Quantitation of human astrovirus by real-time reverse-transcription-polymerase chain reaction to examine correlation with clinical illness

Zhian Zhang, Douglas K. Mitchell, Carol Afflerbach, F. Jakab, Jolan Walter, Yan Jin Zhang, Mary A. Staat, Parvin Azimi, David O. Matson

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Human astroviruses (HAstVs) cause gastroenteritis. Real-time, reverse-transcription-polymerase chain reaction (RT2-PCR) was developed to quantitate HAstV RNA. An 88 bp amplicon from the conserved 3′ genomic region was detected by binding of SYBR Green. RT2-PCR was reproducible, with a correlation coefficient of 0.998-1.00 and PCR efficiency of 94.4-100% (mean 97%). The coefficient of variation was 0.6-2.5%, dynamic range with RNA standard up to 5 × 108 RNA copies (RNACN) and sensitivity 5 RNACN. Of 54 blinded, archived stool samples from children hospitalized because of gastroenteritis tested by RT-PCR, 49 (91%) agreed by RT2-PCR for HAstV-positivity (Cohen κ = 0.81, 95%CI 0.66-0.97). HAstV RNACN in stools ranged from 7.6 × 101 to 3.6 × 1014 copies/0.1 g. Children coinfected with rotavirus had lower RNACN (mean log 4.22/standard deviation = 2.26) than those without coinfection (7.57/3.06; p = .019). Children taking infant formula also had lower RNACN (5.96/2.98) than breast-fed or weaned children (8.73/2.92; p = .027). Higher RNACN tended to occur with longer duration of diarrhea for the episode (r = 0.49, p = .064), but was not associated with change in age, gender, illness day, severity or breast-feeding. RT2-PCR quantitated HAstV RNA and RNACN in stool correlates with features of clinical illness.

Original languageEnglish
Pages (from-to)190-196
Number of pages7
JournalJournal of Virological Methods
Volume134
Issue number1-2
DOIs
Publication statusPublished - Jun 2006

Fingerprint

Mamastrovirus
Reverse Transcription
Polymerase Chain Reaction
RNA
Gastroenteritis
Sick Leave
Infant Formula
Hospitalized Child
Rotavirus
Breast Feeding
Coinfection
Diarrhea
Breast

Keywords

  • Human astrovirus
  • RNA copy number
  • RT2-PCR

ASJC Scopus subject areas

  • Virology

Cite this

Quantitation of human astrovirus by real-time reverse-transcription-polymerase chain reaction to examine correlation with clinical illness. / Zhang, Zhian; Mitchell, Douglas K.; Afflerbach, Carol; Jakab, F.; Walter, Jolan; Zhang, Yan Jin; Staat, Mary A.; Azimi, Parvin; Matson, David O.

In: Journal of Virological Methods, Vol. 134, No. 1-2, 06.2006, p. 190-196.

Research output: Contribution to journalArticle

Zhang, Zhian ; Mitchell, Douglas K. ; Afflerbach, Carol ; Jakab, F. ; Walter, Jolan ; Zhang, Yan Jin ; Staat, Mary A. ; Azimi, Parvin ; Matson, David O. / Quantitation of human astrovirus by real-time reverse-transcription-polymerase chain reaction to examine correlation with clinical illness. In: Journal of Virological Methods. 2006 ; Vol. 134, No. 1-2. pp. 190-196.
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