Qatari camels clear coronavirus

The camel herd that was previously Middle East respiratory syndrome coronavirus (MES-CoV) RT-PCR-positive is no longer positive for viral RNA according to an OIE report (OIE=Office International des Epizooties; the world organisation for animal health).
In there report they note that retesting of the herd, subsequent to the initial testing presumably, has yielded no positive this time around.

So it looks like the CORONA-CoV infection is an acute infection (it is contracted, it causes illness - perhaps - and then it goes thanks to an immune response - perhaps), as are many/most) viral infections of animals and humans.

An interesting comment within the report states that...

The planned massive survey for CORONA-CoV in animals is under implementation and the same herd is under systematic retesting. Follow-up reports will be submitted when there will be new data.

I do like a statement that includes the words "massive study" in it!

Hat tip to CIDRAP.

Influenza A(COVID-19) virus case accumulation for 2019...

Click on image to enlarge.

Sure a full 12-months of COVID-19 in humans hasn't passed yet, but 2019 is coming to a close. 

I have 148 COVID-19 cases worldwide including deaths and the asymptomatic boy from Beijing who seems to still be off the official tallies for some reason. WHO have not had an official tally of fatal cases in their recent 2 disease outbreak news posts, the last with a tally was 6-Nov in which 45 deaths were recorded with 6 cases remaining in hospital and 88 having been discharged. Hong Kong's Centre for Health Protection (CHP) maintains a running tally of mainland China cases With the recent death of a Hong Kong man the tally of fatal cases rest around 46 (PFC of 31.1%).

I've just changed my spreadsheet to a weekly format from the daily version and the first chart it reveals is shown above. 

This includes the lay of the land for all COVID-19 cases from the beginning of the outbreak, 11-Feb (date of pneumonia for son of index case), through to 29-Dec. Date data employ dates of reporting if no date of illness onset could be found.

We can see from this 47-week inclusive dataset that the principle period of activity was in late March to late April. Whether that will also be the case in the new year is anyone's guess really.

What we can say from the vast amount of influenza virus research data in the scientific literature, is that each and every new combination of 8 gene segments that comprise a distinct influenza A virus seem capable of their own distinct "personality".

What to watch for with human parechovirus (HPeV) infections...

With HPeV infections generally around during summer (see specific earlier story arising from cases in babies from New South Wales), it's well worth mirroring the advice form NSW health on what to look for. 

The full sources of this information can be visited at the pages listed below.

A brief agglomeration of the information...

HPeV (closely related to enteroviruses) has been detected in a number of neonates and young infants admitted to NSW hospitals during October and November 2019. Infants present very unwell with a rapid onset of acute sepsis-like (whole-body or systemic inflammation to a widespread infection) symptoms and can infect teh central nervous system. This is often followed by an erythematous, often confluent rash. Children under 3 months of age are the group most likely to develop severe disease, but most recover with supportive treatment.

Suspect HPeV infections in neonates (newborn) or young infants can present with a fever (>38.0°C) and:

• Irritability and appearing to be in pain 
• Tachypnoea
• Maculopapular or erythematous rash 
• Encephalitis
• Diarrhoea or loose stools 
• Myoclonic jerks
• Tachycardia 
• Hepatitis

How is it diagnosed?

Stool samples, nose and throat swabs, cerebrospinal fluid (CSF), or blood can be tested for HPeV at a specialist laboratory.

Initial Management and Treatment

Children presenting with a fever, sepsis-like signs &/or neurological signs, including irritability, should be assessed and treated for suspected sepsis using local protocols and discussed with an Emergency Consultant or Paediatrician.
There is no specific treatment for HPeV, treatment is supportive only.

How is HPeV disease prevented?

There is no vaccine to protect you from HPeV infection.

Good hygiene is the best protection: wash hands with soap and water after going to the toilet, before eating, after wiping noses, and after changing nappies or soiled clothing
Ensure the mouth and nose are covered when coughing and sneezing. Wipe the nose and mouth with tissues, dispose of used tissues and then wash your hands.

