Friday, 18 November 2016

The reality of the post-truth world's impact on science communication...

 We tweet 2each other. 
We write 4each other. 
We're considered elite. 
We don't understand our community. 
We can't reach them. 

Cool. [sarcasm]

Post-truth is now defined by the Oxford dictionary...


Relating to or denoting circumstances in which objective facts are less influential in shaping public opinion than appeals to emotion and personal belief:

‘in this era of post-truth politics, it's easy to cherry-pick data and come to whatever conclusion you desire’

‘some commentators have observed that we are living in a post-truth age’

Thursday, 17 November 2016

Another virus found to remain infectious on hard surfaces...

That headline doesn't bring in the readers. But - as far as we can tell having not been to the Nov 13-17 conference at which the preliminary data were presented during a seminar- it sums up the main finding of a new study on Zika virus (ZIKV).[1,2,4]

A 2016 Puerto Rico strain of the Asian lineage of ZIKV added to blood or a salt/protein solution was dried onto hard, solid surfaces. 

ZIKV was able to be recovered from those surfaces up to 8 hours later when in the presence of blood, but not the salty solution. 
Blood protected the virus. 

ZIKV recovery was achieved after rehydrating the dried material and adding dilutions to cells in culture (Vero E6 cells). There was no news on infectivity at warm temperatures or on cloth, tissues or other porous surfaces on which enveloped viruses like ZIKV usually don't do so well. By the way, when I say "recovered", I mean virus coudl be grown using lab conditions, producing more infectious virus. So the findings show that enough ZIKV remained infectious (or that it retained some infectivity) to start a new infection in lab cultures, despite being held outside the host cells it needs to replicate. 

Can ZIKV virus "live for hours" on surfaces? It's a virus - so it doesn't do much of anything outside of the living cell it completely depends upon for energy and raw materials ("dietary requirements"!). 

The main takeaway is not that the study defined a new route of ZIKV transmission to add to mosquitoes, sex, intrauterine transmission and transfusion.[11] This might have been your interpretation if you'd read...

.."The Zika virus is able to infect people even after sitting out on a counter for several hours, according to new research" [6]..

The study is really about the observations that some disinfecting agents (bleach and peracetic acid) may not work well when the virus is spilt onto these surface in the presence of blood. Isopropyl alcohol and quaternary ammonium/alcohol agents were still effective though.[3] West Nile virus (WNV) and bovine viral diarrhoea virus (BVDV) responded similarly. This is not a new finding for viruses in general, but it's a good one to have. This can be used as a reference for risk assessments for a lab that works with ZIKV or for healthcare facilities that may be dealing with ZIKV infected patients and needing to know how to effectively clean up spills or contaminated rooms.

Should we worry about this new finding?

Does the finding that a ZIKV spill can remain infectious on surfaces add new knowledge to our understanding of the risks of acquiring ZIKV infection? Not as far as we know because we have very limited evidence that ZIKV can infect a human through their epithelial surfaces (mucous membranes) - like we did have for Ebola virus for example. Such a route of infection - from surface to mucous membrane -is the the implied risk here. In other words, getting enough of those spilt infectious viruses into your eye, mouth or onto/into your nether regions. Its possible, but not likley and we have little evidence that its happens. 

We also have little evidence that ingesting something contaminated with infectious ZIKV or breathing it in can result in an infection. 

As ever, little evidence does not equate to zero evinced - we just have few actual data either because theses are such rare events or because we really haven't looked much (my bet).

Rare ZIKV transmission events do happen...

We have seen documented some unusual/infrequent ZIKV transmission events. Laboratory acquired infections [5,12] for example and that case of a severely immunocompromised/chronically ill adult passing ZIKV to his healthy adult son, perhaps via mucous membrane exposure to a high ZIKV load.[8,9] 

Infection of Dengue virus following exposure of a healthcare worker's mucous membranes to an infected IgM-positive patient's blood has also been described previously.[10] 

This route of transmission is certainly in need of some serious study. That said, transmission was not what this study was investigating. 

Infectious fluids such as blood, saliva, breast milk, urine or semen may come into contact with epithelial surfaces in a range of ways. 

Studies that do set out to focus on this interaction and measure how often an infection results from this contact, are needed. 


  1. Research finds Zika virus can live for hours on hard, non-porous surfaces
  2. Zika virus can survive on hard surfaces for hours, researchers say
  3. Study: Zika virus can linger on hard surfaces
  4. Inactivation of Zika Virus on a Hard Non-porous Surface
  6. Zika can survive for hours on hard, nonporous surfaces
  7. Zika virus can live for hours on hard, non-porous surfaces
  8. Scientists just documented the first case of Zika spreading through physical contact
  9. Fatal Zika Virus Infection with Secondary Nonsexual Transmission
  10. Transmission of Dengue Virus without a Mosquito Vector: Nosocomial Mucocutaneous Transmission and Other Routes of Transmission
  11. Zika Virus Disease Cases - 50 States and the District of Columbia, January 1-July 31, 2016.

Wednesday, 9 November 2016

Time to pick ourselves up, learn from our mistakes and do better...

We've all learned some hard lessons in the past 24 hours. We've seen something happen that we can't really comprehend. But such is life. Life is always teaching, always surprising. And we should always be learning from it, from others and from ourselves. We should teach others - both the good and the bad.

Most who read this will be lucky people. Never forget the luck you were born into-nor deny it. Others are not so lucky and they wake up to that every day. 

