The origin and transmission of HIV-1 CRF80_0107 among two major first-tier cities in China

Background: CRF01_AE and CRF07_BC are the two most prevalent HIV-1 genotypes in China, and the co-circulation of these two genotypes has led to the continuous generation of CRF_0107 viruses in recent years. However, little is known about the origin and spread of CRF_0107 viruses thus far. This study focused on HIV-1 CRF80_0107, which we previously identified among the MSM population in Beijing and Hebei Province, to explore the demographic distribution, transmission links, and temporal-spatial evolutionary features of the HIV-1 CRF80_0107 strain in China.

Methods: With the partial pol region fragment of the HIV-1 CRF80_0107 subtype standard sequence as a reference, BLAST was used to search for highly similar sequences in the Los Alamos HIV Sequence Database, followed by preliminary subtype identification via COMET. Further phylogenetic and recombination breakpoint analyses were conducted to verify the subtypes and recombination patterns. We also performed a distance-based molecular network analysis to identify potential relationships among different HIV-positive individuals. In addition, spatiotemporal evolutionary dynamics analysis of the candidate CRF80_0107 sequences was performed via a Bayesian approach.

Results: A total of 36 partial pol gene sequences of HIV-1 CRF80_0107 were identified from 2009 to 2018 from 5 provinces in China. Phylogenetic and spatial-temporal dynamics analyses indicated that CRF80_0107 likely originated in Beijing around 2009 and spread to Guangdong Province around 2012. Population dynamics analysis revealed that CRF80_0107 experienced a significant increase in population size from 2009 to 2011 and then stabilized. The study also found that the number of cases in Guangdong Province was second only to that in Beijing and formed 2 relatively independent transmission clusters in the MSM population in Shenzhen, Guangdong Province.

Conclusions: The HIV-1 CRF80_0107 strain has spread to cities beyond its origin, particularly the MSM population in Shenzhen city, Guangdong Province, which is an area with a high incidence of HIV. This highlights the importance of continuous monitoring for the emergence and dynamic changes of novel HIV-1 recombinant viruses and the necessity of implementing effective preventive measures targeting specific populations in particular regions.