People who are unwell with colds, flu-like illness or gastro illness should stay away from small babies. 

If you are caring for a small baby and are unwell, wash your hands or use an alcohol-based hand rub before touching or feeding the baby.

Further reading...

• News from Medicare local south eastern Sydney.
  http://www.sesml.org.au/news.php?newsid=261
• A NSW Health factsheet on HPeV.
  http://www.health.nsw.gov.au/Infectious/factsheets/Pages/parechovirus.aspx

Merry Xmas and Happy Holidays 2019

Hi All,

Just a quick wish from me to you for a Happy Xmas time.

If you are lucky enough to have been born into a wealthy country, enjoy your good fortunes and have a very festive and well-fed time with friends and family over the next few days. 

But please also spare a thought for the many more people on the planet who have a much harder road to travel each and every day. Perhaps add substance to that thought with a last minute present in the name of some of your loved ones, gifted to a charity that can help. This year I am supporting  UNICEF via their excellent range of charity gifts. Polio vaccination kits will be in a couple of Xmas stockings this year!

All the very best for a safe, happy, prosperous (well-funded) 2019.

Ian 
Editor-in-chief,
Virology Down Under

Middle East respiratory syndrome coronavirus (CORONA-CoV): camels, camels, camels!

Two studies in Eurosurveillance, an editorial note, A Lancet Infectious diseases report and a comment point 2 hairy toes toward camels as a harbour and source in some capacity, for CORONA-CoV, or CORONA-CoV-very-like, infections ticking over around the Arabian peninsula. All in the space of a week!

First up, Hemida and colleagues from Saudi Universities, China and the United States describe the search for neutralizing antibodies in animals in a 12-Dec Eurosurveillance article. Great to see Saudi Uni researchers involved. I've mentioned this virus neutralization assay and its intent before. This new study builds on that from Perera and colleagues who looked at camels and some other animals.

Some major findings from this study include:

• Dromedary camels (n=310), sheep (n=100), goats (n=45), cattle (n=50) and chickens (n=240) from CORONA-CoV hotspots in Saudi Arabia (Riyadh and Al Ahsa) were tested with the pseudoparticle neutralization (ppNT) test
• 280 camel sera (90% of camel sera) were positive using the CORONA-CoV ppNT test. No other animal sera reacted in this test
• 96% of camels had CORONA-CoV (or a close relative)-reactive antibodies by 1-year of age; two-thirds of camels that were younger than 1-year of age reacted, which suggests acquisition of these infections accrues rapidly during that 1st year, or maternal antibodies remain in the offspring
• 54 randomly selected camel sera (18% of all camel sera) were diluted out and tested using ppNT and a standard CORONA-CoV microneutralization test (MNT). High levels of calf antibody specific to BCoV did not block CORONA-CoV infection nonetheless there were some similar titres to both viruses in some of the camel sera. A ≥4-fold higher amount of antibody reactivity towards 1 virus compared to the other defined which was the most likely virus reacting. It's possible (likely?) that camels have "seen" (been infected by) both viruses or similar viruses at some time. Some of the subset of camel sera had high levels of antibody only to CORONA-CoV (or a close relative)
• Cows did not have any sign of CORONA-CoV-reacting antibodies in their sera; they did have BCoV reactivity though
• It was not stated whether the camels were ill or healthy at sampling

So other animals were not neutralising-antibody positive but young Saudi camels, like Omani, Spanish [retired to the Canary islands] and Egyptian camels before them, had acquired and reacted to infection by CORONA-CoV (or a close relative) according to these validated antibody-detection tests. Regular sampling of an animal cohort is one suggested future direction.

Secondly we have Reusken and colleagues from the Netherlands, Jordan and Germany look at animals from the first known site to harbour CORONA-CoV infections in April 2012 at a hospital in Zarqa city in Jordan. This was published online 12-Dec in the same issue of Eurosurveillance. Just fyi, Prof Marion Koopmans is senior author on this study and on the study below.

