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Chapter 6 : Specimen Requirements Selection, Collection, Transport, and Processing

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Abstract:

Proper specimen collection is essential for interpreting test results because of the wide range of viruses, the complexity of virus–host interactions, and changes in testing methodology. Some viruses are part of our normal flora and cause no symptoms. Others, such as human herpes virus 6 (HHV-6), can integrate into germ line cells and be transmitted vertically to children (1, 2). Chronic, suppressed, or latent viruses like human immunodeficiency virus (HIV) or BK virus (BKV) can be reactivated to cause transient, low-level viremia that may or may not need clinical attention (3, 4). Asymptomatic shedding can also result in detection of virions for long periods of time (5–7). In order to recognize and interpret infectious episodes, it is crucial for diagnostic laboratories to receive appropriate specimens for viral testing.

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
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References

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1. Popgeorgiev N, Temmam S, Raoult D, Desnues C . 2013. Describing the silent human virome with an emphasis on giant viruses. Intervirology 56 : 395 412.[PubMed]
2. Arbuckle JH, Medveczky MM, Luka J, Hadley SH, Luegmayr A, Ablashi D, Lund TC, Tolar J, De Meirleir K, Montoya JG, Komaroff AL, Ambros PF, Medveczky PG . 2010. The latent human herpesvirus-6A genome specifically integrates in telomeres of human chromosomes in vivo and in vitro. Proc Natl Acad Sci USA 107 : 5563 5568.[PubMed]
3. Razonable RR, Brown RA, Humar A, Covington E, Alecock E, Paya CV PV16000 Study Group . 2005. A longitudinal molecular surveillance study of human polyomavirus viremia in heart, kidney, liver, and pancreas transplant patients. J Infect Dis 192 : 1349 1354.[PubMed]
4. Jones LE, Perelson AS . 2005. Opportunistic infection as a cause of transient viremia in chronically infected HIV patients under treatment with HAART. Bull Math Biol 67 : 1227 1251.[PubMed]
5. Kalu SU, Loeffelholz M, Beck E, Patel JA, Revai K, Fan J, Henrickson KJ, Chonmaitree T . 2010. Persistence of adenovirus nucleic acids in nasopharyngeal secretions: a diagnostic conundrum. Pediatr Infect Dis J 29 : 746 750.[PubMed]
6. Mark KE, Wald A, Magaret AS, Selke S, Olin L, Huang ML, Corey L . 2008. Rapidly cleared episodes of herpes simplex virus reactivation in immunocompetent adults. J Infect Dis 198 : 1141 1149.[PubMed]
7. Tronstein E, Johnston C, Huang ML, Selke S, Magaret A, Warren T, Corey L, Wald A . 2011. Genital shedding of herpes simplex virus among symptomatic and asymptomatic persons with HSV-2 infection. JAMA 305 : 1441 1449.[PubMed]
8. Yap G, Pok KY, Lai YL, Hapuarachchi HC, Chow A, Leo YS, Tan LK, Ng LC . 2010. Evaluation of Chikungunya diagnostic assays: differences in sensitivity of serology assays in two independent outbreaks. PLoS Negl Trop Dis 4 : e753.[PubMed]
9. Dries V, von Both I, Müller M, Gerken G, Schirmacher P, Odenthal M, Bartenschlager R, Drebber U, Meyer zum Büschenfeld KH, Dienes HP . 1999. Detection of hepatitis C virus in paraffin-embedded liver biopsies of patients negative for viral RNA in serum. Hepatology 29 : 223 229.[PubMed]
10. Von Müller L, Hampl W, Hinz J, Meisel H, Reip A, Engelmann E, Heilbronn R, Gärtner B, Krämer O, Einsele H, Hebart H, Ljubicic T, Löffler J, Mertens T . 2002. High variability between results of different in-house tests for cytomegalovirus (CMV) monitoring and a standardized quantitative plasma CMV PCR assay. J Clin Microbiol 40 : 2285 2287.[PubMed]
11. Hayden RT, Yan X, Wick MT, Rodriguez AB, Xiong X, Ginocchio CC, Mitchell MJ, Caliendo AM College of American Pathologists Microbiology Resource Committee . 2012. Factors contributing to variability of quantitative viral PCR results in proficiency testing samples: a multivariate analysis. J Clin Microbiol 50 : 337 345.[PubMed]
