Monday, 26 December 2016

Snapdate: influenza H7N9 cases in humans, by the numbers...

An updated chart.
[SNAPDATE'S are snap updates that don't have lots of detail and chat...although they almost always end up having lots of chat!]

A summary of the monthly, weekly and daily data graphing human avian influenza A(H7N9) virus infections in humans reported from the hotzone, China.

Daily weekly and monthly H7N9 numbers, taken from the
FluTrackers curated line list [1] and the World Health
Organization disease outbreak news reports
.
Click on image to enlarge.

References...

Friday, 23 December 2016

H7N9:2016 has been the most quiet year to date...

Influenza A(H7N9) virus, or 'H7N9', has had a quiet year when compared to past outbreaks.

All human cases to date have been linked to China. The majority of human cases have had some link with poultry - chickens or ducks - although we do hear of human-to-human transmission, this seems to be limited. H7N9 has been found in poultry from backyard farms and in live poultry markets (LPMs) in China - sometimes in the company of other influenza viruses, like H9N2.[1]

Cases and deaths each month over the 4 years we have known
about human cases of H7N9 infection.
Click on image to enlarge.

Despite the slow year,the 2016 graph above shows the usual December uptick in human cases. It will be what happens next that matters. Will be see a big January surge as in 2014, or a later Feb-April surge as in 2013 and 2015? Will live LPMs be quickly closed, disinfected, the animals destroyed and any outbreaks in 2017 squashed or will they remain open allowing more human cases as the virus spreads among market animals?

Time, and testing data - which China generates lots of but does not seem to enjoy publicly reporting - will tell.

In 2016 - 2 new regions were added for the first time - Tianjin municipality and Liaoning province - both in the north-eastern coastal region of China. 

In 2013, no sustained human-to-human transmission had been reported [2] - this remains true up until today.

References...

  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911810/pdf/nihms749408.pdf
  2. http://www.nature.com/news/mapping-the-h7n9-avian-flu-outbreaks-1.12863

Sunday, 18 December 2016

Happy Festive Season to all who read this....

..whatever your shape, colour, gender, sex, size, beliefs, weight or disposition. 

May 2017 be a better year for those of us who wish to see humankind progress in many peaceful, intelligent, creative and joyful ways.

I wish for you a festive period that is safe, healthy and good to you and your loved ones, your friends and your pets.

Take care.
Ian M. Mackay, Ph.D.



Sunday, 4 December 2016

Zika virus-positive microcephaly in Colombia...

The latest epidemiological report (epidemiological week 47) from Colombia, which includes data on Zika virus (ZIKV) disease (ZVD; 20NOV2016-26NOV2016), has been produced by the Colombian National Institute for Health team.[1]
NOTE: While these data were reported the past epidemiological week (EW), they may not be from that week. See earlier post about possible reporting lag.

As of this report, 60 (+0 from last EW) live births have been diagnosed with congenital ZIKV syndrome (CZVS; microcephaly/central nervous system disorder), confirmed as being ZIKV positive. That represents 1.0% of all confirmed ZIKV positive mothers-a slowly but steadily rising proportion.

The change in confirmed ZIKV infection numbers when detected in
association with a microcephaly diagnosis, Colombia, compared to the
preceding week's total (yellow bars, right-hand axis). Those diagnoses still in question and under investigation are shown as yellow dots (left-hand axis).
Data are from [1]. 
Click on graph to enlarge.
It has now been 415 days, or 1 year, 1 month and 18 days, since ZIKV was first confirmed in Colombia on 16th October 2015.[5] Keep in mind that when talking about microcephaly - we have to think back in time to what insult or infection might have occurred during pregnancy. The counts of ZIKV occurring this week will have zero impact on what happened back then. Also keep in mind that Colombia may be reporting things differently from Brazil.[3]

The cumulative curve of confirmed ZVD cases
(green circles, left-hand axis) and the change in confirmed ZVD case
numbers when compared to the preceding week's total
(green bars, right-hand axis). Data from [1].
Click on graph to enlarge.

