Showing posts with label urine. Show all posts
Showing posts with label urine. Show all posts

Sunday, 3 April 2016

Usefulness of urine samples for Zika virus testing...

There is a narrow window of Zika virus (ZIKV) detectability in the blood (viraemia) based on the RT-PCR testing of serum samples from symptomatic cases. I've talked a little about this in a smaller, earlier post: Zika virus disease samples...don't pass urine (by)..

Little is known about asymptomatic infections and viraemia.

A decent number of studies have shown that urine may be a better sample for testing using molecular methods because of prolonged viral shedding (viruria) and sometimes higher viral load compared to serum samples.

The following is a list of some of the peer-reviewed literature and some public health advisories that have mentioned seeking ZIKV in urine using molecular techniques.


Australian Department of Health
Blood & Urine: 1st 14 days post symptom onset
http://www.health.gov.au/internet/main/publishing.nsf/Content/ohp-zika-health-practitioners.htm#toc05

European CDC
Blood: 3-5d post onset
Urine: up 10 10d

Public Health England
Blood: Anyone with travel history and current/past symptoms suggetsing ZIKV infection
Urine: Pregnant woman with current symptoms/male with current symptoms and a pregnant partner
https://www.gov.uk/guidance/zika-virus-sample-testing-advice 

United States CDC
Serum\CSF: Must be collected as primary test substrate
Urine: Can also be submitted
                                     
Kutsuna et al
In 1/2 cases, ZIKV RNA detected in urine when serum negative

Gourinat et al
Detected in urine of 6/6 symptomatic patients between 10 to 20 days after onset (7-20d better than serum), often with higher viral loads from urine samples than from serum. Serum positive in 4/6 but only until rash observed (2-3d post onset). Urine levels rise slightly after disease and rash onset - “preferred for virus detection”.



Shinohara et al
ZIKV RNA detected in urine 7 days after symptom onset; serum equivocal at 2 days post-onset

Besnard et al
Urine positive in 2 cases up to 8 days post-onset, in one case after serum was negative

Brasil et al
Of 88 women, 72 (82%) had positive results for ZIKV on PCR in blood, urine, or both; 60 in serum specimens; 46 in urine samples; 34 in both specimens; 12 in urine specimens only; 26 in blood specimens only; median number of PCR cycles for serum specimens - 33.0; median number of PCR cycles for urine specimens - 29.0.

Roze et al
Urine positive in 2/2 cases when serum was negative. 15-21 days after neurological symptom onset.

Barzon et al
Urine and had 106-fold higher viral loads than serum. Both sample types positive from 5 days after symptom onset, Urine positive until 22 days after onset-saliva until 29 days.


The outcome here is that urine is a sample that looks like it should be requested perhaps much more often than it is. Also, the language around recommending the collecting of urine is not as clear as it appears that it should be - including by some other public health agencies 

As it stands, a negative serum RT-PCR test for ZIKV does not hold a lot of meaning because of the narrow detection window using blood. 

Urine has proven itself useful for detection and confirmation of ZIKV infection - a process that is key to learning more about the virus and its impact(s) on infected humans. 

Use urine. Welcome the wee. Take the...well you get the point.

Saturday, 6 February 2016

Urine found to contain infectious Zika virus...again...

In what is becoming a trend of "part-of-the-story" science releases from Brazil's Zika virus (ZIKV) epidemic, we saw an overnight media report of the "first" finding of infections ZIKV in urine and saliva samples.[1,2]

It was not the first in urine. 

There was an earlier report from 2014 that described RNA and infectious virus in the urine of a Canadian traveller who had returned from Thailand, where she presumably acquired her ZIKV infection.[3]

Rushing out appallingly weak stories into scientific journals that exhibit very little peer review [4] and poorly worded or  thought out statements to describe ZIKV findings is not helping the situation in Brazil. In particular, it is doing nothing to investigate the link between ZIKV infection and congenital malformations or Guillain Barre syndrome. At all. 