12. Madej RM, Davis J, Holden MJ, Kwang S, Labourier E, Schneider GJ . 2010. International standards and reference materials for quantitative molecular infectious disease testing. J Mol Diagn 12 : 133 143.[PubMed]
13. Popowitch EB, O'Neill SS, Miller MB . 2013. Comparison of the Biofire FilmArray RP, Genmark eSensor RVP, Luminex xTAG RVPv1, and Luminex xTAG RVP fast multiplex assays for detection of respiratory viruses. J Clin Microbiol 51 : 1528 1533.[PubMed]
14. Moscicki AB, Shiboski S, Hills NK, Powell KJ, Jay N, Hanson EN, Miller S, Canjura-Clayton KL, Farhat S, Broering JM, Darragh TM . 2004. Regression of low-grade squamous intra-epithelial lesions in young women. Lancet 364 : 1678 1683.[PubMed]
15. Saslow D, Solomon D, Lawson HW, Killackey M, Kulasingam SL, Cain JM, Garcia FA, Moriarty AT, Waxman AG, Wilbur DC, Wentzensen N, Downs LS Jr, Spitzer M, Moscicki AB, Franco EL, Stoler MH, Schiffman M, Castle PE, Myers ER, Chelmow D, Herzig A, Kim JJ, Kinney W, Herschel WL, Waldman J . 2012. American Cancer Society, American Society for Colposcopy and Cervical Pathology, and American Society for Clinical Pathology screening guidelines for the prevention and early detection of cervical cancer. J Low Genit Tract Dis 16 : 175 204.[PubMed]
16. Halperin SA, Shehab Z, Thacker D, Hendley JO . 1983. Absence of viremia in primary herpetic gingivostomatitis. Pediatr Infect Dis 2 : 452 453.[PubMed]
17. Harel L, Smetana Z, Prais D, Book M, Alkin M, Supaev E, Mendelson E, Amir J . 2004. Presence of viremia in patients with primary herpetic gingivostomatitis. Clin Infect Dis 39 : 636 640.[PubMed]
18. Zuckerman RA . 2009. The clinical spectrum of herpes simplex viremia. Clin Infect Dis 49 : 1302 1304.[PubMed]
19. Malm G, Forsgren M . 1999. Neonatal herpes simplex virus infections: HSV DNA in cerebrospinal fluid and serum. Arch Dis Child Fetal Neonatal Ed 81 : F24 F29.[PubMed]
20. Kimura H, Futamura M, Kito H, Ando T, Goto M, Kuzushima K, Shibata M, Morishima T . 1991. Detection of viral DNA in neonatal herpes simplex virus infections: frequent and prolonged presence in serum and cerebrospinal fluid. J Infect Dis 164 : 289 293.[PubMed]
21. Benedetti J, Corey L, Ashley R . 1994. Recurrence rates in genital herpes after symptomatic first-episode infection. Ann Intern Med 121 : 847 854.[PubMed]
22. Corey L, Wald A, Patel R, Sacks SL, Tyring SK, Warren T, Douglas JM Jr, Paavonen J, Morrow RA, Beutner KR, Stratchounsky LS, Mertz G, Keene ON, Watson HA, Tait D, Vargas-Cortes M Valacyclovir HSV Transmission Study Group . 2004. Once-daily valacyclovir to reduce the risk of transmission of genital herpes. N Engl J Med 350 : 11 20.[PubMed]
23. Berrington WR, Jerome KR, Cook L, Wald A, Corey L, Casper C . 2009. Clinical correlates of herpes simplex virus viremia among hospitalized adults. Clin Infect Dis 49 : 1295 1301.[PubMed]
24. MacCannell T, Umscheid CA, Agarwal RK, Lee I, Kuntz G, Stevenson KB . 2011. Guideline for the prevention and control of norovirus gastroenteritis outbreaks in healthcare settings. Infect Control Hospital Epidemiol 32 : 939- 969.
25. Frange P, Touzot F, Debré M, Héritier S, Leruez-Ville M, Cros G, Rouzioux C, Blanche S, Fischer A, Avettand-Fenoël V . 2012. Prevalence and clinical impact of norovirus fecal shedding in children with inherited immune deficiencies. J Infect Dis 206 : 1269 1274.[PubMed]
26. Sukhrie FH, Teunis P, Vennema H, Copra C, Thijs Beersma MF, Bogerman J, Koopmans M . 2012. Nosocomial transmission of norovirus is mainly caused by symptomatic cases. Clin Infect Dis 54 : 931 937.[PubMed]
27. Sawinski D, Goral S . 2014. BK virus infection: an update on diagnosis and treatment. Nephrol Dial Transplant.[PubMed]