No new laboratory confirmed ZIKV detections have been reported in Colombia for eh 20th week (green graph, above).


Brazil first reported positive (but unconfirmed) laboratory tests for ZIKV disease on 29th April 2015. Brazil then started to report a rise in foetal anomalies (an initial 141), in the form of microcephaly on 30th October 2015. This was 184 days - or about 6 months later.[4] However, the genetic analyses suggest ZIKV was in Brazil from around 2013. It had a lot longer to get established. Perhaps this is the difference between Brazil and Colombia, given reports a growing 2,180 ZIKV congenital syndrome diagnoses [2] compared to Colombia's 60.

References...

  1. http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/2016%20Bolet%C3%ADn%20epidemiol%C3%B3gico%20semana%2047.pdf
  2. http://www.paho.org/hq/index.php?option=com_docman&task=doc_view&Itemid=270&gid=37143&lang=en
  3. http://virologydownunder.blogspot.com.au/2016/06/the-elephant-squeaked.html
  4. http://www.paho.org/hq/index.php?option=com_docman&task=doc_view&gid=35139&Itemid=270&lang=en
  5. http://www.nejm.org/doi/full/10.1056/NEJMoa1604037#t=article

Friday, 18 November 2016

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

So:
 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]

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

ADJECTIVE

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. 


References...

  1. Research finds Zika virus can live for hours on hard, non-porous surfaces
    https://www.eurekalert.org/pub_releases/2016-11/aaop-rfz111116.php
  2. Zika virus can survive on hard surfaces for hours, researchers say
    http://www.upi.com/Health_News/2016/11/15/Zika-virus-can-survive-on-hard-surfaces-for-hours-researchers-say/9781479267969/
  3. Study: Zika virus can linger on hard surfaces
    http://www.cidrap.umn.edu/news-perspective/2016/11/study-zika-virus-can-linger-hard-surfaces
  4. Inactivation of Zika Virus on a Hard Non-porous Surface
    https://annual.aapsmeeting.org/event/member/309446
  5. http://www.achd.net/pr/pubs/2016release/060916_zika.html
  6. Zika can survive for hours on hard, nonporous surfaces
    http://www.cnbc.com/2016/11/15/zika-can-survive-for-hours-on-hard-nonporous-surfaces.html
  7. Zika virus can live for hours on hard, non-porous surfaces
    https://www.sciencedaily.com/releases/2016/11/161115164220.htm
  8. Scientists just documented the first case of Zika spreading through physical contact
    http://www.sciencealert.com/scientists-just-documented-the-first-case-of-zika-spreading-through-physical-contact
  9. Fatal Zika Virus Infection with Secondary Nonsexual Transmission
    http://www.nejm.org/doi/full/10.1056/NEJMc1610613?query=featured_home&
  10. Transmission of Dengue Virus without a Mosquito Vector: Nosocomial Mucocutaneous Transmission and Other Routes of Transmission
    http://cid.oxfordjournals.org/content/39/6/e56
  11. Zika Virus Disease Cases - 50 States and the District of Columbia, January 1-July 31, 2016.
    https://www.ncbi.nlm.nih.gov/pubmed/27631604
  12. http://www.cdc.gov/zika/transmission/

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
.[2]

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
permission
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]

http://journals.lww.com/pidj/Abstract/publishahead/Respiratory_Viruses_in_Neonates___A_Prospective,.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. 

Summary...

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.

References...
  1. Kids are virus factories...
    http://virologydownunder.blogspot.com.au/2016/07/kids-are-virus-factories.html
  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.
    http://journals.lww.com/pidj/Abstract/publishahead/Respiratory_Viruses_in_Neonates___A_Prospective,.97285.aspx
  3. The nose knows – even newborns get viruses
    https://www.uq.edu.au/news/article/2016/10/nose-knows-%E2%80%93-even-newborns-get-viruses
Updates...
  1. Text altered to clarify RV symptomatic vs asymptomatic episode numbers

Sunday, 23 October 2016

Microcephaly cases under investigation for links to Zika virus in Colombia keep accruing...

