Objective To analyze the effective reproduction number (Re) of HIV⁃1 main epidemic strains in Shenzhen by using system dynamics method. Methods HIV⁃1 gene sequence of new reports of HIV infected individuals in Shenzhen from 2005 to 2019 was downloaded from the HIV Sequence Database. After sorting out the sequence and determining the subtype, the HIV Gene Sequences Database was employed to perform clustering and grouping. The TempEst v1.5.3 software was used to perform linear regression analysis of genetic evolution and time after the construction of maximum likelihood tree for the grouped sequence sets of various subtypes subclusters. The BEAST v2.6.3 software was run to perform system dynamics analysis and calculate Re. Results (1) A total of 6619 sequences were enrolled finally to perform analysis, therein there were 2390 CRF01_AE subtype sequences, 2886 CRF07_BC subtype sequences, 983 CRF55_01B subtype sequences, 294 CRF08_BC subtype sequences, and 66 CRF59_01B subtype sequences. (2) The results of Re average value calculation revealed that among CRF01_AE, CRF07_BC, and CRF55_01B subtypes, the highest Re average value went to CRF01_AE_C1⁃1 (1.357), CRF07_BC_N⁃14 (1.553), and CRF55_01B_C1 (1.464), respectively; furthermore, CRF08_BC and CRF59_01B subtypes exerted relatively high Re average values of 1.511 and 1.574, respectively. (3) The results of dynamic Re calculation indicated that the Re values of various CRF01_AE subclusters subgroups exhibited an overall downward trend, and the value of Re fluctuated around 1 after 2010. The Re values of CRF59_01B and CRF55_01B demonstrated an upward trend after 2018, and were more than 1. In 2019, 10 subgroups of CRF07_BC and CRF08_BC expressed Re value >1. Conclusion The transmission ability of different subtypes of HIV⁃1 in Shenzhen is different. It is necessary to focus on monitoring the epidemic dynamics of HIV⁃1 strains with Re>1 to guide the precise prevention and control of HIV⁃1.

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