28. Egli A, Infanti L, Dumoulin A, Buser A, Samaridis J, Stebler C, Gosert R, Hirsch HH . 2009. Prevalence of polyomavirus BK and JC infection and replication in 400 healthy blood donors. J Infect Dis 199 : 837 846.[PubMed]
29. Costa C, Cavallo R . 2012. Polyomavirus-associated nephropathy. World J Transplant 2 : 84 94.[PubMed]
30. Drachenberg CB, Papadimitriou JC, Hirsch HH, Wali R, Crowder C, Nogueira J, Cangro CB, Mendley S, Mian A, Ramos E . 2004. Histological patterns of polyomavirus nephropathy: correlation with graft outcome and viral load. Am J Transplant 4 : 2082- 2092.
31. Behzad-Behbahani A, Klapper PE, Vallely PJ, Cleator GM, Khoo SH . 2004. Detection of BK virus and JC virus DNA in urine samples from immunocompromised (HIV-infected) and immunocompetent (HIV-non-infected) patients using polymerase chain reaction and microplate hybridisation. J Clin Virol 29 : 224- 229.
32. Randhawa P, Uhrmacher J, Pasculle W, Vats A, Shapiro R, Eghtsead B, Weck K . 2005. A comparative study of BK and JC virus infections in organ transplant recipients. J Med Virol 77 : 238 243.[PubMed]
33. Garces JC . 2010. BK virus-associated nephropathy in kidney transplant recipients. Ochsner J 10 : 245 249.[PubMed]
34. Campbell GL, Marfin AA, Lanciotti RS, Gubler DJ . 2002. West Nile virus. Lancet Infect Dis 2 : 519 529.[PubMed]
35. Tilley PA, Fox JD, Jayaraman GC, Preiksaitis JK . 2006. Nucleic acid testing for west nile virus RNA in plasma enhances rapid diagnosis of acute infection in symptomatic patients. J Infect Dis 193 : 1361 1364.[PubMed]
36. Tilley PA, Walle R, Chow A, Jayaraman GC, Fonseca K, Drebot MA, Preiksaitis J, Fox J . 2005. Clinical utility of commercial enzyme immunoassays during the inaugural season of West Nile virus activity, Alberta, Canada. J Clin Microbiol 43 : 4691 4695.[PubMed]
37. Leruez-Ville M, Vauloup-Fellous C, Couderc S, Parat S, Castel C, Avettand-Fenoel V, Guilleminot T, Grangeot-Keros L, Ville Y, Grabar S, Magny JF . 2011. Prospective identification of congenital cytomegalovirus infection in newborns using real-time polymerase chain reaction assays in dried blood spots. Clin Infect Dis 52 : 575 581.[PubMed]
38. Legrand F, Berrebi D, Houhou N, Freymuth F, Faye A, Duval M, Mougenot JF, Peuchmaur M, Vilmer E . 2001. Early diagnosis of adenovirus infection and treatment with cidofovir after bone marrow transplantation in children. Bone Marrow Transplant 27 : 621 626.[PubMed]
39. Allard A, Albinsson B, Wadell G . 1992. Detection of adenoviruses in stools from healthy persons and patients with diarrhea by two-step polymerase chain reaction. J Med Virol 37 : 149 157.[PubMed]
40. Stránská R, Schuurman R, de Vos M, van Loon AM . 2004. Routine use of a highly automated and internally controlled real-time PCR assay for the diagnosis of herpes simplex and varicella-zoster virus infections. J Clin Virol 30 : 39 44.[PubMed]
41. Rübben A, Baron JM, Grussendorf-Conen EI . 1997. Routine detection of herpes simplex virus and varicella zoster virus by polymerase chain reaction reveals that initial herpes zoster is frequently misdiagnosed as herpes simplex. Br J Dermatol 137 : 259 261.[PubMed]
42. Johnson G, Nelson S, Petric M, Tellier R . 2000. Comprehensive PCR-based assay for detection and species identification of human herpesviruses. J Clin Microbiol 38 : 3274 3279.[PubMed]
43. Lilie HM, Wassilew SW, Wolff MH . 2002. Early diagnosis of herpes zoster by polymerase chain reaction. J Eur Acad Dermatol Venereol 16 : 53 57.[PubMed]
44. Espy MJ, Uhl JR, Sloan LM, Buckwalter SP, Jones MF, Vetter EA, Yao JD, Wengenack NL, Rosenblatt JE, Cockerill FR III, Smith TF . 2006. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin Microbiol Rev 19 : 165 256.[PubMed]
45. Hall CB, Long CE, Schnabel KC, Caserta MT, McIntyre KM, Costanzo MA, Knott A, Dewhurst S, Insel RA, Epstein LG . 1994. Human herpesvirus-6 infection in children. A prospective study of complications and reactivation. N Engl J Med 331 : 432 438.[PubMed]
