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Background  Malaria in Nigeria is principally due to  Plasmodium falciparum  and, to a lesser extent to  Plasmodium malariae  and  Plasmodium ovale .  Plasmodium vivax  is thought to be absent in Nigeria in particular and sub-Saharan Africa in general, due to the near fixation of the Duffy negative gene in this population. Nevertheless, there are frequent reports of  P. vivax  infection in Duffy negative individuals in the sub-region, including reports from two countries sharing border with Nigeria to the west (Republic of Benin) and east (Cameroon). Additionally, there were two cases of microscopic vivax-like malaria from Nigerian indigenous population. Hence molecular surveillance of the circulating  Plasmodium  species in two states (Lagos and Edo) of southwestern Nigeria was carried out.    Methods  A cross-sectional survey between September 2016 and March 2017 was conducted. 436 febrile patients were included for the present work. Venous blood of these patients was subjected to RDT as well as microscopy. Further, parasite DNA was isolated from positive samples and PCR diagnostic was employed followed by direct sequencing of the 18S rRNA of  Plasmodium  species as well as sequencing of a portion of the promoter region of the Duffy antigen receptor for chemokines. Samples positive for  P. vivax  were re-amplified several times and finally using the High Fidelity Taq to rule out any bias introduced.    Results  Of the 256 (58.7%) amplifiable malaria parasite DNA,  P. falciparum  was, as expected, the major cause of infection, either alone 85.5% (219/256; 97 from Edo and 122 from Lagos), or mixed with  P. malariae  6.3% (16/256) or with  P. vivax  1.6% (4/256). Only one of the five  P. vivax  isolates was found to be a single infection. DNA sequencing and subsequent alignment of the 18S rRNA of  P. vivax  with the reference strains displayed very high similarities (100%). Remarkably, the T-33C was identified in all  P. vivax  samples, thus confirming that all vivax-infected patients in the current study are Duffy negative.    Conclusion  The present study gave the first molecular evidence of  P. vivax  in Nigeria in Duffy negative individuals. Though restricted to two states; Edo in South–South and Lagos in South-west Nigeria, the real burden of this species in Nigeria and sub-Saharan Africa might have been underestimated, hence there is need to put in place a country-wide, as well as a sub-Saharan Africa-wide surveillance and appropriate control measures.    Electronic supplementary material  The online version of this article (10.1186/s12936-018-2588-7) contains supplementary material, which is available to authorized users.

malaria journal

Molecular identification of Plasmodium species responsible for malaria reveals Plasmodium vivax isolates in Duffy negative individuals from southwestern Nigeria