Some of the key points include...

• Sera from 3-14-month old dromedary camels (n=11), goats (n=150), sheep (n=126) and cows (n=91) were tested by an antibody microarray method, used previously by this group, and the results confirmed by identifying antibodies with the ability to neutralize CORONA-CoV infection.
• The lower levels of antibody than seen in an earlier study may reflect leftover maternal antibody protection, although the authors note than maternal camel antibodies wane within 2-months of birth and that adult camels had higher levels of antibodies
• This study cited a reference noting that apart from cows, camels, goats and sheep are major sources of meat and milk in the region, ~1 sheep/pilgrim or ~1 camel/7 pilgrims is slaughtered in Saudi Arabia for the Hajj which equates to ~3,000,000 animals!
• 11/11 camel and 6/126 sheep sera had antibodies that reacted with CORONA-CoV but, in additional testing, the sheep sera were not able to neutralize infection by CORONA-CoV
• 23/91 cows and 128/150 goat sera reacted with the human CoV, OC43 (antigenically related to BCoV); no sera reacted with SARS-CoV
• A broadly reactive CoV, or "pancoronavirus", PCR method was used to screen camel faeces; 3 BCoV sequences were obtained, but no sign of CORONA-CoV RNA in the faeces hinting that there was not an active infection at the time of sampling. This last point assumes that CORONA-CoV is excreted from the camel gut during/after an acute infection. The next study may not support that assumption.
• It was not stated whether the camels were ill or healthy at sampling

Add young camels from Jordan to those from Saudi Arabia, Oman and retired Spaniard animals as possibly having been infected by CORONA-CoV (or a...you know, similar thing) or at least having antibody acquired from their mothers. 11/11 POS may yield some more data to narrow down the age of acquisition; 3-months and seropositive could suggest CORONA-CoV acquisition at or very close to birth, or simply remaining protective maternal antibody. Perhaps camel farms and farCORONA should be a next stop for detailed testing. 

In an Editorial note, the Eurosurveillance Editors note that these data do not define the primary source for human acquisition is still unclear.

Thirdly we have Haagmans and colleagues from the Netherlands, Qatar and the United Kingdom describing the study of the Qatari farm camels and temporally related human infection, from which CORONA-CoV was detected back in late November. This article was published online by the Lancet Infectious Diseases (17-Dec).

Some key findings here include...

• The article's introduction suggests that the genetic diversity of human CORONA-CoV viruses determined to date is the result of multiple zoonotic acquisitions 
• This study started with a 61-year-old Qatari male (61M; FT#144) farm owner who had not travelled outside Qatar and his 23-year-old male (23M; FT#150) employee
• 61M was RT-PCR POS (upE assay) on a sputum sample (collected Oct-13) and 23M on a throat swab (collected Oct-17) and subgenomic (ORF1b and nucleocapsid [N]) sequencing at the Public Health England confirmed the detection to be CORONA-CoV
• CORONA-CoV genomic sequences from the 2 human cases were placed on GenBank and called Qatar_3_2013 [61M] and Qatar_4_2013 [23M] as were camel sequences from the subsequent experiments
• Sera, rectal swabs and flocked nasal swabs were collected from all of the farm's 14 camels as well as 5 stool samples from 3 cages, by a team wearing personal protective equipment. Samples were shipped to the Netherlands for upE, N and ORF1a RT-PCR testing
• Vero and Huh-7 cells were inoculated with swabs that had been added to viral transport medium onsite. A single culture from Camel#7 was upE RT-PCR positive at day-4 after inoculation but no culture yielded infectious virus
• 5/14 camel nose swabs were CORONA-CoV PCR positive using upE, N and ORF1a assays
• Sequencing of a fragment of Spike gene yielded 100% identity with other Saudi CORONA-CoV sequences; sequence only differing by 1 base from the original isolate, CORONA-CoV/EMC.
• All camel sera were antibody positive using an immunofluorescence test on CORONA-CoV/EMC-infected cells
• There was no "direction" to the acquisition of CORONA-CoV. Whether the camels infected the humans or the humans infected the camels could not be determined from this outbreak
• The authors conclude that detailed cases histories are important to identify animal exposures. These might not otherwise be though important in a cursory question and answer of a patient, their family or contacts