46. De Bolle L, Naesens L, De Clercq E . 2005. Update on human herpesvirus 6 biology, clinical features, and therapy. Clin Microbiol Rev 18 : 217 245.[PubMed]
47. Campadelli-Fiume G, Mirandola P, Menotti L . 1999. Human herpesvirus 6: an emerging pathogen. Emerg Infect Dis 5 : 353 366.[PubMed]
48. Corti M, Villafañe MF, Trione N, Mamanna L, Bouzas B . 2011. Human herpesvirus 6: report of emerging pathogen in five patients with HIV/AIDS and review of the literature. Rev Soc Bras Med Trop 44 : 522 525.[PubMed]
49. Levy JA, Ferro F, Greenspan D, Lennette ET . 1990. Frequent isolation of HHV-6 from saliva and high seroprevalence of the virus in the population. Lancet 335 : 1047 1050.[PubMed]
50. Ghany MG, Strader DB, Thomas DL, Seeff LB American Association for the Study of Liver Diseases . 2009. Diagnosis, management, and treatment of hepatitis C: an update. Hepatology 49 : 1335 1374.[PubMed]
51. CDC . 2013. Testing for HCV infection: an update of guidance for clinicians and laboratorians. MMWR Morb Mortal Wkly Rep 62 : 362365.
52. Ghany MG, Nelson DR, Strader DB, Thomas DL, Seeff LB American Association for Study of Liver Diseases . 2011. An update on treatment of genotype 1 chronic hepatitis C virus infection: 2011 practice guideline by the American Association for the Study of Liver Diseases. Hepatology 54 : 1433 1444.[PubMed]
53. DeBiasi RL, Tyler KL . 2004. Molecular methods for diagnosis of viral encephalitis. Clin Microbiol Rev 17 : 903 925.[PubMed]
54. Peeling RW, Artsob H, Pelegrino JL, Buchy P, Cardosa MJ, Devi S, Enria DA, Farrar J, Gubler DJ, Guzman MG, Halstead SB, Hunsperger E, Kliks S, Margolis HS, Nathanson CM, Nguyen VC, Rizzo N, Vázquez S, Yoksan S . 2010. Evaluation of diagnostic tests: dengue. Nat Rev Microbiol 8( Suppl) : S30 S37.[PubMed]
55. Bag AK, Curé JK, Chapman PR, Roberson GH, Shah R . 2010. JC virus infection of the brain. AJNR Am J Neuroradiol 31 : 1564 1576.[PubMed]
56. Berger JR, Khalili K . 2011. The pathogenesis of progressive multifocal leukoencephalopathy. Discov Med 12 : 495 503.[PubMed]
57. Berger JR, Miller CS, Mootoor Y, Avdiushko SA, Kryscio RJ, Zhu H . 2006. JC virus detection in bodily fluids: clues to transmission. Clin Infect Dis 43 : e9 e12.[PubMed]
58. Garnett CT, Erdman D, Xu W, Gooding LR . 2002. Prevalence and quantitation of species C adenovirus DNA in human mucosal lymphocytes. J Virol 76 : 10608 10616.[PubMed]
59. Chung PW, Huang YC, Chang LY, Lin TY, Ning HC . 2001. Duration of enterovirus shedding in stool. J Microbiol Immunol Infect 34 : 167 170.[PubMed]
60. Cinek O, Witso E, Jeansson S, Rasmussen T, Drevinek P, Wetlesen T, Vavrinec J, Grinde B, Ronningen KS . 2006. Longitudinal observation of enterovirus and adenovirus in stool samples from Norwegian infants with the highest genetic risk of type 1 diabetes. J Clin Virol 35 : 33- 40.
61. Kupila L, Vuorinen T, Vainionpäā R, Marttila RJ, Kotilainen P . 2005. Diagnosis of enteroviral meningitis by use of polymerase chain reaction of cerebrospinal fluid, stool, and serum specimens. Clin Infect Dis 40 : 982 987.[PubMed]
62. Yamamoto N, Wakabayashi T, Murakami K, Hommura S . 2003. Detection of CMV DNA in the aqueous humor of AIDS patients with CMV retinitis by AMPLICOR CMV test. Ophthalmologica 217 : 45 48.[PubMed]
63. Ginocchio CC, Wang XP, Kaplan MH, Mulligan G, Witt D, Romano JW, Cronin M, Carroll R . 1997. Effects of specimen collection, processing, and storage conditions on stability of human immunodeficiency virus type 1 RNA levels in plasma. J Clin Microbiol 35 : 2886 2893.[PubMed]
64. Holodniy M, Kim S, Katzenstein D, Konrad M, Groves E, Merigan TC . 1991. Inhibition of human immunodeficiency virus gene amplification by heparin. J Clin Microbiol 29 : 676 679.[PubMed]
65. Jagodzinski LL, Weston HR, Liu Y, O'Connell RJ, Peel SA . 2012. Efficient quantification of HIV-1 in heparin plasma spiked with cultured HIV-1 by the Roche Cobas TaqMan and Abbott RealTime HIV-1 tests. J Clin Microbiol 50 : 2804 2806.[PubMed]
