Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine

Yun, Heather C.; Young, Adam N.; Caballero, Manuel Y.; Lott, Lisa; Cropper, Thomas L.; Murray, Clinton K.

Specimen processing was performed as previously described [17] . Respiratory specimens were characterized daily by PCR on Applied Biosystems (ABI) 7500 and 7900HTFast (Applied Biosystems, CA) and the ViiA 7 real-time PCR systems. Specimens were tested for Ad ( panAd and serotypes 4, 7, 14, 3, 11, 21, 2, and 5); rhinovirus; influenza A, including H1 and H3; influenza B, enterovirus, human coronaviruses OC43 and 229E, bocavirus, human metapneumovirus (HMPV), parainfluenza virus type 3 (HPIV), S pyogenes, Streptococcus pneumoniae, Mycoplasma pneumoniae, and Chlamydophila pneumoniae. All primer and probe sequences used have been previously reported (Association of Public Health Laboratories guidelines for realtime reverse transcription-PCR assays of influenza respiratory viruses; non-influenza respiratory viruses from clinical respiratory specimens; respiratory bacterial pathogens) [18, 19] . Influenza A and B, enterovirus and rhinovirus thermocycling conditions were 30 minutes at 50°C, 10 minutes at 95°C, followed by 15 seconds at 95°C and 35 seconds at 60°C for 45×. Coronaviruses, HMPV, and HPIV thermocycling conditions were 10 minutes at 48°C, 10 minutes at 95°C, followed by 15 seconds at 95°C and 1 minute at 60°C for 45×. Streptococcus pneumoniae, S pyogenes, and bocavirus thermocyling conditions were 10 minutes at 95°C followed by 15 seconds at 95°C and 45 seconds at 60°C for 45×. Thermocycling conditions for M pneumoniae and C pneumoniae were 2 minutes at 50°C, 10 minutes at 95°C, followed by 15 seconds at 95°C and 1 minute at 60°C for 40×.