Longitudinal characterization of mixed-genotype SARS-CoV-2 infections in a military cohort reveals compartmentalized viral populations
{"Mixed-genotype":[0],"severe":[1,182],"acute":[2,183],"respiratory":[3,184],"syndrome":[4,185],"coronavirus":[5,186],"2":[6,187],"(SARS-CoV-2)":[7,188],"infections":[8,197,300],"are":[9,198],"a":[10,127,216,244,272,280],"concern":[11],"due":[12],"to":[13,23,94,100,113,144,204,229,321,328],"the":[14,39,107,162,333],"potential":[15,308],"generation":[16],"of":[17,49,109,164,181,268,277,288,294,335],"novel":[18],"recombinants":[19,180],"that":[20,121,246],"give":[21],"rise":[22],"new":[24],"variants.":[25],"To":[26,233],"better":[27],"understand":[28],"intra-host":[29,231],"viral":[30],"dynamics,":[31],"we":[32,69,152,242],"analyzed":[33,215],"specimens":[34,221],"from":[35,38,102,148,156,190,222,237],"24":[36,66],"participants":[37],"U.S.":[40],"Military":[41],"Health":[42],"System's":[43],"Epidemiology,":[44],"Immunology,":[45],"and":[46,75,89,116,169,207,255,279,291,301,314,331],"Clinical":[47],"Characteristics":[48],"Emerging":[50],"Infectious":[51],"Diseases":[52],"with":[53,58,192,220,240,257],"Pandemic":[54],"Potential":[55],"COVID-19":[56],"cohort":[57],"suspected":[59,67],"mixed-genotype":[60,97],"SARS-CoV-2":[61,296],"infections.":[62,98,177],"From":[63],"an":[64,140,227],"initial":[65],"cases,":[68,151],"confirmed":[70],"17":[71],"as":[72,130,132],"genuine":[73,154],"coinfections":[74,155,191],"graded":[76],"them":[77],"by":[78,126,252],"evidence:":[79],"7":[80,90],"were":[81,84,87,91],"\\"strong\\";":[82],"4":[83],"\\"moderate\\";":[85],"6":[86],"\\"weak\\";":[88],"deemed":[92],"unlikely":[93],"be":[95],"true":[96,235,304],"Access":[99],"swabs":[101],"multiple":[103,223],"body":[104,224],"sites":[105],"across":[106],"course":[108],"infection":[110,306],"allowed":[111,263],"us":[112],"observe":[114],"compartmentalization":[115,278],"shifts":[117],"in":[118,173,324],"variant":[119,260],"dominance":[120],"would":[122],"have":[123],"been":[124],"missed":[125],"single-timepoint":[128],"analysis,":[129],"well":[131],"one":[133],"recombinant":[134,281],"Omicron":[135],"BA.1/BA.2":[136],"genome.":[137],"By":[138],"using":[139],"evidence-based":[141],"bioinformatic":[142,157,171,238],"framework":[143,245],"assess":[145,230],"sequencing":[146],"data":[147,218],"well-characterized":[149],"clinical":[150,292],"distinguished":[153],"artifacts.":[158],"Our":[159],"findings":[160],"emphasize":[161],"importance":[163],"both":[165],"extensive":[166],"specimen":[167],"collection":[168],"careful":[170],"approaches":[172],"ascertaining":[174],"dual":[175],"genotype":[176],"IMPORTANCE:":[178],"Novel":[179],"arise":[189],"different":[193],"lineages,":[194],"but":[195],"mixed":[196,250,269,295],"not":[199],"screened":[200],"for":[201,249,332],"despite":[202],"risk":[203],"public":[205,312],"health,":[206],"most":[208],"surveillance":[209],"relies":[210],"on":[211],"single":[212,273],"swabs.":[213],"We":[214],"longitudinal":[217],"set":[219],"sites,":[225],"providing":[226],"opportunity":[228],"dynamics.":[232],"distinguish":[234],"coinfection":[236],"artifacts":[239,310],"confidence,":[241],"applied":[243],"grades":[247],"evidence":[248,320],"genotypes":[251,270],"incorporating":[253],"lineage":[254],"clade":[256],"manually":[258],"validated":[259],"calls.":[261],"This":[262,283],"investigation":[264],"beyond":[265],"abundance":[266],"levels":[267],"within":[271],"specimen,":[274],"including":[275],"observations":[276],"virus.":[282],"work":[284],"enables":[285],"further":[286],"study":[287],"evolutionary,":[289],"immunological,":[290],"implications":[293],"genotypes.":[297],"Detecting":[298],"dual-genotype":[299,305],"discriminating":[302],"between":[303],"vs":[307],"bioinformatics-based":[309],"support":[311],"health":[313],"military":[315],"readiness.":[316],"These":[317],"efforts":[318],"provide":[319],"bolster":[322],"decision-making":[323],"molecular":[325],"epidemiological":[326],"studies":[327],"track":[329],"transmission":[330],"choice":[334],"effective":[336],"countermeasures.":[337]}
Authors
- Brian K. Agan (ORCID: https://orcid.org/0000-0002-5114-1669)
- Kyle A. Long (ORCID: https://orcid.org/0009-0003-6426-3758)
- Stephanie A Richard (ORCID: https://orcid.org/0000-0002-0530-384X)
- Katrin Mende
- Anthony C Fries (ORCID: https://orcid.org/0000-0001-7556-1353)
- Bishwo N. Adhikari (ORCID: https://orcid.org/0000-0003-4840-9609)
- Logan J. Voegtly (ORCID: https://orcid.org/0000-0003-0580-3702)
- Mark P. Simons (ORCID: https://orcid.org/0000-0002-4316-9709)
- Robin H. Miller (ORCID: https://orcid.org/0000-0001-6279-6401)
- Kimberly A. Bishop‐Lilly (ORCID: https://orcid.org/0000-0002-5744-8493)
- Adrian C. Paskey (ORCID: https://orcid.org/0000-0003-4575-3092)
- David R. Tribble (ORCID: https://orcid.org/0000-0003-3077-9505)
- Francisco Malagón (ORCID: https://orcid.org/0000-0002-8459-2802)
- J. Alexander Chitty (ORCID: https://orcid.org/0000-0002-7416-9226)
- Regina Z. Cer (ORCID: https://orcid.org/0000-0002-2395-980X)
- Charlotte Lanteri
- Simon D. Pollett
- Timothy H. Burgess
- Haven Miner
Institutions
- Leidos (United States) (US)
- Henry M. Jackson Foundation (US)
- Naval Medical Research Command (US)
- Defense Threat Reduction Agency (US)
- Uniformed Services University of the Health Sciences (US)
- United States Air Force (US)
- Joint Base San Antonio (US)
Publication Details
- Journal
- Microbiology Spectrum
- Published
- 2026-09-14
- DOI
- https://doi.org/10.1128/spectrum.01806-26
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00