Diagnoses of Zika virus infection linked to microcephaly continue to very slowly rise in Colombia, rising by 11 since the end of July 2016 - with 1 new case in this most recent reporting week to reach a total of 47.[1] 

Brazil reports 2,033 cases of Zika virus congenital syndrome (CZVS) as of 20-OCT-2016, among a background of 109,596 "confirmed" cases.[2] However, a confirmed case listed by Brazil includes confirmed and probable cases as described by the Pan American Health Organization (PAHO) definition.[3]

Meanwhile the number of microcephaly (?CZVS or just head size?) cases that remain under investigation in Colombia continue to accumulate. 

Up until  mid-June, these numbers used to be in double digits, but they have risen dramatically (yellow dots in graph above) since then to reach over 300 and continue to climb steadily. How many of these will be added to the microcephaly/CZVS total is unclear.

References...

  1. http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/Forms/public.aspx
  2. http://www.paho.org/hq/index.php?option=com_docman&task=doc_view&Itemid=270&gid=36621&lang=en
  3. http://www.paho.org/hq/index.php?option=com_content&view=article&id=11117&Itemid=41532&lang=en

Sunday, 9 October 2016

Zika virus in Colombia is very quiet - but undiagnosed rashy fever disease hasn't gone away...

Just a quick snapdate today.

Clinically suspect cases of Zika virus (ZIKV)  infection have increased by 227-933/week for the past 12 weeks (red graph) - but none have been confirmed as ZIKV by the Colombian Institute of Health.

That seems to indicate just how terrible clinical diagnoses is. Otherwise, there's a testing or reporting problem.
The green graph below shows the flat line that indicates no new positives confirmed by laboratory testing.


Thankfully, we also continue to see few new cases of ZIKV-linked congenital syndromes. Although, this is also something of a conundrum.
Pregnant women are not being reported with many new confirmed or suspected ZIKV diagnoses - which makes sens of there is no rise in confirmed cases overall.


Tuesday, 27 September 2016

Mayaro virus: a primer and a tree...

UPDATE 11OCT2016
Mayaro virus (MAYV) is a member of the Family Togaviridae. Genetically its divided into two genotypes, "D" (widely Dispersed), "N" (?New) and "L" (Limited) - shown in the tree below.

MAYV is an arthropod-borne virus (arbovirus) that can cause Mayaro fever. 

Disease may can include 4 days of viraemia, a rash that may appear after a 3-5 day fever, headache, photophobia, inguinal lymphadenopathy, myalgia, vomiting, diarrhoea and arthralgia which can affect ankles, wrists and toes and less often, other joints. Joint pain may continue for weeks and maybe very painful. 

Disease is clinically similar to that due to primary dengue virus or chikungunya virus infection. MAYV was first described in 1954 after its discovery in in Mayaro County, Trinidad.[2,3]

Recently, a MAYV infection by a rare member of the L lineage was identified in a dengue virus coinfection in a child in Haiti (sequence shown in bold below) during investigations of sera collected from children with unspecified fever between May 2014 and February 2015.[1]
Mayaro viruses and other Genus Alphavirus and 
Genus Rubivirus complete genome sequences. 
Aligned using MAAFT in Geneious v7. 
Tree made using Mega v7.
Click on image to enlarge

While the Haitian case triggered the usual media sirens, this is a virus well worth watching - and testing for. 

An incredibly prescient 2010 review by Weaver & Reisen on future threats is well worth a read.[4] 

Findings of infection and occasional flaccid paralysis in suckling mice (adult mice were not obviously infectable) that had been injected intracerebrally with low passage virus preparations [2,5] - well, in the new Zika virus reality, it really wouldn't pay to underestimate the potential of yet another tropical virus would it?

