Emergence of two new lineages of the cosmopolitan dengue virus serotype 2 in Yunnan, China, 2024.

Abstract

BACKGROUND Dengue fever has become a significant epidemic in South and Southeast Asia. Recently, Yunnan Province in southwestern China, which borders these regions, has also experienced a significant outbreak. This study aims to investigate the genetic diversity of the dengue virus (DENV) and identify potential sources of transmission in Xishuangbanna, Yunnan Province in 2024. METHODS In 2024, we investigated 321 suspected cases of dengue fever in Yunnan Province. We screened dengue fever patients using a combination of DENV NS1 antigen and Pan-qPCR methods, and performed serotype typing using specific qPCR. We also performed phylogenetic and molecular clock analyses to understand the genotypes and transmission sources. RESULTS DENV infection was detected in 101 of 321 specimens. Serotype and genotype analysis were performed on 88 of the 98 positive samples. The results showed that 81 cases belonged to the cosmopolitan genotype and cosmopolitan_asian-pacific subtype of DENV serotype 2 (DENV-2), while only 1 case was classified as genotype I and subtype 1L of DENV serotype 1 (DENV-1). Notably, samples within the cosmopolitan_asian-pacific subtype were primarily divided into two distinct lineages. Further analysis of whole genome sequences, focusing on phylogenetic history and spatiotemporal dynamics, indicated that lineage-1 likely originated in Thailand, while lineage-2 may have originated in Cambodia. In addition, we analyzed all available DENV-2 sequences from Yunnan in the GenBank database and found that DENV-2 genotypes in the Xishuangbanna region were more diverse and complex. CONCLUSIONS This study identifies two new lineages of cosmopolitan DENV-2 in Yunnan, originating from Thailand and Cambodia, respectively.