27C. neoformans var. grubii (C. neoformans) is an environmentally acquired pathogen causing 181 000 28 HIV-associated deaths each year. We used whole genome sequencing (WGS) to characterise 699 29 isolates, primarily C. neoformans from HIV-infected patients, from 5 countries in Asia and Africa. We 30 found that 91% of our clinical isolates belonged to one of three highly clonal sub-clades of VNIa, 31 which we have termed VNIa-4, VNIa-5 and VNIa-93. Parsimony analysis revealed frequent, long 32 distance transmissions of C. neoformans; international transmissions took place on 13% of VNIa-4 33 branches, and intercontinental transmissions on 7% of VNIa-93 branches. The median length of 34 within sub-clade internal branches was 3-6 SNPs, while terminal branches were 44.5-77.5 SNPs. The 35 short median internal branches were partly driven by the large number (12-15% of internal 36 branches) of polytomies in the within-sub-clade trees. To simultaneously explain our observation of 37 no apparent molecular clock, short internal branches and frequent polytomies we hypothesise that 38 C. neoformans VNIa spends much of its time in the environment in a quiescent state, while, when it 39 is sampled, it has almost always undergone an extended period of growth. Infections with VNIa-93 40 were associated with a significantly reduced risk of death by 10 weeks compared with infections 41 with VNIa-4 (Hazard Ratio = 0.45, p = 0.003). We detected a recombination in the mitochondrial 42 sequence of VNIa-5, suggesting that mitochondria could be involved in the propensity of this sub-43 clade to infect HIV-uninfected patients. These data highlight the insight into the biology and 44 epidemiology of pathogenic fungi which can be gained from WGS data. 45 46 3