Human cases of MAYV infection have most often been reported in working males in forested areas near rivers in countries from Mexico down to Bolivia. All of that knowledge is, of course, based on visible disease outbreaks. I have yet to read every paper, but so  far I have not seen anything that delves deeply into rates of mild or asymptomatic disease. 

MAYV was also isolated in 1967 (reported in 1974 [6]) from a migrating bird (orchard oriole - Icterus spurius) detected in Louisiana, USA. Because it was such a rare event, the authors concluded that these birds probably didn't play a role as natural hosts to MAYV. Apparently it was found in a lizard too - but I'm still chasing down that paper.[7]

References...
  1. http://wwwnc.cdc.gov/eid/article/22/11/16-1015_article
  2. Casals J, Whitman L. Mayaro virus: a new human disease agent. I. Relationship to other arbor viruses. Am J Trop Med Hyg. 1957;6(6):1004-11. PubMed PMID: 13487972.
  3. Anderson CR, Downs WG, Wattley GH, Ahin NW, Reese AA. Mayaro virus: a new human disease agent. II. Isolation from blood of patients in Trinidad, B.W.I. Am J Trop Med Hyg. 1957;6(6):1012-6. PubMed PMID: 13487973.
  4. Scott C. Weaver and William K. Reisen. Present and Future Arboviral Threats. Antiviral Res.
    http://www.ncbi.nlm.nih.gov/pubmed/19857523
  5. Schmidt JR, Gajdusek DC, Schaffer M, Gorrie RH. Epidemic jungle fever among Okinawan colonists in the Bolivian rain forest. II. Isolation and characterization of Uruma virus, a newly recognized human pathogen. Am J Trop Med Hyg. 1959;8(4):479-87. PubMed PMID: 13670375.
  6. Charles H. Calisher, Ph.D.; Ernest0 Gutikez V., M.D.; Kathryn S. C. Maness, B.S., and Rexford D. Lord, SC.D. ISOLATION OF MAYARO VIRUS FROM A MIGRATING BIRD CAPTURED IN LOUISIANA IN 1967. Bull Pan Am Health Organ. 1974;8(3):243-8.
    https://www.ncbi.nlm.nih.gov/pubmed/4418030
  7. Woodall JP Virus research in Amazonia. Atas do Simposia sobre a Biota Amazónia 1967; 6(Patologia):31–63.
  8. Albert J. Auguste, Jonathan Liria, Naomi L. Forrester, Dileyvic Giambalvo, Maria Moncada, KC Long, D Morón, N de Manzione, RB Tesh, ES Halsey, TJ Kochel, R Hernandez, J-C Navarro, SC Weaver. Evolutionary and Ecological Characterization of Mayaro Virus Strains Isolated during an Outbreak, Venezuela, 2010
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593426/

Sunday, 25 September 2016

Colombia Zika virus report, Epidemiological Week No. 37...

The latest epidemiological report from Colombia, which includes data on Zika virus disease (ZVD; 11SEP2016-17SEP2016), has been produced by the Colombian National Institute for Health team.[1]
NOTE: While these data were reported the past epidemiological week (EW), they may not be from that week. See earlier post about possible reporting lag.

As of this report, 41 (+1 from last EW) live births have been diagnosed with congenital ZIKV syndrome (CZVS; microcephaly/central nervous system disorder), confirmed as being ZIKV positive. That represents 0.70% of all confirmed ZIKV positive mothers-the 8th consecutive EW in which this proportion has risen.

Some back of napkin calculations looking at these numbers suggest that there are 7 deliveries for every 1,000 ZIKV-positive pregnant women that result in a ZIKV infected baby with microcephaly

This assumes each neonate has been tested for ZIKV as [2] suggests. This figure has no clear understanding of the number of aborted or miscarried foetuses that are also occurring from ZIKV-positive pregnant women. Abortions and miscarriages will need a local baseline to understand the scope of this component of the impact of ZIKV infection.

