Prevalence and genetic variation of salivary gland hypertrophy virus in wild populations of the tsetse fly Glossina pallidipes from southern and eastern Africa

► Prevalence of GpSGHV showed significant variations in Glossina pallidipes wild populations. ► Twenty-one synonymous and six non-synonymous SNPs were detected in five GpSGHV putative ORFs. ► Low genetic diversity and random distribution was observed among 23 GpSGHV haplotypes. ► Molecular-based strategies can be widely used to manage the GpSGHV in tsetse fly colonies.