66. Forman MS, Valsamakis A, . 2011. Specimen collection, transport, and processing: virology, p 1276–1296. In Landry ML (ed), Manual of Clinical Microbiology, 10th ed, vol 2. ASM Press, Washington, D.C.
67. Levin MJ, Leventhal S, Masters HA . 1984. Factors influencing quantitative isolation of varicella-zoster virus. J Clin Microbiol 19 : 880 883.[PubMed]
68. Hernes SS, Quarsten H, Hagen E, Lyngroth AL, Pripp AH, Bjorvatn B, Bakke PS . 2011. Swabbing for respiratory viral infections in older patients: a comparison of rayon and nylon flocked swabs. Eur J Clin Microbiol Infect Dis 30 : 159- 165.
69. Daley P, Castriciano S, Chernesky M, Smieja M . 2006. Comparison of flocked and rayon swabs for collection of respiratory epithelial cells from uninfected volunteers and symptomatic patients. J Clin Microbiol 44 : 2265 2267.[PubMed]
70. Loeffelholz MJ, Pong DL, Pyles RB, Xiong Y, Miller AL, Bufton KK, Chonmaitree T . 2011. Comparison of the FilmArray Respiratory Panel and Prodesse real-time PCR assays for detection of respiratory pathogens. J Clin Microbiol 49 : 4083 4088.[PubMed]
71. Rand KH, Rampersaud H, Houck HJ . 2011. Comparison of two multiplex methods for detection of respiratory viruses: FilmArray RP and xTAG RVP. J Clin Microbiol 49 : 2449 2453.[PubMed]
72. Sung RY, Chan PK, Choi KC, Yeung AC, Li AM, Tang JW, Ip M, Tsen T, Nelson EA . 2008. Comparative study of nasopharyngeal aspirate and nasal swab specimens for diagnosis of acute viral respiratory infection. J Clin Microbiol 46 : 3073 3076.[PubMed]
73. Lee K, Park HD, Kang ES . 2013. Reduction of the HIV seroconversion window period and false positive rate by using ADVIA Centaur HIV antigen/antibody combo assay. Ann Lab Med 33 : 420 425.[PubMed]
74. Aberg JA, Gallant JE, Ghanem KG, Emmanuel P, Zingman BS, Horberg MA . 2014. Primary care guidelines for the management of persons infected with HIV: 2013 update by the HIV medicine association of the Infectious Diseases Society of America. Clin Infect Dis 58 : e1 e34.[PubMed]
75. Tomblyn M, Chiller T, Einsele H, Gress R, Sepkowitz K, Storek J, Wingard JR, Young JA, Boeckh MJ . 2009. Guidelines for preventing infectious complications among hematopoietic cell transplantation recipients: a global perspective. Biol Blood Marrow Transplant 15 : 1143 1238.[PubMed]
76. Holland JL, Louie L, Simor AE, Louie M . 2000. PCR detection of Escherichia coli O157:H7 directly from stools: evaluation of commercial extraction methods for purifying fecal DNA. J Clin Microbiol 38 : 4108 4113.[PubMed]
77. Kermekchiev MB, Kirilova LI, Vail EE, Barnes WM . 2009. Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples. Nucleic Acids Res 37 : e40.[PubMed]
78. Schrader C, Schielke A, Ellerbroek L, Johne R . 2012. PCR inhibitors - occurrence, properties and removal. J Appl Microbiol 113 : 1014 1026.[PubMed]
79. Shulman LM, Hindiyeh M, Muhsen K, Cohen D, Mendelson E, Sofer D . 2012. Evaluation of four different systems for extraction of RNA from stool suspensions using MS-2 coliphage as an exogenous control for RT-PCR inhibition. PLoS One 7 : e39455.[PubMed]
80. Buckwalter SP, Sloan LM, Cunningham SA, Espy MJ, Uhl JR, Jones MF, Vetter EA, Mandrekar J, Cockerill FR III, Pritt BS, Patel R, Wengenack NL . 2014. Inhibition controls for qualitative real-time PCR assays: are they necessary for all specimen matrices? J Clin Microbiol 52 : 2139 2143.[PubMed]
81. Hoorfar J, Malorny B, Abdulmawjood A, Cook N, Wagner M, Fach P . 2004. Practical considerations in design of internal amplification controls for diagnostic PCR assays. J Clin Microbiol 42 : 1863 1868.[PubMed]
82. Stacey GN . 2011. Cell culture contamination. Methods Mol Biol 731 : 79 91.[PubMed]
83. Steinau M, Patel SS, Unger ER . 2011. Efficient DNA extraction for HPV genotyping in formalin-fixed, paraffin-embedded tissues. J Mol Diagn 13 : 377 381.[PubMed]