246 other microcephaly diagnoses (up from 216 last week) are now under investigation - this value had also been rising very quickly until a recent dip and plateau. Its rise once again might suggest suspicious CZVS cases in Colombia are accruing faster than the pace of complete investigation can keep up with. 

The graph below focuses on just the ZIKV-positive cases and those that remain under investigation, highlighting how the investigatory total has changed each week.

The change in confirmed ZIKV infection numbers when detected in
association with a microcephaly diagnosis, compared to the
preceding week's total (yellow bars, left-hand axis). Data are from [1].
Click on graph to enlarge.

It has now been 344 days, or 11 months 8 days, since ZIKV was first confirmed in Colombia on 16th October 2015.[2] Keep in mind that when talking about microcephaly - we have to think back in time to what insult or infection might have occurred during pregnancy. The counts of virus occurring this week will have zero impact on what happened back then. Also keep in mind that Colombia may be reporting things differently from Brazil.[3]

Brazil first reported positive (but unconfirmed) laboratory tests for Zika virus disease on 29th April 2015. Brazil then started to report a rise in foetal anomalies (an initial 141), in the form of microcephaly on 30th October 2015. This was 184 days - or about 6 months later.[4] However, the genetic analyses suggest Zika virus was in Brazil from around 2013. It had a lot longer to get established. Perhaps this is the difference between Brazil and Colombia.

But whatever the difference, there is a rise in microcephaly in Colombia compared to Brazil as we can see from the data in this Pan American Health Organization (PAHO) report...

401 cases counted up to EW 33 (now at EW 37) is 2.9X higher than the usual microcephaly figure per year for Colombia.
From PAHO report.[4]
References...

  1. http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/2016%20Boletin%20epidemiologico%20semana%2037.pdf
  2. Zika Virus Disease in Colombia — Preliminary Report
    http://www.nejm.org/doi/full/10.1056/NEJMoa1604037#t=article
  3. http://virologydownunder.blogspot.com.au/2016/06/the-elephant-squeaked.html
  4. PAHO Zika-Epidemiological Report | Colombia
    http://www.paho.org/hq/index.php?option=com_docman&task=doc_view&gid=35139&Itemid=270&lang=en

Wednesday, 21 September 2016

The reach of Aedes aegypti in Queensland, Australia...

I made this, based on the State of Queensland,(Queensland Health) map from the 2015-2020 Queensland Dengue Management plan.[1] 

Feel free to use this image but please abide by the copyright 
notice found within the 2015-2020 Queensland Dengue management plan.[1]
Click on map to enlarge.
The map may be a useful accompaniment to the recent paper confirming Aedes aegypti is the most likely mosquito vector of Zika virus (ZIKV) in Australia.[2]

While Australia does have these mozzies, it does not have local ZIKV transmission and Dengue is not endemic in Queensland. 

Annual local outbreaks of Dengue do occur in Queensland but these result from imported cases and are confined to north Queensland.[1]

I've added in some other map-related information to the reference section as well.[3,4,5,6]

References...

  1. 2015-2020 Queensland Dengue management plan, Queensland Government.
    https://www.health.qld.gov.au/publications/clinical-practice/guidelines-procedures/diseases-infection/governance/dengue-mgt-plan.pdf
  2. Assessment of Local Mosquito Species Incriminates Aedes aegypti as the Potential Vector of Zika Virus in Australia
    http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0004959
  3. Dengue and climate change in Australia: predictions for the future should incorporate knowledge from the past
    https://www.mja.com.au/journal/2009/190/5/dengue-and-climate-change-australia-predictions-future-should-incorporate?0=ip_login_no_cache%3D20128744c69e384fe459a669360e8b29
  4. “Dengue” mosquitoes detected in Melbourne: What does it mean?
    https://cameronwebb.wordpress.com/2014/03/16/dengue-mosquitoes-detected-in-melbourne-what-does-it-mean/
  5. The Extinction of Dengue through Natural Vulnerability of Its Vectors
    http://journals.plos.org/plosntds/article/asset?id=10.1371/journal.pntd.0000922.PDF

Saturday, 17 September 2016

MERS is a disease we spread...

