Heterogeneity in the response of different subtypes of Drosophila melanogaster midgut cells to viral infections

This article belongs to the Section Viral Immunology, Vaccines, and Antivirals.Single-cell RNA sequencing (scRNA-seq) offers the possibility to monitor both host and pathogens transcriptomes at the cellular level. Here, public scRNA-seq datasets from Drosophila melanogaster midgut cells were used to compare the differences in replication strategy and cellular responses between two fly picorna-like viruses, Thika virus (TV) and D. melanogaster Nora virus (DMelNV). TV exhibited lower levels of viral RNA accumulation but infected a higher number of cells compared to DMelNV. In both cases, viral RNA accumulation varied according to cell subtype. The cellular heat shock response to TV and DMelNV infection was cell-subtype- and virus-specific. Disruption of bottleneck genes at later stages of infection in the systemic response, as well as of translation-related genes in the cellular response to DMelNV in two cell subtypes, may affect the virus replication.This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (CAPES)—Finance Code 001 to J.M.F.S., Generalitat Valenciana grant PROMETEO2019/012, CSIC grant PIE202020E94 and Spain Agencia Estatal de Investigación—FEDER grant PID2019-103998GB-I00 to S.F.E., T.N. and F.L.M. received a PQ-fellowship from CNPq.Peer reviewe