Don't blame others for the place we find ourselves in. Be a better person yourself. Teach your children to be good people, to be accepting, forgiving and giving people. Be inclusive. Study, be kind. Don't give in to anger and hatred - they are easy to sow but hard to repair and in the end make nobody happy.

Make the world a better place and remember to bring everyone along with you. Boy, girl, any colour, shade, height, nationality or belief. Help others see the things you see and learn to appreciate what they see and share with you. Understand the patterns and changes in their lives and help them view our global community for the joys its tribes can bring - we share many things.

But do rage against the threats to progress and social justice that we now face all over the world. Do not stop calling out that which harkens back to darker days and ways of life otherwise we will find ourselves waking into those days.

We can be better than this and we should always strive to be.

Saturday, 5 November 2016

During the first 4 weeks of life "common cold" viruses occur frequently and can make your little one sick....

UPDATE #1 08NOV2016
Not much is known about the number of, and burden due to, virus infections that happen during the very first four weeks of life - called the "neonatal period".

I've talked previously about the Observational Research in Childhood Infectious Diseases (ORChID) study.[1]

In this post I'm talking about the latest publication it has produced - Respiratory Viruses in Neonates: A Prospective, Community-Based Birth Cohort Study

The enrolled cohort and the samples...

From this study, 157/164 enrolled neonates (74 males, 47.1%) provided 574 nasal swab specimens (1-5 per neonate).

These swabs represented 552-weeks of data and represented 88% of the number of parent-collected samples that were expected to be returned by mail-which is good. 

A big thankyou to the parents who took part in this really big study.[3] Weekly sampling is no easy job!

Testing of samples for viruses...

Respiratory viruses were sought in the nucleic acids purified from these swabs using sensitive real-time polymerase chain reaction (rtPCR) techniques. 

Since most respiratory viruses have an RNA genome, we often added a reverse-transcription step (RT-rtPCR). 

The viral targets were:
  • rhinoviruses (RVs)
    • we also sought out the species and genotype of each RV using a nested, conventional RT-PCR
  • respiratory syncytial virus (RSV)
  • influenza virus (IFV) A and B
  • parainfluenza virus (HPIV) 1, 2, 3 and 4
  • adenoviruses (AdVs)
  • human metapneumovirus (HMPV)
  • human coronaviruses (HCoV) 229E, OC43, NL63 and HUK1
  • human bocavirus (HBoV) type 1
  • human polyomavirus WU and KI 

Viruses were found from early on...

You can see from the paper's [2] reprinted supplementary figure below, that there is a lot of respiratory virus activity during those first four weeks of new life. 

The first detection of a virus occurred at two days of age and the first infections linked to symptoms occurred during the first week - both infections by distinct viruses belonging to the species Rhinovirus A.

Of 157 neonates, 29 yielded a virus-positive swab. There were 13 ill neonates among the 29 (45% of infected neonates), 3 others who did not return symptom diaries and 13 neonates (45%) who remained asymptomatic, despite the finding of a virus up their nose.

Rhinovirus detection: with and without illness...

Among the 29 neonates shown, 21 had at least 1 RV infection during the first four weeks of life. This resulted in 31 RV(+) specimens. 

Unfortunately there were a fair number of completely untypeable RVs (white boxes). There were also some genotypes that did not match up with a previously described type at the time of the analysis (black boxes). These will require further study to sequence the viral protein 1 (VP1) region - or their entire genome - to get a better of idea of what they are and whether they are previously unknown RVs.

Among the 21 RV positive neonates (72% of all neonates)...

  • 8 had symptoms (38% of RV positive neonates)
  • 3 did not return symptom diaries (14%)
  • 10 did not have symptoms.
    These 10 RV infections represent 48% of the 21 positive neonates, or 56% of those who returned diaries. 

An RV(+) sample was considered linked to a symptomatic episode if it was collected 7-days before or after the episode.

Figure reprinted on Virology Down Under blog with
from Wolters Kluwer. Source is Supplementary Digital
Content Fig 1 from “Respiratory Viruses in Neonates: A Prospective,Community-Based Birth Cohort Study.”
Pediatric Infectious Disease Journal, 2016. [1],.97285.aspx

While RVs are often burdened by tales of glorious wimpiness, that does not usually hold up to close scrutiny. 

It also turned out that in our study, RVs were not the only viruses to be detected in the absence of any symptoms. The only detections of RSV, IFV B and HCoV-NL63 were also made in the absence of any symptoms. 


Most of the neonates had at least one virus detected during the first four weeks of life, but only 40% showed any obvious signs of illness. 

Rhinoviruses were the most frequently detected viruses and 38% of infected neonates were linked to an illness. Other viruses - like RSV and an IFV - sometimes attributed to much more severe disease, were found less frequently than RVs and when detected, did not seem to have caused symptoms. 

Respiratory virus infections start from birth and most do not cause symptoms in the neonatal period. But you can be sure these infections are teaching the newly developing immune systems all about the tiny invaders they will face for the rest of their 'lives'. These encounters create the immunological tools we all need to defend against a world shared by many challenges.

  1. Kids are virus factories...
  2. Respiratory Viruses in Neonates: A Prospective, Community-Based Birth Cohort Study.
    Sarna, M,  Alsaleh, A, Lambert SB, Ware, RS, Mhango, LP, Mackay, IM, Whiley DM, Sloots TP, Grimwood K. Published ahead of print. Pediatric Infectious Disease Journal, 2016.,.97285.aspx
  3. The nose knows – even newborns get viruses
  1. Text altered to clarify RV symptomatic vs asymptomatic episode numbers