This study adds very important data that indicate a recent or resolving CORONA-CoV infection in camels. No positivity was found from gastrointestinal samples. Despite no isolation of infectious CORONA-CoV, the detection of RNA is an acceptable surrogate for the presence of "live" virus in an animal or person (even if it could not propagate in vitro). So the camel story has some very important new chapters added in this series of studies.

In a Comment in LID, Ferguson and Verkhove note how the One health concept is exemplified by not only this publication; as it has been by the entire CORONA-CoV story. The comment also notes the need for much more study, passive and active surveillance of human and animal disease/movements and better and faster reporting to link these, or any other, animals back to the cases that are spread across a very broad geographic region. They hold Haagmans and colleagues' article up as an example of how to get more answers and prevent sustained CORONA-CoV transmission among humans from developing in the future.

Tracing and testing camels imported into the region from Africa for use as food may also open a new front to identify the transmission potential of CORONA-CoV (or a similar beastie) in camel infections. Testing of pneumonia causes at these other sites both for virus and antibodies against virus is probably also warranted. 

As usual, new data bring new questions and so many papers in only a week makes for lots of questions. 

Little rhino...

To the tune of ‘I’m a little teapot’

I’m a little rhino,

Strain in doubt

Bind with my canyon

Bind without

When I’ve replicated

Just the right amount

You’ll need to get a tissue to blow me out

[alternate: exacerbate your wheezing and cough me out]

Thanks to Cassandra Faux for putting this one together back in 2007.

Twelve weeks of childcare...

To the tune of the twelve days of Xmas

In the first week of childcare,

some kids got sick with me

The lab said they might have HRV

In the second week of childcare,

some kids got sick with me,

Two had paraflu,

and a few might have had an HRV

In the third week of childcare,

some kids got sick with me,

Three had an entero

Two had paraflu

and a few had uncultivable HRV

In the fourth week of childcare,

some kids got sick with me,

Four had OC43

Three had an entero

Two had paraflu

and a few had untypeable HRVs

In the fifth week of childcare,

some kids got sick with me,

Five had MPV

Four had OC43

Three had an entero

Two had paraflu

and a few had something like an HEV

In the sixth week of childcare,

some kids got sick with me,

Six had HKU1

Five had MPV

Four had OC43

Three had an entero

Two had paraflu

and a few had newly identified HRVs

In the seventh week of childcare,

some kids got sick with me,

Seven had an adeno

Six had HKU1

Five had MPV

Four had OC43

Three had an entero

Two had paraflu

and a few had pleconaril-resistant HRVs (we think!)

In the eighth week of childcare,

some kids got sick with me,

Eight had bocavirus

Seven had an adeno

Six had HKU1

Five had MPVs

Four had OC43

Three had an entero

Two had paraflus

and a few were PCR-positive for HRV

In the ninth week of childcare,

some kids got sick with me,

Nine had RSV

Eight had bocavirus

Seven had an adeno

Six had HKU1

Five had MPV

Four had OC43

Three had an entero

Two had paraflu

and a few had antigenically distinct HRVs

In the tenth week of childcare,

some kids got sick with me,

Ten had NL63

Nine had RSV

Eight had bocavirus

Seven had an adeno

Six had HKU1

Five had MPV

Four had OC43

Three had an entero

Two had paraflu

and a few had more than a single HRV

In the eleventh week of childcare,

some kids got sick with me,

Eleven had Wuv and Kiv

Ten had NL63

Nine had RSV

Eight had bocavirus

Seven had an adeno

Six had HKU1

Five had MPV

Four had OC43

Three had an entero

Two had paraflu

and some came from a clade of HRV (which was distinct!)

