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Volume 25, Number 8—August 2019
Research Letter

Prolonged Zika Virus RNA Detection in Semen of Immunosuppressed Patient

Christina PetridouComments to Author , David Bonsall, Aleem Ahmed, Mark Roberts, Carolyn Bell, Mariateresa de Cesare, Rory Bowden, Victoria Graham, Daniel Bailey, Andrew Simpson, and Emma AaronsComments to Author 
Author affiliations: Rare and Imported Pathogens Laboratory, Public Health England Porton, Salisbury, UK (C. Petridou, V. Graham, D. Bailey, A. Simpson, E. Aarons); University of Oxford, Oxford, UK (D. Bonsall, M. de Cesare, R. Bowden); Leicester Royal Infirmary, Leicester, UK (A. Ahmed); Worcestershire Royal Hospital, Worcester, UK (M. Roberts); South Warwickshire National Health System Foundation Trust, Warwick, UK (C. Bell)

Main Article


Serial Zika virus genome sequence and culture results from semen of a patient with immunosuppression, United Kingdom*

Sample no. Days after symptom onset RT-PCR Ct value† Sequence coverage, %‡ Average read depth Sequencing platform§ Mutations detected Culture result
1 13 19 99.9 (min depth 2), 88.4 (min depth 40) 386.9 MinION Reference Frozen sample: unsuccessful
2 46 26 ND NA NA Fresh sample: unsuccessful
3 167 Subthreshold ND NA NA ND
4 194 No RNA detected¶ ND NA NA ND
5 241 31 Unsuccessful NA NA ND
6 257 34 44 (min depth 2), 0 (min depth 40) 3.3 MinION None Frozen sample: unsuccessful
7 278 No RNA detected¶ ND NA NA ND
8 326 26 76 (min depth 2), 6 (min depth 40) 13.2 MinION None Fresh sample: unsuccessful
9 396 29 ND NA NA ND
10 515 24 98.1 (min depth 5) 33.3 MiSeq K3272E, Syn2921 Fresh sample: unsuccessful
11 687 39 ND NA NA ND
12 941 32 ND NA NA ND

*Ct, cycle threshold; min, minimum; NA, not applicable; ND, not done; RT-PCR, reverse transcription PCR.
†Before PCR, nucleic acid was extracted from samples 1–7 using the EZ1 Virus Mini Kit (QIAGEN, Samples 8–12 were extracted using the MagNA Pure 96 DNA and Viral NA Small Volume Kit (LifeScience-Roche Diagnostics Corporation, Ct values <40 with acceptable amplification curves are interpreted as positive, but results for samples with Ct values >35 are confirmed by re-extraction and repeat PCR in triplicate, where possible.
‡Conservative read-depth thresholds were selected for comparative analyses of the day 13 (sample 1) and day 515 (sample 10) consensus genomes.
§MinION (Oxford Nanopore Technologies,; MiSeq (Illumina,
¶Confirmed on reextraction and repeat PCR testing.

Main Article

Page created: July 16, 2019
Page updated: July 16, 2019
Page reviewed: July 16, 2019
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