Multivariate longitudinal count data arise in biological studies, where responses may be over-dispersed, correlated within subjects and over time, measured at irregular times, and exhibit unobserved subgroup structure. Our goal was to develop a model that can accommodate over-dispersion, longitudinal dependence, cross-outcome dependence, covariate effects, irregular observation times, and covariate-dependent latent-class membership. We propose a latent-class Poisson-lognormal mixed model for clustering heterogeneous multivariate count trajectories. Estimation is performed using a variational EM algorithm designed for scalable inference. Simulation studies show accurate parameter estimation, strong latent-class recovery, and reliable selection of the number of classes, as compared to state-of-the-art approaches. We also applied the proposed approach to longitudinal neutrophil RNA-seq data from hospitalized COVID-19 patients as an illustration. The proposed framework provides a flexible approach for clustering complex longitudinal biological count data. Implementation code is available at https://github.com/PengqiLiu-Mc/latent-class-mpln-mixed-models.

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