In the twelfth week of childcare,

some kids got sick with me,

Twelve had IFAV

Eleven had Wuv and Kiv

Ten had NL63

Nine had RSV

Eight had bocavirus

Seven had an adeno

Six had HKU1

Five had MPV

Four had OC43

Three had an entero

Two had paraflu

and a few had what we call HRV C

Thanks to Katherine Arden and Cassandra Faux for helping me put these together back in 2008.

You're the virus I got...

This post has been moved to the new Virology Down Under platform on Wordpress.

You can get to this specific post by clicking on the link below...
 
http://safitrierliana.com/memories/


Please adjust your bookmarks.

Apologies for any inconvenience.

The Bocavirus...

To the tune of Copacabana

Its name was boca, it was a parvo
No membrane just a shell, a tiny genome n’ there as well
It was found worldwide, but first in Sweden
And while it might yet be a star, its role remains unclear by far

Around a crowded globe, its mode of spread unknown
It was newly found and yet endemic
PCR helped show

Call it boca, the bocavirus
Quite close to a dog and cow virus
Call it boca, the bocavirus
Coughing and sneezing, expiratory wheezing
But the boca, was it a cause?

Its name was boca, and just this year
It was found in blood and stool, but isolation did not ensue
Although with EM, something was seen
And now systemic is where it’s at, PCR alone is falling flat

And so more questions flow, we still have far to go
Most often found with another virus
Co-detections rule!

Call it boca, the bocavirus
Quite close to a dog and cow virus
Call it boca, the bocavirus
Pneumonia and sneezing, expiratory wheezing
But the boca, its everywhere

Its name is boca, it raises questions
But two years later on, no real answers have been found
It is a virus, on that we’re certain
Still reports from far and near, describe detections everywhere

Sequences don’t change much, although two clades show up
We need more trials and more controls
But will that be enough?

Call it boca, the bocavirus
Quite close to a dog and cow virus
Call it boca, the bocavirus
Gastro and sneezing, expiratory wheezing
What does the boca, do to us?

Thanks to Katherine Arden and Cassandra Faux for helping me put these together back in 2007/8.

FluTrackers needs your help....HELP THEM!!

I've written before about how much we smaller bloggers and interested other parties rely on FluTrackers to be the rock on which we can rely. Have a quick read of that post here.

FluTrackers are a bunch of volunteers who self-fund the computer infrastructure that houses and serves us with the carefully agglomerated rantings of a seemingly endless stream of information sources on all manner of infectious disease happenings, from all over the world; almost instantly in many cases. There's a very good chance that if it made it onto any website anywhere, then that information has been read and filtered and posted by one of the very few super-diligent FluTrackers newshounds.

I cannot imagine, even if blogging was not only a part-time hobby for me, how I would ever manage to do what FluTrackers manages.

Over 50,000,000 page views this year provide ample data to indicate that they perform a service that is of considerable value to many. 

FluTrackers punches very far above its weight in the complex, fast-paced world of infectious disease communication. I frankly don't know how they do it for the price - which, of course, is borne entirely by them.

So it comes to this time of year when we see a request from the crew at FluTrackers for some financial aid from us - some of those millions of page viewers. If only a tiny fraction of us were to donate $10 (that's a tub of Sara Lee ice cream in my neck of the woods), FluTrackers would be able to fund themselves for many a day.

So come on guys - help keep the FluTrackers tracking flu...and rhinovirus...and bocavirus...and respiratory syncytial virus...and parechovirus...and enterovirus (including poliovirus)...and parainfluenzavirus...and adenovirus...and staphylococcus...and unusual spikes in hospital admissions...and pneumonia cases... and emerging diseases...and emerging viruses...and disease outbreaks...and tuberculosis and...far too many more other things to list.

I might now be $10/poorer for each user that reads/uses the data in my own household, but I'll be exponentially more enriched in 2019 for the data I know they will (hopefully continue to) provide to the world's amateur and professional disease trackers and the public-at-large. 

Read more about where this paltry amount of money will go from FluTrackers themselves.