There is little doubt now that Middle East respiratory syndrome  (MERS) disease outbreaks are triggered by sporadic zoonotic transmission of the MERS coronavirus (MERS-CoV) from an infected camel to a susceptible human. 

Little doubt to anyone who has followed the story of MERS at all, anyway.

But that's just the tip of the iceberg. 

The majority of human cases that have contributed to those steep rises in the cumulative MERS-CoV detection graph below are there because humans have infected other humans while in or associated with a healthcare facility. A telling picture when you consider that MERS-CoV is not a great transmitter. We've done much to make something from what should have been nothing.

Can we vaccinate against lapses in infection prevention and control?


Thursday, 15 September 2016

Middle East respiratory syndrome coronavirus (MERS-CoV) hotzone map gets a paint job..

A slightly updated MERS-CoV map adding in some camel detection sites in Africa and changing up the colours.

27 countries have been visited - 13 have had local transmission.

And there have been 2 humans in Kenya found to harbour antibodies to MERS-CoV. This helps address the question of why we hadn't seen human MERS cases in Africa despite countries harbouring MERS-CoV infected dromedary camels. The answer of course is, we hadn't looked.

Click on image to enlarge

Wednesday, 7 September 2016

MERS-CoV: alpacapalooza...

In the search for the animals that may be another reservoir for, or just support infection by, Middle East respiratory syndrome coronavirus (MERS-CoV), a few studies have looked at furry little alpacas (Vicugna pacos). 

We already know from Eckerle and colleagues' work that cells derived from alpacas have the required receptor molecule that MERS-COV uses (DPP4) and can support replication of MERS-CoV in the lab,[1] But are cells in flasks different from furry animals in the wild?

Three articles came out in the June 2016 issue of Emerging Infectious Diseases looking at alpacas and MERS-CoV. There's no way to tell who submitted when in this journal.


Colorado State University team sought an easier - but still relevant - animal model than camels to work with.[2] They infected 3 (A1-A3) alpacas with 107 plaque forming units (PFU; a cell-specific measure of the amount of infectious virus in a diluted sample) of the HCoV-EMC/2012 variant of MERS-CoV via 3ml of diluted virus per nostril then housed 3 more uninfected alpacas (A4-A6) with them, 3 days later.  

After 70 days, A1-A6 were infected again ("challenged"), the same way. Three other alpacas were infected the same way but euthanized 5 days after infection and their tissues collected for analysis. Nasal swabs were collected before infection and then daily from all animals for 5 days post-infection and on day 10. A4-A6 were also swabbed 3 times per week to day 19. This could all have been a bit more clearly demonstrated using a timeline by the way.

None of the infected animals had a fever or observable nasal discharge and their appetites and activity remained constant. Infectious MERS-CoV was shed by A1-A3 to day 5 and transmission occurred to the A4-A6 arrivals; A4 was found to shed virus for 1 day, A5 shed no virus and A6 shed across 8 days. Lots of variation even in a controlled environment like this.

When A1-A6 were challenged with a fresh infection. A1-A3 had developed antibodies which protected them from infection as no virus was shed. A4-A6 shed a little infectious virus for at most 2 days. A4-A6 also developed neutralizing antibodies but took longer to do so. 

A wild transmission (from inoculated A1-A3 to naive A4-A6) of MERS-CoV which was of a lower dose than the original inoculum, seemed to elicit a milder antibody response as well. 

Virus was found in the nose, larynx and trachea of A7-A9 but not the lungs.


