Approaches to diagnosis of respiratory tract infections. A diagnostic test that could identify patients before the onset of symptoms (but after exposure) who will later become ill would be an indispensible tool for guiding individual treatment decisions when antiviral supplies may be limited. Furthermore,Host Genomic Signatures Detect H1N1 Infectionthese early results may forecast epidemic/pandemic spread, potentially mitigating pandemic intensity [6]. Although previous studies with dengue, melioidosis, tuberculosis, candidiasis, and sepsis have focused on diagnosis in patients as they present with active disease [7,8,9,10,11,12], we utilized human influenza challenge cohorts with a defined inoculation event coupled with dense serial sampling to explore the ability of modern genomic and statistical techniques to accurately classify CASIN site individuals with multiple subtypes of influenza infection as early as possible following viral exposure. Through this method, we have demonstrated the potential for a robust host gene response signature in pre-symptomatic human infection and suggest the utility of this approach for detecting pandemic H1N1 infection in an acute care setting.Results Healthy Volunteers Demonstrate Variable Clinical Responses to Inoculation with Seasonal Influenza H1N1 and H3NFor the H1N1 challenge we inoculated 24 volunteers age 20?5 with influenza A (A/Brisbane/59/2007). Nine (38 ) of the 24 inoculated subjects developed symptoms consistent with viral upper respiratory infection with confirmed shedding of challenge virus (Fig. 1). This infection rate is similar to previous viral challenge studies [13], and occurs despite similar MedChemExpress ML-240 patient profiles, vaccination history, and baseline influenza hemagglutination and neutralization titers (Sup Tables s1 and s2). Subjects exhibited variability of time to initiation of symptoms as well as maximal severity of symptoms achieved (Fig. s1), but symptom onset began an average of 61.3 hours after inoculation (range 24?08 hrs, median 72 hrs). Subjects who became ill experienced maximal symptoms on average 102.7 hours after inoculation (range 60?20 hours, median 108 hrs). For symptomatic subjects, the average total 5 day symptom score was 19.7 (range 6?4) with an average daily peak of 7.4 (range 4?3, Table s3). For the H3N2 challenge (A/Wisconsin/67/2005) 23727046 reported previously [4,14], we inoculated 17 volunteers (mean age 27 years; range 22?1 years). For the 9 (53 ) symptomatic-infected subjects, symptom onset began earlier than in the H1N1 challenge(Fig. 1) at an average of 49.3 hours after inoculation (range 24?4 hours, median 48 hrs). Subjects who became ill experienced maximal symptoms on average 90.6 hours after inoculation (range 60 to 108 hours, median 96 hours). For these subjects the average total 5 day symptom score was 21.1 (range 6?3) with an average daily peak of 7.3 (range 2?3). For both challenge studies, only those individuals achieving both clear clinical and virologic endpoints were analyzed as true influenza `infection’ (see Methods, Table s3). In our challenge studies there were four major outcome groups despite historical and immunologic screening and similar inoculations [13]. Most individuals fall within our two 
analysis groups ?those who are symptomatic-infected or asymptomatic-uninfected. However, a few individuals demonstrate mixed phenotypes and are either symptomatic-uninfected (symptoms but no viral shedding detected, see Methods) or asymptomatic-infected individuals.Approaches to diagnosis of respiratory tract infections. A diagnostic test that could identify patients before the onset of symptoms (but after exposure) who will later become ill would be an indispensible tool for guiding individual treatment decisions when antiviral supplies may be limited. Furthermore,Host Genomic Signatures Detect H1N1 Infectionthese early results may forecast epidemic/pandemic spread, potentially mitigating pandemic intensity [6]. Although previous studies with dengue, melioidosis, tuberculosis, candidiasis, and sepsis have focused on diagnosis in patients as they present with active disease [7,8,9,10,11,12], we utilized human influenza challenge cohorts with a defined inoculation event coupled with dense serial sampling to explore the ability of modern genomic and statistical techniques to accurately classify individuals with multiple subtypes of influenza infection as early as possible following viral exposure. Through this method, we have demonstrated the potential for a robust host gene response signature in pre-symptomatic human infection and suggest the utility of this approach for detecting pandemic H1N1 infection in an acute care setting.Results Healthy Volunteers Demonstrate Variable Clinical Responses to Inoculation with Seasonal Influenza H1N1 and H3NFor the H1N1 challenge we inoculated 24 volunteers age 20?5 with influenza A (A/Brisbane/59/2007). Nine (38 ) of the 24 inoculated subjects developed symptoms consistent with viral upper respiratory infection with confirmed shedding of challenge virus (Fig. 1). This infection rate is similar to previous viral challenge studies [13], and occurs despite similar patient profiles, vaccination history, and baseline influenza hemagglutination and neutralization titers (Sup Tables s1 and s2). Subjects exhibited variability of time to initiation of symptoms as well as maximal severity of symptoms achieved (Fig. s1), but symptom onset began an average of 61.3 hours after inoculation (range 24?08 hrs, median 72 hrs). Subjects who became ill experienced maximal 
symptoms on average 102.7 hours after inoculation (range 60?20 hours, median 108 hrs). For symptomatic subjects, the average total 5 day symptom score was 19.7 (range 6?4) with an average daily peak of 7.4 (range 4?3, Table s3). For the H3N2 challenge (A/Wisconsin/67/2005) 23727046 reported previously [4,14], we inoculated 17 volunteers (mean age 27 years; range 22?1 years). For the 9 (53 ) symptomatic-infected subjects, symptom onset began earlier than in the H1N1 challenge(Fig. 1) at an average of 49.3 hours after inoculation (range 24?4 hours, median 48 hrs). Subjects who became ill experienced maximal symptoms on average 90.6 hours after inoculation (range 60 to 108 hours, median 96 hours). For these subjects the average total 5 day symptom score was 21.1 (range 6?3) with an average daily peak of 7.3 (range 2?3). For both challenge studies, only those individuals achieving both clear clinical and virologic endpoints were analyzed as true influenza `infection’ (see Methods, Table s3). In our challenge studies there were four major outcome groups despite historical and immunologic screening and similar inoculations [13]. Most individuals fall within our two analysis groups ?those who are symptomatic-infected or asymptomatic-uninfected. However, a few individuals demonstrate mixed phenotypes and are either symptomatic-uninfected (symptoms but no viral shedding detected, see Methods) or asymptomatic-infected individuals.
