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Research Article - (2011) Volume 2, Issue 1

Molecular evolutionary studies of lassa virus nucleoprotein

Lawrence Ehis Okoror1* and Omovigho Iyobosa Okoro2

1Department of Microbiology and Biotechnology, College of Natural Sciences, Joseph Ayo Babalola University, PMB 5006, Ilesha, Osun State Nigeria.

2Department of Microbiology, Faculty of Natural Sciences, Ambrose Alli University, PMB 14, Ekpoma. Edo State. Nigeria.

*Corresponding Author:
Lawrence Ehis Okoror,
Department of Microbiology and Biotechnology
College of Natural Sciences, Joseph Ayo Babalola University
PMB 5006, Ilesha, Osun State
E-mail: LEO [email protected], OIO [email protected]
Visit for more related articles at Translational Biomedicine


Background: Lassa virus is the cause of Lassa fever with high morbidity and mortality. Molecular evolution was studied through virulence diversity through to provide insight as to despite circulating antibodies there is still yearly epidemic outbreaks. 

Methods and Findings: The nucleotide sequences of 18 Lassa virus genomic RNA encoding Lassa virus nucleoprotein isolates collected from different parts of the world were obtained from the GenBank and nucleotide substitution among them studied using the computer program MEGA4. The genetic distances among strains were predicted by pairwise nucleotide differences. The rate of synonymous substitution was high 5.889 per nucleotide per year and nonsynonymous was higher at 49.664. The average predicted rate of synonymous and nonsynonymous using modified Nei-Gojobori (assuming transition/transversion bias = 2) was 27.9 which was taken as the genetic distance between strains. The average number of synonymous sites is 150.741. The average number of nonsynonymous sites is 392.259. The phylogenetic tree was inferred by unweighted pairwise grouping in MEGA4 and using neighbour-joining method. The time of emergence of Lassa virus was predicted to be around January 1920. However the first human appearance of the virus was predicted to be around May 1959. (±24months). In synonymous substitution the rate of (G-----T) rare was high. The nucleotide frequencies were 0.314 (A), 0.246 (T/U), 0.204 (C) and 0.235 (G). The transition/transversion ratio k1 = 14.991 (purines) and k2 = 69.916 (pyrimidines). The overall transition/transversion bias R=16.662 with a total of 620 position in the final data set. These figures are far higher than an earlier study using Lassa virus glycoprotein. The nucleotide diversity was also very high using the Taijima’s model in MEGA 4. 

Conclusion: The divergence within strains always coincides with the period of epidemic which goes to confirm that the cause of epidemic outbreak should be the emergence of new strain.


Lassa virus, nucleoprotein, arena viruses,


Lassa virus belongs to a very large group of heamorrhagic fever viruses-arena viruses which is responsible for high rate of morbidity and mortality in areas of West Africa. Among the six arena viruses known so far only one –Lassa virus (LASV) is known to cause illness in humans. There are an estimated 300,000 to 500,000 cases of Lassa fever each year [1,2,3,4,5] with mortality rate of 15% to 20% for hospitalized patients and as high as 50% during epidemics [2,6,7]. The LASV genome is comprised of two ambisense, single stranded RNA molecules, designated small (S) and large (L) [8]. Two genes on the S segment encode NP, GP1, and GP2; whereas, the L segment encodes the viral polymerase (L protein) and RING finger Z matrix protein. GP1 and GP2 subunits result from post-translational cleavage of a precursor glycoprotein (GPC) by the protease SKI-1/S1P [9,10]. GP1 serves a putative role in receptor binding, while the structure of GP2 is consistent with viral transmembrane fusion proteins [11,12].

Over the years many aspects of Lassa fever have been defined including the clinical presentation, epidemiology, immunology, pathology, physiology and therapy [13,14] with sparse reports on molecular evolution. The exact seasonality of Lassa virus is still not understood and therefore increase in availability of rodent host (Mastomys natalensis) may increase the risk of infection or transfer of the virus to humans. Lassa virus infection has continued unabated despite the presence of circulating antibodies against the infection in the areas of epidemics with emergence of newer strains which might likely be the cause of new outbreaks [15], hence a detailed evolutionary study at molecular level becomes essential. Serological data did not provide information on seasonality and the origin of human to human infection.