84. McKinney MD, Moon SJ, Kulesh DA, Larsen T, Schoepp RJ . 2009. Detection of viral RNA from paraffin-embedded tissues after prolonged formalin fixation. J Clin Virol 44 : 39- 42.
85. Inoue T, Nabeshima K, Kataoka H, Koono M . 1996. Feasibility of archival non-buffered formalin-fixed and paraffin-embedded tissues for PCR amplification: an analysis of resected gastric carcinoma. Pathol Int 46 : 997 1004.[PubMed]
86. Zhao FH, Hu SY, Bian JJ, Liu B, Peck RB, Bao YP, Pan QJ, Frappart L, Sellors J, Qiao YL . 2011. Comparison of ThinPrep and SurePath liquid-based cytology and subsequent human papillomavirus DNA testing in China. Cancer Cytopathol 119 : 387 394.[PubMed]
87. Tirumala R, Clary KM . 2013. Dual Sample Collection and Comparison of COBAS HPV Testing Using SurePath and ThinPrep Media. Rochester General Hospital, Rochester, New York, USA, Daytona Beach, Florida.
88. Dickinson B . 2011. BD SurePath™ Preservative Fluid. Material Safety Data Sheet:Becton Dickinson. Franklin Lakes, NJ.
89. Druce J, Garcia K, Tran T, Papadakis G, Birch C . 2012. Evaluation of swabs, transport media, and specimen transport conditions for optimal detection of viruses by PCR. J Clin Microbiol 50 : 1064 1065.[PubMed]
90. Johnson FB . 1990. Transport of viral specimens. Clin Microbiol Rev 3 : 120 131.[PubMed]
91. Abad FX, Pintó RM, Bosch A . 1994. Survival of enteric viruses on environmental fomites. Appl Environ Microbiol 60 : 3704 3710.[PubMed]
92. Jerome KR, Huang ML, Wald A, Selke S, Corey L . 2002. Quantitative stability of DNA after extended storage of clinical specimens as determined by real-time PCR. J Clin Microbiol 40 : 2609 2611.[PubMed]
93. Krajden M, Minor JM, Rifkin O, Comanor L . 1999. Effect of multiple freeze-thaw cycles on hepatitis B virus DNA and hepatitis C virus RNA quantification as measured with branched-DNA technology. J Clin Microbiol 37 : 1683 1686.[PubMed]
94. Krafft AE, Russell KL, Hawksworth AW, McCall S, Irvine M, Daum LT, Connoly JL, Reid AH, Gaydos JC, Taubenberger JK . 2005. Evaluation of PCR testing of ethanol-fixed nasal swab specimens as an augmented surveillance strategy for influenza virus and adenovirus identification. J Clin Microbiol 43 : 1768 1775.[PubMed]
95. Frisbie B, Tang YW, Griffin M, Poehling K, Wright PF, Holland K, Edwards KM . 2004. Surveillance of childhood influenza virus infection: what is the best diagnostic method to use for archival samples? J Clin Microbiol 42 : 1181 1184.[PubMed]
96. CDC . 2014. How U.S. Clinical Laboratories Can Safely Manage Specimens from Persons Under Investigation for Ebola Virus Disease, on Department of Health and Human Services. http://www.cdc.gov/vhf/ebola/hcp/safe-specimen-management.html. Accessed 9/11/14.
97. Khare R, Espy MJ, Cebelinski E, Boxrud D, Sloan LM, Cunningham SA, Pritt BS, Patel R, Binnicker MJ . 2014. Multiplex detection of gastrointestinal pathogens: a comparative evaluation of two commercial panels using clinical stool specimens. J Clin Microbiol Electronically published ahead of print.
98. Mohamed S, Penaranda G, Gonzalez D, Camus C, Khiri H, Boulmé R, Sayada C, Philibert P, Olive D, Halfon P . 2014. Comparison of ultra-deep versus Sanger sequencing detection of minority mutations on the HIV-1 drug resistance interpretations after virological failure. AIDS 28 : 1315 1324.[PubMed]
99. Téllez-Sosa J, Rodríguez MH, Gómez-Barreto RE, Valdovinos-Torres H, Hidalgo AC, Cruz-Hervert P, Luna RS, Carrillo-Valenzo E, Ramos C, García-García L, Martínez-Barnetche J . 2013. Using high-throughput sequencing to leverage surveillance of genetic diversity and oseltamivir resistance: a pilot study during the 2009 influenza A(H1N1) pandemic. PLoS One 8 : e67010.[PubMed]
100. Orozovic G, Orozovic K, Lennerstrand J, Olsen B . 2011. Detection of resistance mutations to antivirals oseltamivir and zanamivir in avian influenza A viruses isolated from wild birds. PLoS One 6 : e16028.[PubMed]