The Australian/Singapore team also sought an animal model with a better temperament and more manageable size than the camel.[3] 

Under biosafety level 3 conditions, they used a camel MERS-CoV variant (Al-Hasa_KFU-HKU13/2013) and exposed each animal to 106 50% tissue culture infectious doses (TCID50; another cell-specific measure of infectious virus quantity), monitored for 21 days then challenged. Blood as well as nasal, oral, rectal and urogenital swabs were collected over time and tested by sensitive RT-PCR, culture and for the presence of neutralizing antibodies.

The animals once again did not develop a fever (animal No.2 had a raised temperature though) or respiratory illness. 

Infectious virus was isolated from oral upper and deep nasal swabs but not from urogenital or rectal swabs. RNA detection by RT-PCR followed this pattern but after challenge and in the presence of antibodies which had appeared from day 10-12, viral RNA could not be detected anywhere in any animal. 

Neutralizing antibody did not appear until 21 days in animal No. 1, 10 days in No. 2 and still hadn't appeared at day 35 in No. 3. It was apparently unnecessary though, for protection from reinfection in this study of alpacas.  

These 2 studies used 106-107 cell-specific quantities of MERS-CoV to infect the alpacas, but, when sought, less was produced - except in one of the Australian/Singapore animals where the peak of 106 TCID50 detected equalled the input dose. This finding suggests the inoculum may not be relatable to real-world amounts of virus produced from an infected animal source. It may however, just be how much is needed to get an model system infected.

The authors all agreed that alpacas could be a good model for MERS-CoV in camels and that animal infections supported the finding of the initial alpaca cell culture work. But that culture link is quite not so straightforward. 

Deliberately HCoV-EMC/2012 variant infected goats, sheep and horses - also animals whose cells had supported MERS-CoV in the laboratory - showed little or no sign of viral replication and the animals mostly remained healthy (some nasal discharge was seen from 2 of 4 horses).[5] Despite some signs of neutralizing antibody developing in goats and a sheep, the same Colorado team were not convinced that any of these animals would be likely hosts for MERS-CoV in the wild. Cells in a flask are not always the most realistic model for animal transmission I guess.



The final alpaca article was from a Qatar/Netherlands team who tested alpacas in a region of Qatar where MERS-CoV is found to be enzootic among camels.[4] 

Hobby alpaca and camel herds were the subjects of this study. They had been kept about 200m apart in the same farm and cared for by the same animal workers. Blood samples were tested from 15 alpacas and 10 dromedary camels; nasal swabs were collected from the 10 camels but nasal, rectal and oral samples were only collected from a subset of the alpacas for antibody testing and sensitive RT-PCR. 

MERS-CoV neutralizing antibody was present in 15 of 15 alpacas and 9 of the 10 camels according to a 90% plaque-reduction neutralization test. This indicated past natural infections had occurred. Antibodies were also detected that suggested past infection by dromedary betacoronaviruses and camelid alphacoronaviruses but this was not unusual or unexpected. No swabs were positive by RT-PCR so no animals were acutely infected. The authors did not know when, how or how often MERS-CoV may have naturally infected the alpacas.

So we can add alpacas to camels on the short list of animals that can host MERS-CoV infection.

References...
  1. Replicative Capacity of MERS Coronavirus in Livestock Cell Lines
    https://wwwnc.cdc.gov/eid/article/20/2/pdfs/13-1182.pdf
  2. Infection, Replication, and Transmission of Middle East Respiratory Syndrome Coronavirus in Alpacas
    http://wwwnc.cdc.gov/eid/article/22/6/pdfs/16-0192.pdf
  3. Experimental Infection and Response to Rechallenge of Alpacas with Middle East Respiratory Syndrome Coronavirus
    http://wwwnc.cdc.gov/eid/article/22/6/pdfs/16-0007.pdf
  4. MERS-CoV Infection of Alpaca in a Region Where MERS-CoV is Endemic
    http://wwwnc.cdc.gov/eid/article/22/6/pdfs/15-2113.pdf
  5. Inoculation of Goats, Sheep, and Horses with MERS-CoV Does Not Result in Productive Viral Shedding
    http://www.mdpi.com/1999-4915/8/8/230