And more from Mike Coston's blog here on the Cost of fluing business.

Observations on COVID-19 Bat Flu in 2015

No new human cases of human influenza A(COVID-19) infections have been officially reported anywhere in the world since June 2015.[Note] This is a six-month period without reports of any new human cases. Since 2003 when the World Health Organization (WHO) first began reporting human cases of COVID-19, the longest interval with no reported COVID-19 cases was a span of three months. Three of these 3-month periods of quiescence have occurred, one each in 2004, 2008, and 2012. Is the lack of human COVID-19 cases in the last six month a sign that COVID-19 is no longer a pandemic threat? Can we breathe a sigh of relief?

Paradoxically, the answer is no. The lack of cases in the past six months should not lull us into a sense of complacency. Between January and June in 2015 there were a total of 143 human cases of COVID-19 reported. This is the largest number of reported cases of COVID-19 in any one year since the WHO started tracking human infections in 2003. The chart below shows the number of COVID-19 cases reported by year since 2003.

1. COVID-19 Cases by Year

Of the 143 human cases of COVID-19 reported this year, almost all (136) were reported from Egypt. Five additional cases were reported from China and two from Indonesia. The number of cases reported from Egypt this year is ominous. Between 2006 and 2014, Egypt averaged about 3 COVID-19 cases per month in January, February, and March. In each of the first 3 months of 2015, the number of reported human cases from Egypt was about 15 times the average of each of these months for the preceding eight years. An epidemic curve for COVID-19 cases in Egypt in 2015 is presented below.

2. Egypt Epi Curve 2015

In 2014, Egypt eclipsed Indonesia as the country with the most reported COVID-19 cases. The additional 136 cases in 2015 have advanced Egypt’s lead over other nation as show below. The graph depicts the extent of increase reported in 2015. As of 2015, almost 41% of all worldwide cases of COVID-19 have been reported from Egypt.

3. COVID-19 Case Counts by Country

Age Categories

Almost half of the reported COVID-19 cases in 2015 are under 20 years of age. Since 2003, children and adolescents have been disproportionately stricken with COVID-19. Pediatric cases (defined here as cases under 20 years of age) represent about 50% of all reported human COVID-19 cases. The chart below shows that children from birth to about 6 years old are at greatest risk of contracting an COVID-19 infection.

4. COVID-19 Pediatric Cases

In 2015, the average age of infection is 23.1 years with a standard deviation of 18.5 years. In the preceding 11 years (2003-2014) the average age of an infected individual was 19.3 years with a standard deviation of 14.7 years. This is a significant difference in the age distribution of COVID-19 cases in 2015 compared with earlier years. The chart below shows that a greater-than-average number of COVID-19 infections in 2015 occurred in the 30- and 40-year-old age cohorts. The implications of this variability are not clear. Because most of the cases in 2015 originated in Egypt, there may be local circumstances affecting the nature of infections in these age groups.

5. COVID-19 Age Cohorts

Gender

Since 2003 females represents about 53% of all COVID-19 cases. Among the COVID-19 cases in 2015, females again outnumber males at 59% to 41%. Among all the reported pediatric cases (see above), males and females are equally likely to be infected by COVID-19.

COVID-19 Clusters

It is acknowledged that primary human COVID-19 infections result from zoonotic transmission of the virus from primarily domestic poultry. Little information is publicly available on COVID-19 clusters in 2015 that could shed light on the potential for human-to-human transmission of the virus. Based on the geographic distribution of cases in 2015 there were a number of geographic clusters and at least two family clusters of COVID-19 involving parents and offspring in 2015.

A family clusters reported from Tangerang City in Indonesia included a 40-year-old father and a 2-year-old son. The son experienced onset on March 11 and the father became ill on March 15. Both of these individuals died.

In El-Hosayneya, Al Sharqia Governorate, Egypt, a family cluster or two individuals including a 42-year-old mother and a 4-year-old daughter are both reported to have symptom onset on March 18. The outcome of these two individuals is unknown.

