Abstract: Objective To analyze blood samples from patients with falciparum malaria and vivax malaria in border areas of Yunnan Province, using 18S rRNA-based nested PCR, and compare 18S rRNA sequences. Methods Blood or filter blood samples with positive microscopic results for Plasmodium falciparum or P. vivax infection were collected from Laza, Nankajiang, Mangdong and Nawei of Myanmar, and from Mengla, Tengchong and Yingjiang of Yunnan Province between 2004 and 2011. 18S rRNA-based nested PCR was conducted on the samples, and PCR products were sequenced and blasted. Phylogenetic tree was constructed using the neighbor-joining method with MEGA software（version 6.06）. Results Microscopic examination revealed P. falciparum infection in 256 samples and P. vivax infection in 219 samples. The 18S rRNA-based PCR further confirmed P. falciparum infection in 242 samples, P. vivax infection in 176 samples, and mixed infection in 57 samples. The consistency rate was 81.7% （388/475） between microscopic and PCR results. The inconsistency rate significantly correlated with parasite density （Spearman’s r=-0.408， P<0.05）. Sequence alignment revealed 11 and 10 homologous sequences for P. falciparum and P. vivax 18S rRNA gene, comprising 2.9%（6/205） and 22.5%（27/120） variable sites, respectively. The 18S rRNA of P. falciparum clustered with that from Cameroon（GenBank accession number KC428742）, but was distantly related with the S-type 18S rRNA from the Netherlands （U36465） and Brazil （U36466 and U36467）. The 18S rRNA of P. vivax clustered with A-type 18S rRNA from Thailand （U07367）, but was distantly related with the C-type 18S rRNA from Thailand（U07368）. Conclusion Nested PCR revealed mixed infection in 57 samples among those identified with single infection by microscopy. There is no significant difference in 18S rRNA sequence in seven counties/cities in Yunnan Province.

Key words: Plasmodium falciparum, Plasmodium vivax, 18S rRNA gene, Nested PCR, Phylogenetic analysis