I urge that everyone take a deep breath and perhaps involve a lot more more peer review - even for media releases.

And on the use of urine, just because previous studies have not sought infectious ZIKV (or other viruses) using culture techniques, or have not found it when they did look,[5,6] is not reason not rule out urine or any fluid as possibly contained infectious virus. When RNA is detected but RT-PCR, there is a real risk of infectious virus being present and there is a decent chance that culture will fail to detect that because it isn't a hugely sensitive technique at times and because of the many infectivity-degrading specimen handling steps between collection and culture. 

Whether that RNA detection, or this infectious virus detection for that matter, equates with an "infectious dose" of virus (enough virus to start an actual infection before the body's defences contain the virus) is the next issue to consider. Also, would mucous membranes onto which virus-contaminated saliva might be propelled, have the receptors to bind virus and the cells to support ZIKV replication? More questions.

Seriously though, has Ebola taught research studies nothing? Look everywhere and expect everything.

References...

  1. https://agencia.fiocruz.br/fiocruz-detecta-presenca-de-virus-zika-com-potencial-de-infeccao-em-saliva-e-urina
  2. http://edition.cnn.com/2016/02/05/health/zika-urine-saliva/index.html?sr=fbcnni020516zika-urine-saliva0438PMStoryGalLink&linkId=21012904
  3. First case of Zika virus infection in a returning Canadian traveler.
    http://www.ncbi.nlm.nih.gov/pubmed/25294619
  4. Ophthalmological findings in infants with microcephaly and presumable intra-uterus Zika virus infection
    http://www.scielo.br/pdf/abo/v79n1/0004-2749-abo-79-01-0001.pdf.
  5. Detection of Zika virus in urine.
    http://www.ncbi.nlm.nih.gov/pubmed/25530324
  6. Value of Routine Dengue Diagnostic Tests in Urine and Saliva Specimens
    http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0004100
  7. Detection of Zika virus in saliva.
    http://www.ncbi.nlm.nih.gov/pubmed/26071336

Friday, 29 January 2016

Zika virus disease samples...don't pass urine (by)..

It is becoming anecdotal in the Tweet'verse that Zika virus (ZIKV) viraemia (virus in the blood) can only be detected for 5 days - presumably after illness onset  - I need to chase that down.

But blood is not the only sample to test. 

In fact it may even be one of the less informative samples to test if trying to detect signs of a current or very recent infection. A lot of that being done in the Americas, and as a result, in laboratories worldwide, right now.

Urine has been shown to be positive for ZIKV RNA beyond 5 days, sometimes when blood is completely negative by highly sensitive polymerase chain reaction (PCR) methods.[1,2,3] Saliva has also been of use,[4] but urine seems to outperform it for PCR purposes.

In particular - beyond 10 days in the study by Gourinat et al.[3]
From Emerging Infectious Diseases article,Vol. 21, No. 1,
January 2015 Detection of Zika Virus in Urine.[3]
References...
  1. http://jtm.oxfordjournals.org/content/jtm/23/1/tav011.full.pdf
  2. http://www.eurosurveillance.org/images/dynamic/EE/V19N04/art20683.pdf
  3. http://wwwnc.cdc.gov/eid/article/21/1/pdfs/14-0894.pdf
  4. http://www.sciencedirect.com/science/article/pii/S138665321500133X

Saturday, 4 April 2015

Ebola - the lesser transmission risks are still risks...

The United Nations (UN) Foundation blog has used some pretty strong language in their latest post of the 5 Things to Know on Ebola This Week.

Number 2 on their list stated (by highlighting)...
First detected case of Ebola transmitted through sexual intercourse
Earlier research suggested that three months of abstinence or condom use among male survivors would suffice to prevent the transmission of Ebola through intercourse. But an Ebola patient in Liberia who died last week had just one known risk factor: her boyfriend was an Ebola survivor, treated last September. This is the first case detected of the Ebola virus being transmitted through sexual intercourse, which has necessitated updated recommendations. Read the full story here: http://unfoundationblog.org/ebola/5-things-to-know-on-ebola-this-week-10/#sthash.2HkUbbYT.dpuf
While there is reported to be ongoing testing (and presumably virus genotyping), I've yet to hear publicly the outcome of such testing. 