Tables

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TABLE 1

Specimen Information for respiratory disease [e.g., pharyngitis, laryngotracheobronchitis (croup), bronchitis, bronchiolitis, pneumonitis]

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
Generic image for table
TABLE 2

Specimen information for exanthems (e.g., maculopapular, diffuse, dermatomal, vesicular)

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
Generic image for table
TABLE 3

Specimen information for neurological infections (e.g., meningitis, meningoencephalitis, encephalitis, encephalopathy)

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
Generic image for table
TABLE 4

Specimen information for infections with joint pain (e.g., fever, polyarthralgia, polyarthritis, tenosynovitis)

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
Generic image for table
TABLE 5

Specimen information for hepatic infections (e.g., jaundice, elevated liver enzymes, dark urine, abdominal pain)

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
Generic image for table
TABLE 6

Specimen information for gastroenteritis (e.g., diarrhea, abdominal pain, vomiting)

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
Generic image for table
TABLE 7

Specimen information for genital infections (e.g., lesions, atypical squamous cells)

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
Generic image for table
TABLE 8

Specimen information for retroviruses

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
Generic image for table
TABLE 9

Specimen information for congenital infections (e.g., intrauterine, perinatal, postnatal)

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
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TABLE 10

Specimen information for infectious mononucleosis

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
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TABLE 11

Specimen information for hemorrhagic fevers

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6
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TABLE 12

Specimen information for other infections, like ocular (e.g., conjunctivitis, retinitis, endophthalmitis), heart (e.g., myocarditis, pericarditis), and renal infections (e.g., hemorrhagic cystitis, nephropathy)

Citation: Khare R, Grys T. 2016. Specimen Requirements Selection, Collection, Transport, and Processing, p 57-77. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch6

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