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.



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...

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]

  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.
  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.
  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

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 extan;shed. 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]

  2. Zika Virus Disease in Colombia — Preliminary Report
  4. PAHO Zika-Epidemiological Report | Colombia

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]


  1. 2015-2020 Queensland Dengue management plan, Queensland Government.
  2. Assessment of Local Mosquito Species Incriminates Aedes aegypti as the Potential Vector of Zika Virus in Australia
  3. Dengue and climate change in Australia: predictions for the future should incorporate knowledge from the past
  4. “Dengue” mosquitoes detected in Melbourne: What does it mean?
  5. The Extinction of Dengue through Natural Vulnerability of Its Vectors

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.

  1. Replicative Capacity of MERS Coronavirus in Livestock Cell Lines
  2. Infection, Replication, and Transmission of Middle East Respiratory Syndrome Coronavirus in Alpacas
  3. Experimental Infection and Response to Rechallenge of Alpacas with Middle East Respiratory Syndrome Coronavirus
  4. MERS-CoV Infection of Alpaca in a Region Where MERS-CoV is Endemic
  5. Inoculation of Goats, Sheep, and Horses with MERS-CoV Does Not Result in Productive Viral Shedding

Sunday, 4 September 2016

There (might be) something in the air tonight... [UPDATE]

UPDATE No.1 06SEPT2016
One of the early pieces of science-based news to come out of the May-2015 Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak in South Korea was a June-2015 piece asking whether air conditioning may have played one (of many?) key role in facilitating the spread of virus from infectious patients, within healthcare facilities.[1]

In a publication that came out in April 2016 (yes, the literature did not see much detail on the South Korean outbreak for quite some time), authors described a study to collect and test air and swabs from surfaces in and outside patient's rooms, and their restrooms, in 2 hospitals that housed 3 male cases of MERS pneumonia.

Whenever RT-PCR is used for this sort of work, it brings with it the question of whether infectious virus-containing droplets were captured, or only bits of non-infectious RNA viral genome was detected. This group, like those in the last post (who did not collect air samples), attempted to grow infectious virus. They could confirm that it was infectious virus by observing cell changes in infected laboratory cultures which were also RT-PCR positive. Also the same approach as that described by the South Korean study reviewed in the last post.[3] Additionally, the infected cell cultures also reacted to an anti-Spike protein antibody in a fluorescent test and they even saw some actual virus from swab cultures (not captured air samples?) using electron microscopy.

Some interesting findings from the use of these test on air and swabs samples included:

  • All airs samples from both hospitals were RT-PCR positive and these included the detection of MERS-CoV of RNA in room, restroom and common corridor air. Infectious virus was grown in cells from from 4 of 7 (57%) samples.
  • 42 of 68 (62%) surface swab samples tested positive for MERS-CoV RNA by RT-PCR and included elevator button and rails, doorknobs and handrails inside and outside a patient's room, telephone button, toilet seat, call button, patient pillow, nasal prong, toilet seat, TV, keyboard, stethoscope and air exhaust dampers. Infectious MERS-CoV was isolated from 15 swabs of some of these items including an elevator button, nasal prong, patient pillow, TV, bed handrail, keyboard, stethoscope, toilet seat and an air exhaust damper

This study really addresses three big issues. 

Firstly MERS-CoV from very ill patients late in their disease course, thoroughly contaminates a hospital room and its surrounds - not just with detectable genetic material, but with infectious, viable MERS-CoV virus. 

Secondly, surface contamination was detected from swabs collected 3-7 hours after daily room cleaning suggesting either that cleaning was insufficient or that new virus was quickly laid down on cleaned surfaces (with no lasting anti-viral effect from the cleaning solution). 

Thirdly, the capture of infectious virus from the air implies that the virus maybe present in droplets or droplet nuclei with implications for the level of personal protective equipment required for healthcare workers and visitors to an infected person bedside. It also pertains to the distance away from a case that is considered "safe" for an uninfected person to be. Six feet may not be nearly enough distance, at least if that is a prolonged period in a room.

More data to explain how MERS-CoV is associated with hospital outbreaks. Why it has been allowed to get away with this is a matter for infection prevention and control specialists in each and every healthcare facility to address.


After this was published, Van Kerkhove and colleagues wrote a letter to the editor to make some points about the study noting:

  • an absence of negative control sampling from areas where MERS-CoV patients were not housed.
    Absolutely. I'd even suggest a few different sites in very distant hospital areas from where MERS patients were housed, given the possible human-spread of virus around a facility during and the possibility of silent or subclinical infection in patients admitted to hospitals for other reasons during times of outbreak. This will explore whether false positive laboratory results are occurring.
  • other studies have reported surface contamination that did not yield viable virus. Van Kerkhove note that these negative findings need to be published to balance the literature. Always.
    However, it's well known that virus culture is insensitive compared to RT-PCR methods so it
    may fail to detect infectious virus which may be enough to infect a human . It may also be that infectious virus capable of infecting another person who comes into contact with it is not always present in the air or on surfaces. It may be that the surfaces often simply have non-infectious "bits" of virus detected by RT-PCR -these cannot cause a new infection. But in this study infectious virus was able to be isolated from air and surfaces...unless Van Kerkhove and colleagues are implying contamination of the cultures in some way.
  • the need to replicate these findings in other studies.
    But as is often the case, let's not wait on those findings to recognise that infectious droplets and contaminated surfaces now have some more data to support them and that they fit nicely into a picture of hospital transmission. Precautionary principle.
A second letter was also written by Myoung-don Oh,[7] noting:

  • few infected cells in the cultures / slow growth.
    This isn't too surprising, it may just reflect that there was a low amount of virus in the air, added to the cell cultures compared to that used from the control virus (cell adapted?) stock.
    This may mean that the risk from airborne transmission in these rooms is low. However, since we don't know what amount of MERS-CoV is required to start a new human infection, this is a moot point.
  • the sequences of the room samples were too different from each other.
    This is a bit surprising since within an outbreak, MERS-CoV doesn't usually vary much at all. I'll have a look at how much South Korea's MERS-CoV Spike gene sequences varied and come back to this point.

Both letters were replied to.[8]


  1. Did poor ventilation lead to MERS 'superspread' in Korea?
  2. Extensive Viable Middle East Respiratory Syndrome (MERS) Coronavirus Contamination in Air and Surrounding Environment in MERS Isolation Wards
  3. Korea contamination: Middle East respiratory syndrome coronavirus in the room..
  4. Interpreting Results From Environmental Contamination Studies of Middle East Respiratory Syndrome Coronavirus
  6. Transmissibility of Middle East Respiratory Syndrome by the Airborne Route
  7. Interpreting Results From Environmental Contamination Studies of Middle East Respiratory Syndrome Coronavirus
  8. Reply to Kerkhove et al and Oh
  1. Added in detail on letter by Van Kerkhove and colleagues [4], and rebuttal authors [5]