Lassa virus was first identified in Northern Nigeria in 1969, although reports have it that the virus co-evolved with the rodent host over a period of 9 million years. A study of the molecular evolution will provide better and concise information as to the origin of the virus in humans and its seasonality. The recent identification of two new strains point to the fact that the virus is in constant genetic change which has made this study necessary. Evolutionary study of the virus which is a determinant of the virulence diversity have been reported to give a knowledge of possible vaccine development for the virus and also give an in site into the host parasite relationship. A further study may eventually lead to the explanation as to why despite the circulating antibodies against Lassa virus, outbreaks still occur yearly.


The computer program MEGA 4 and CLC workbench 4 enabled us to separately estimate the rate of synonymous and nonsynonymous substitution as wells as study the entire evolution of Lassa virus nucleoprotein using 18 nucleotide sequences identified over the years and deposited in Genbank which included their genetic distances, evolutionary rate, neighbor joining methods of evolutionary studies, phylogenetic tree, substitution frequency and pattern. The genetic distances between strains were estimated using pairwise nucleotide differences. The substitution pattern as well as transition and tranversional substitution and frequency of parallel independently occurring at the same site of different evolutionary lineages were studied. Multiple sequence alignment of the sequences were also carried out and viewed in genedoc to observe for evolutionary conservation.

Nucleotide Sequences

Sequences used in this study were from Genbank and are as follows:

L._virus_DGD112_NP, L._virus_DGD104_NP, L._virus_DGD87_NP,

L._virus_DGD43_NP, L._virus_DGD35_NP, L._virus_DGD28_NP,

L._virus_DGD13_NP, L._virus_DGD4_NP, L._virus_TA846_NP,

L._virus_TA820_NP, L._virus_TA817_NP, L._virus_TA491_NP,

L._virus_TA471_NP, L._virus_TA464_NP, L._virus_TA462_NP,

L._virus_TA444_NP, L._virus_TA341_NP, L._virus_TA416_NP.

A graph of evolutionary differences representing their evolutionary distance was plotted against the time of identification of the new strain in order to determine the time of emergence of the virus using only human isolates since 1972. The dates of isolation of all the human strains used were extracted from Bowen et al. [16].


Alignment of the 18 nucleotide sequences of Lassa virus strains demonstrated insertion and deletions as well as substitutions among the strains collected over the years from different parts of the world. It also showed some conserved areas over the years especially regions of suspected high functionality. Of the 628 sites of substitution, 488 were conserved. There were 399 nondegenerate sites, 101 two fold degenerate sites and 46 four fold degenerate sites.

The rate of synonymous substitution was high 5.889 per nucleotide per year and nonsynonymous was higher at 49.664. The average predicted rate of synonymous and nonsynonymous using modified Nei-Gojobori (assuming transition/transversion bias = 2) was 27.9 which was taken as the genetic distance between strains. The average number of synonymous sites is 150.741. The average number of nonsynonymous sites is 392.259. The phylogenetic tree was inferred by unweighted pairwise grouping in MEGA4 and using neighbour-joining method (Fig. 1). The time of emergence of Lassa virus was predicted to be around January 1920 (±24 months). And the time of emergence of the virus in humans was predicted to be May 1959 about ten years before the first Lassa virus report in Nigeria. In synonymous substitution the rate of (G-----T) was high. The nucleotide frequencies were 0.314 (A), 0.246 (T/U), 0.204 (C) and 0.235 (G). The transition/transversion ratio k1=14.991 (purines) and k2=69.916 (pyrimidines). The overall transition/transversion bias R=16.662 with a total of 620 position in the final data set. These figures are far higher than an earlier study using lassa virus glycoprotein. The nucleotide diversity was also very high using the Taijima’s model in MEGA 4. Of the 628 sites 399 were non degenerate while 101 were two fold degenerate and 46 four fold degenerate. The neighbour joining method was used to explore the evolutionary relationship of isolates using Kt as the genetic distance (Fig. 1). This is based on the principle that the sum of the branch length at each cluster stage is to be minimised. Thus this method is suitable for estimating genetic relationship among isolates without taking into account evolutionary rate or isolation time. The nucleotide diversity was high at 0.099905. Amino acid substitution was high where 99 of the total 209 sites were conserved. The graph of the nucleotide distance against their time of identification of new human strains (Fig 2) predicted the first human infection to be around May 1959 using the 1972 Josiah strain as a reference strain.


Figure 1: Phylogenetic tree inferred by neighbour-joining method of lassa virus. Numbers represent estimated branch lengths in nucleotide. Notice that all strains of lassa virus evolved from one focal point.