Perhaps the results are known behind closed doors and perhaps that testing has firmly pointed to a sexual transmission route. The UN post above certainly seems very sure and it also seems that this event has triggered an update to recommendations. There is solid literature about the presence of infectious Ebola virus in seminal fluids so the possibility shouldn't be far beyond belief.[4]

Another possible, albeit also unproven, transmission route is urine. This fluid seems to me to be a far more likely source of trouble. One cannot abstain from urination. So why worry about urine as a risk for transmission of Ebola virus? An EVD case study last year showed very nicely that infectious Ebola virus could be cultured from urine for about 12 days longer than it could be from blood.[1] Viral RNA has also been found in urine for four weeks.[1,2] 

Perhaps urine should be a more noteworthy concern for its potential to remain infectious after blood test become negative. This concern might be greater wherever toilet and hand-washing facilities and sewers, are minimal or poorly maintained.

Urine and seminal fluids are not considered to be major transmission routes for Ebola virus. But let's not forget that it was probably an unlikely transmission event, and route - a single jump from an animal to a human - that triggered >25,000 EVD cases in this epidemic. Even a rare risk must be given serious consideration when such a large public health impact can realistically result.

References...

  1. Kreuels B, Wichmann D, Emmerich P et al. A Case of Severe Ebola Virus Infection Complicated by Gram-Negative Septicemia. N Engl J Med. 2014 Oct 22. 371:2394-2401
  2. Lyon GM, Mehta AK, Varkey JB et al. Clinical Care of Two Patients with Ebola Virus Disease in the United States.  N Engl J Med. 2014 Nov 12. 371:2401-2409
  3. Ebola Virus Disease (EVD). Key questions and answers concerning water, sanitation and hygiene. World Health Organization. http://apps.who.int/iris/bitstream/10665/137181/1/WHO_EVD_WSH_14_eng.pdf?ua=1
  4. Mackay IM, Arden KE. Ebola virus in the semen of convalescent men. Lancet Infect Dis. 2015 Feb;15(2):149-50.

Friday, 30 May 2014

MERS-CoV in the Netherlands...a detail analysis of cases

Red arrow indicates where Dutch 
MERS-CoV case sequences sit.
Click on tree to enlarge
This comes from a shiny newly released Eurosurveillance report from Dutch researchers. 

I've marked up my earlier tree to show where (based on partial 4,000nt fragment) the sequence from the Netherlands MERS-CoV positive cases (near identical) sits.

I've also charted Case 1's laboratory testing course, to show the variability of virus detection when a very thorough sampling and testing investigation is conducted. 

Viral RNA remained detectable in the blood for all days tested demonstrating viraemia (well, RNAaemia technically) from day-4 onwards. Urine was not positive but a faecal sample was, on day-5. The latter has implication for infection control in hospital settings whereby flushing toilets creating aerosols could be another contributor to spread.

Reverse transcription real-time polymerase chain reaction (RT-rtPCR) results are shown as positive (tall bars), negative (stumpy bars) or not tested (empty space) plotted against day of sampling.
Click on image to enlarge.

This is, as far as I'm aware, is only the second time human faeces or urine have been found to contain signs of MERS-CoV.

A throat swab was positive early on and then again after a 2-day period of negativity. This points to the possibility of shedding for over a week, when associated with cough. But given that this case was part of a tour group and they didn't all become symptomatic, MERS-CoV still didn't spread efficiently or result in disease very often (if it did spread), for whatever reason(s). Antibody testing would be interesting here too.

It would also be very interesting to know whether virus was being shed during the initial diarrhoea in Case 1, which predated his return to the Netherlands by about 8-days, or whether that was unrelated to the MERS-CoV infection. Perhaps testing faeces for gastrointestinal viruses would be useful, or interesting, here.