Local population structure and patterns of Western Hemisphere dispersal for<i>Coccidioides spp</i>., the fungal cause of Valley Fever

Engelthaler, David M.; Roe, Chandler C.; Litvintseva, Anastasia P.; Driebe, Elizabeth M.; Schupp, James M.; Gade, Lalitha; Waddell, Victor; Komatsu, Kenneth; Arathoon, Eduardo; Logemann, Heidi; Thompson, George R.; Chiller, Tom; Barker, Bridget; Keim, Paul

doi:10.1101/024778

Cited by 13 publications

(29 citation statements)

References 59 publications

(40 reference statements)

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“…Coccidioides posadasii was assigned to three populations: Arizona, Guatemala, and Mexico/Texas. Our results are generally consistent with the results of Engelthaler and co‐workers (), which used the software package BAPS in which we both find three populations of C. posadasii and assign similar individuals to similar populations. However, within populations, we observed a higher amount of shared ancestry from other populations.…”

Section: Resultssupporting

confidence: 91%

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Gene exchange between two divergent species of the fungal human pathogen,Coccidioides

et al. 2018

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The fungal genus Coccidioides is composed of two species, Coccidioides immitis and Coccidioides posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what is the expected size of shared haplotypes that might be inherited from the last common ancestor of the two species and find a cutoff to find what haplotypes have conclusively been exchanged between species. Finally, we precisely identified the breakpoints of the haplotypes that have crossed the species boundary and measure the allele frequency of each introgression in this sample. We find that introgressions are not uniformly distributed across the genome. Most, but not all, of the introgressions segregate at low frequency. Our results show that divergent species can share alleles, that species boundaries can be porous, and highlight the need for a systematic exploration of gene exchange in fungal species.

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Section: Resultssupporting

confidence: 91%

“…We only included genomes with paired-end reads from Illumina technology (MiSeq, HiSeq 2500, or Genome Analyzer). Using this filter, we obtained 51 C. posadasii genomes and 27 C. immitis genomes from two previous studies (Litvintseva et al 2014;Engelthaler et al 2016). The geographic provenance of these isolates is shown in Fig.…”

Section: Population Genomic Datamentioning

confidence: 99%

Gene exchange between two divergent species of the fungal human pathogen,Coccidioides

et al. 2018

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“…These studies helped to elucidate the deserts of Southern Arizona and the Central Valley of California as the primary areas of endemicity. Interestingly, these areas are populated distinctly by two separate species, C. posadasii and C. immitis [4]. The San Joaquin Valley region is the primary endemic region for C. immitis, which is found in Central and Southern California and Washington [11].…”

Section: Geographic Distributionmentioning

confidence: 99%

“…Serious, life-threatening complications are often the result of dissemination which frequently manifests as disease of the skin, bone, or central nervous system [1,2]. Two genetically distinct species, Coccidioides immitis and Coccidioides posadasii, lead to clinically indistinct diseases, often discerned only by the geographic location of acquisition [3][4][5]. This article reviews the epidemiology of Coccidioides spp.…”

Section: Introductionmentioning

confidence: 99%

Update on the Epidemiology of Coccidioidomycosis

Stewart

Thompson

2016

Curr Fungal Infect Rep

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Coccidioidomycosis is an illness caused by the soildwelling, dimorphic fungi, Coccidioides immitis and Coccidioides posadasii, which are found primarily in niche ecological zones of the Western Hemisphere. The bulk of infections due to Coccidioides are found within the endemic areas of Arizona, California, Mexico, and Central America. Outcomes run the gamut from asymptomatic to a self-limited or even chronic pulmonary process, up to severe disseminated, and life-threatening disease. Patients at particular risk include the elderly, pregnant women, and members of certain ethnicities. Recent changes in the epidemiology and our overall understanding of coccidioidomycosis that pose a particular challenge to healthcare professionals include the rising incidence of disease, identification of infections thought to be acquired outside the previously described zones of endemicity, and the risks posed to the immunosuppressed population due to the increasing use of immunomodulatory pharmaceutical agents.

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“…The two etiological agents of coccidioidomycosis, C. immitis and C. posadasii , are two sibling species that diverged about 5 million years ago (21). The species are thought to be phenotypically similar but some key differences have been reported.…”

Section: Introductionmentioning

confidence: 99%

Strong population structure in Venezuelan populations ofCoccidioides posadasii

Teixeira

Alvarado

Roe

et al. 2019

Preprint

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28Coccidioides posadasii is a pathogenic fungus that causes coccidioidomycosis in many arid regions of 29 the Americas. One of these regions is bordered by the Caribbean Sea, and the surrounding 30 landscape may play an important role in the dispersion of C. posadasii across South America 31 through southeastern Mexico, Honduras, Guatemala and Venezuela. Comparative phylogenomic 32 analyses of C. posadasii reveal that clinical strains from Venezuela are genetically distinct from the 33 North American populations found in Arizona (AZ), Texas, Mexico, and the rest of South America 34 (TX/MX/SA). We find evidence for admixture between the Venezuela and the North American 35 populations of C. posadasii in Central America. As expected, the proportion of Venezuelan alleles in 36 the admixed population decreases as latitude (and distance from Venezuela) increases. Our results 37 indicate that the population in Venezuela may have been subjected to a recent bottleneck, and 38shows strong population structure. This analysis provides insight into potential for Coccidioides 39 spp. to invade new regions. 40

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Local population structure and patterns of Western Hemisphere dispersal forCoccidioides spp., the fungal cause of Valley Fever

Cited by 13 publications

References 59 publications

Gene exchange between two divergent species of the fungal human pathogen,Coccidioides

Gene exchange between two divergent species of the fungal human pathogen,Coccidioides

Update on the Epidemiology of Coccidioidomycosis

Strong population structure in Venezuelan populations ofCoccidioides posadasii

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