Figure 2: Evolution rate of Lassa virus and the first human infection. The 1972 strain was taken as the stand point for first case. Using 4 strains and assuming that they all evolved at a constant rate, the evolutionary distance was plotted against time of emergence. A dotted line from the point of joins at the dot plot, backwards will terminate at the month of first emergence. Or the slope of the plot in months minus the proposed first emergence date will give the date of first emergence of human straisn. The dot plot was done in SPSS version 17.

Discussion and Conclusion

The phylogenetic tree was inferred with 18 Lassa virus nucleoprotein nucleotide sequences using MEGA 4 and this was consistence with results from other studies [17,18]. Okoror et al., [18] studied the Lassa virus glycoprotein nucleotide sequences using MEGA 4 while Takeda compared 18 nucleotide of capsid protein VP1 in 18 isolates of EV70 in two separate studies with earlier study using oligonucleotide mapping of the entire genome [19]. The emergence of Lassa virus was predicted to be 1920 (±24 months) which opposes earlier studies that suggested that the virus probably co-evolve millions of years ago with the rodent host. However the rodent strain might be different from the human strain since all the strains compared in this study were all human strains. It is suggested that as soon as the strains crosses the species barrier to infect humans there will be a mutation in the nucleotide sequences. This study also revealed that the divergence times are usually during the period of high epidemics which confirms that the emergence of newer strains were responsible for the yearly epidemic outbreaks. The concentration of strains at the period of epidemics also inferred that the variations in strains is usually location dependent rather time dependent. The occurrence of epidemics at the same time in all the endemic areas also supportive of the fact that newer strains are responsible for epidemics in different locations. The fact that epidemics occur at the same time in different areas by different strains of the virus confirms earlier report by Banseh [20] who suggested that the virus vary with location. In this study therefore we suggest that the virus vary according to both location and time. The high rate of transition/transversion at the same time shows that there is co-circulation of genetically and antigenically different strains in the population. This goes to point that the nucleoprotein is suitable for evolutionary studies but the glycoprotein is more suited for vaccine development if the study by Okoror et al. [18] is anything to compare with.

The nucleotide substitution rates of the Lassa virus nucleoprotein gene obtained here (27.6) weighted average for both synonymous and nonsynonymous per nucleotide per year were higher than those of an earlier study by Okoror et al., [18]. This goes to confirm that the Lassa virus nucleoprotein is best suited for evolutionary studies than the glycoprotein since it gives a better insight of the periodic nucleotide changes especially with a nucleotide diversity as high as 0.099905. This is in opposition to earlier studies in non-structural protein gene [21], nucleoprotein gene [21,22] and PB2 of influenza [23] A virus and for haemagglutinin [24] and NS genes [25] of influenza B virus; they were in the range of 1.1 x 10-3 to 2.3x10-3 substitutions per nucleotide per year for the observed nucleotide differences. There was a high remarkable feature of the nucleotide substitution patterns of Lassa virus transitions, i.e., low transversions. The relative frequency of transitions (C*- -U and A*- ->G) was almost 70% (R = 16.662 in the 620 sites in the final data sets in all three estimations, i.e., in total substitutions, at the third position of codons, and at fourfold-degenerate sites.

This is an indication that transitions were found in almost all the sites in the data set. Although transitions in naturally occurring mutations are known to be much more frequent than expected from random substitutions [26,27], the frequency of transitions in Lassa virus glycoprotein gene was much higher than that reported for the pseudogene DNA of human origin (55.6% on average) [26], for the third codon position of the Mahoney and Sabin strains of type 1 poliovirus (77.1%). This study is in opposition with earlier report by Takeda et al. [17] which suggested that the short period for the analysis of the EV70 VP1 gene was responsible for its high transition since this study analysed sequences that were isolated close to 40 years ago. Such high frequency was also observed for Lassa virus glycoprotein which was analysed for a shorter period of time. Hence the time of isolation is not a parameter to judge is transition. This study also suggests that virulence diversity in arenaviruses as studied is essential for the development of vaccine against the virus as earlier reported by Jahrling and Peters and other reports [28,29,30]. It is also suggested that the reasons for a yearly epidemic outbreak is due to the fact that each time the rodents strain crosses the species barrier there is always a re-modification of genetic or molecular make-up of the virus, hence not been recognised by already circulating antibodies.

Author Contribution: OLE conceived the study and did all the computational study as well as wrote the paper. OOI was actively involved in interpretation of the results and the proof reading of the final manuscript up to the point of submission. She also supervised most of the evolutionary analysis.

Conflicting Interest: There was no conflicting interest.



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