related virus sequence with our Ibadan strain. The phylogenetic tree generated revealed that the Ibadan prototype Clade A strain co-clustered with sequences close to the vaccine Edmonston Zagreb stain with 98% bootstrap value (Figure 1), suggesting the possibility of common ancestral origin. Molecular Epidemiology of Measles virus in Nigeria classifies isolates into two distinct groups within genotype B3, B3 cluster 1 and B3 cluster 2^7,8. The B3 genotype was assigned after exhaustive genetic analysis of MV strains from Lagos and Ibadan in 1999⁸.

Figure 1. Phylogenetic tree of the partial nucleoprotein gene sequence of the measles virus.

The study isolate is shown in bold red font; clinical strains from Nigeria are shown in blue font. Clades are indicated beside the black horizontal lines. The GenBank accession numbers are indicated first in the sequence labels, bootstrap values are indicated if ≥ 50%, phylogenetic tree was constructed using the Neighbor joining algorithm in MEGA 6.0 with 1,000 bootstrap replicates.

Our current study describes isolation of a different strain of measles from the previously described genotypes (MViIbadan/NIE/11.10). This virus was recovered from the throat swab of a 3 year old child with no documented history of vaccination at Oni Memorial Children Hospital in Ibadan Nigeria in November 2010.

Measles virus of genotype A has previously been detected in acute cases of measles in South and North America, China, Japan, Eastern Europe, Finland and the UK and South Africa over the last 40 years¹⁰, but there had not been any report of Clade A virus in West Africa. The virus isolated in this study is from a child who had never received any form of measles vaccination and there was no activities involving measles virus vaccine in the laboratory as at the time of virus isolation. Molecular epidemiologic information has revealed circulation of several measles genotype in Africa in recent times. Clade B viruses is reported to be endemic in central and western parts of sub-Saharan Africa while genotypes D2 and D4 has been continually detected southern and eastern parts of Africa and genotype C2 in northern Africa^11–14 but no virus of Clade A has been reported in Africa recently.

In this study, although we did not independently investigate the immediate or remote factors that could have led to the introduction/emergence of this virus genotype in Nigeria, we postulate that the virus could have been probably imported from another continent or could have been an undetected circulating strain. This is because active molecular surveillance is not in place in Nigeria, and the last report of MV molecular epidemiology was in 2005⁸. This leaves a huge gap in research information and multiple introductions of diverse measles genotypes might have taken place undetected over time. We therefore advocate for the establishment of an institution of a national surveillance program, and the inclusion of molecular epidemiology alongside national and global authorities, such as the WHO and Federal Ministry of Health Nigeria, to help achieve measles elimination goals in the country and globally.

Data availability

The sequence of the identified isolate has been deposited in GenBank under the accession number LN876569.1.

Ethical statement

Ethical approval was obtained from Oyo State, Hospital Management Board (Ibadan, Nigeria), approval number OY/HMB/REC-140010, to conduct this study. The parent of the infected child reported in this study also provided written informed consent for sequencing of the sample and use in research before the sample was collected.