{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T18:45:10Z","timestamp":1785437110076,"version":"3.56.0"},"posted":{"date-parts":[[2026,6,1]]},"group-title":"Genomics","reference-count":37,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"award":["K01AI153544"],"award-info":[{"award-number":["K01AI153544"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>\n                    Within host diversity (WHD) in\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    is increasingly used to infer transmission and treatment response, but it lies at low allele frequencies where sequencing error and reference mapping artifact can be mistaken for signal.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>In a cohort in Accra, Ghana, we measured WHD using deep short read whole genome sequencing and LoFreq with a depth-conditional detection limit and an artifact-aware mask and assessed reproducibility using within-patient biological replicates.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Findings<\/jats:title>\n                  <jats:p>\n                    Among 83 single strain infections, about a fifth of called variants were recurrent artifact, and the corrected WHD burden was modest (median 16 variants per patient). WHD was higher in\n                    <jats:italic>M. africanum<\/jats:italic>\n                    than in lineage 4 (median 26 versus 14; p = 0.002) and was not explained by host or clinical features. Over the first two months of treatment the within host bacterial population drifted and cleared without detectable positive selection. Patients with an unfavorable two-month outcome carried higher baseline WHD (median 20.5 versus 14.0; p = 0.014). Shared within host variants did not mark transmission, and a single sputum undercaptured diversity.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Interpretation<\/jats:title>\n                  <jats:p>WHD in early treatment is modest, lineage-patterned, and drift-dominated, and reading it for clinical or epidemiological signal depends first on measuring it defensibly.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Research in context<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Evidence before this study<\/jats:title>\n                    <jats:p>\n                      We searched PubMed, Semantic Scholar, and Scopus (via Consensus) through July 2026 for within-host\n                      <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                      diversity, using terms combining \u201cwithin-host \/ minority \/ intra-host variants\u201d, \u201csequencing error \/ artifact\u201d, \u201ctransmission\u201d, \u201ctreatment outcome\u201d, and \u201c\n                      <jats:italic>M. africanum<\/jats:italic>\n                      \/ West Africa\u201d. Within-host\n                      <jats:italic>M. tuberculosis<\/jats:italic>\n                      diversity is real but small and inconsistently measured, and low frequency calls are strongly shaped by sequencing and mapping artifact[1\u20135]. Shared minority variants have been proposed to sharpen transmission inference[1], while baseline diversity has not predicted treatment outcome[6]. Artifact-aware within-host data that include\n                      <jats:italic>M. africanum<\/jats:italic>\n                      , which causes a large share of West African tuberculosis, are lacking[7,8].\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Added value of this study<\/jats:title>\n                    <jats:p>\n                      Using a depth-conditional empirical limit of detection with a monomorphic site false positive check, we provide an artifact-aware within-host diversity measurement in a Ghanaian cohort: a modest burden (median 16 iSNVs) an\n                      <jats:italic>M. africanum<\/jats:italic>\n                      elevation, weak host association, no transmission signal, and marked single-sputum undercapture.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Implications of all the available evidence<\/jats:title>\n                    <jats:p>Within-host diversity holds public health promise as densely captured minority variants could refine transmission chain reconstruction, flag mixed infection, and surface emerging drug resistance earlier than consensus genomes allow. Realizing that promise requires sampling and measurement dense enough to recover the signal that single sputum specimens miss.<\/jats:p>\n                  <\/jats:sec>\n                <\/jats:sec>","DOI":"10.64898\/2026.05.27.727477","type":"posted-content","created":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T13:05:12Z","timestamp":1780319112000},"source":"Crossref","is-referenced-by-count":0,"title":["Within-host diversity of\n                  <i>Mycobacterium tuberculosis<\/i>\n                  : weak host association and no transmission signal in a Ghanaian cohort"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2120-6011","authenticated-orcid":false,"given":"Marie Nancy","family":"S\u00e9raphin","sequence":"first","affiliation":[{"name":"Department of Epidemiology, University of Florida, College of Public Health and Health Professions, College of Medicine, Gainesville, FL, USA"},{"name":"Department of Medicine, University of Florida, College of Medicine, Gainesville, FL, USA"},{"name":"Emerging Pathogens Institute, University of Florida, Gainesville, FL USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane Sandra","family":"Afriyie-Mensah","sequence":"additional","affiliation":[{"name":"Unit of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana"},{"name":"Department of Medicine, University of Ghana Medical School, Accra, Ghana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Asare-Baah","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, University of Florida, College of Public Health and Health Professions, College of Medicine, Gainesville, FL, USA"},{"name":"Department of Medicine, University of Florida, College of Medicine, Gainesville, FL, USA"},{"name":"Emerging Pathogens Institute, University of Florida, Gainesville, FL USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Chariker","sequence":"additional","affiliation":[{"name":"Kentucky INBRE Bioinformatics Core, University of Louisville School of Medicine, Louisville, Kentucky, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Domotey","sequence":"additional","affiliation":[{"name":"Unit of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ernest","family":"Kwarteng","sequence":"additional","affiliation":[{"name":"Unit of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magalie","family":"Zoungrana","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Florida, College of Medicine, Gainesville, FL, USA"},{"name":"Emerging Pathogens Institute, University of Florida, Gainesville, FL USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheila","family":"Mireku Appah","sequence":"additional","affiliation":[{"name":"Chest Clinic TB Laboratory, Unit of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Honesty Mensah","family":"Ganu","sequence":"additional","affiliation":[{"name":"Chest Clinic TB Laboratory, Unit of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael Amo","family":"Omari","sequence":"additional","affiliation":[{"name":"Chest Clinic TB Laboratory, Unit of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026072913350887000_2026.05.27.727477v2.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanmic.2024.06.003"},{"key":"2026072913350887000_2026.05.27.727477v2.2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000217"},{"key":"2026072913350887000_2026.05.27.727477v2.3","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00062-18"},{"key":"2026072913350887000_2026.05.27.727477v2.4","doi-asserted-by":"publisher","DOI":"10.1038\/s41437-020-00377-7"},{"key":"2026072913350887000_2026.05.27.727477v2.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2019.08.010"},{"key":"2026072913350887000_2026.05.27.727477v2.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2020.102747"},{"key":"2026072913350887000_2026.05.27.727477v2.7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0000744"},{"key":"2026072913350887000_2026.05.27.727477v2.8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0003370"},{"key":"2026072913350887000_2026.05.27.727477v2.9","unstructured":"World Health Organization. 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