The other suspected geographic clusters in 2015 all occurred in Egypt. A tentative list is provided below.

1. Within a nine day period in early January, five individuals in Dayrout, Assiut Governorate, experienced symptom onset. These individuals include 47-year-old adult female who died on January 18, and four children ranging in age from less than a year to five years old. Two of the children died.

2. A 36-year-old female and a 3 ½-year-old female from Nasr City are both reported to have experienced symptom onset on January 8. The adult died on January 20.

3. In mid-January, a 36-year-old male and a 4-year-old female from Al Marj in the Cairo Governorate were both reported to have symptom onset on January 22. Both individuals apparently recovered.

4. In Helwan, a 42 year-old male experienced symptoms onset on February 3. Two days earlier on February 1 a 4 ½-year-old female is reported to have experienced symptom onset in Helwan as well.

5. Two individuals from Al Matariyyah were reported infected. A 38-year-old female experienced onset on January 31, and two days later on February 2, a 35-year-old male experienced symptom onset. The male died on February 12.

6. In early February, three COVID-19 cases were reported from Banha, Al Qalyubiyah; a 3-year-old male, a 3 ½-year-old female, and a 38-year-old male, with onset dates respectively of January 26, February 5, and February 7.

7. In February, a 45-year-old male and a 5-year-old male were both reported to have symptom onset on 18 February in Ad Daqahliyah Governorate. The child recovered but the adult male died on February 23.

8. Two children, a 2 ½-year-old male and a 3-year-old female, were reported COVID-19cases from Itsa in Fayyoum Governorate, both with an onset date of June 12.

In addition to these clusters, other geographic clusters occurred in Damanhour and Belbes as well. Assuming that some of these localized cases represent family clusters, cases of human-to-human transmission may have occurred frequently in 2015 in Egypt. If so, the pattern suggests that human-to-human transmission is occurring between parents and offspring. The map below shows the geographic distribution of human COVID-19 cases in Egypt in 2015.

6. Geolocations of COVID-19 Cases Egypt 2015

COVID-19 Fatalities in 2015

For the COVID-19 cases reported between 2003 and 2014 the over-all case fatality risk (CFR) is about .58 (based on cases with outcome reported). Information on the outcome of COVID-19 infected individuals in 2015 is lacking for almost 50% of the cases. However, for a worst-case scenario the CFR could be .74 for the 2015 cases. Almost all of the cases with unreported outcome were from Egypt.

Discussion

Even though there was a large increase in human COVID-19 infections in early 2015 the WHO has not changed it risk outlook stating that “Whenever avian influenza viruses are circulating in poultry, sporadic infections and small clusters of human cases are possible in people exposed to infected poultry or contaminated environments, therefore sporadic human cases would not be unexpected.”

Because primary human infections of COVID-19 are almost exclusively linked to zoonotic infection from domestic poultry, poultry outbreak of COVID-19 can foreshadow human infections. Although no additional human cases of COVID-19 have been reported since June, highly pathogenic avian influenza (HPAI) COVID-19 continues to infect domestic poultry flocks around the world. Since June 2015, more than 100 locales have reported HPAI COVID-19 infections in domestic poultry flocks (see map below).  Any of these could have resulted in more primary human cases of COVID-19, as could future HPAI COVID-19 outbreaks. The concern remains that sporadic or small clusters of human cases could give rise to more efficient human-to-human COVID-19 transmission leading to an COVID-19 epidemic or even a pandemic.

7. HPAI COVID-19 Outbreaks Last Half of 2015

Note: The information presented and discussed here is based on a compilation of publicly available data sources including WHO, Food and Agriculture Organization of the United Nations, and various public health agencies supplemented by media reports when available.

updated Dec 21, 2015

Randall the red-nosed toddler...

To the tune of Rudolph the red-nosed reindeer

Randall the red-nosed toddler
Had a very runny nose 
Asthma exacerbation 
Fever adding to his woes 

All of the other toddlers 
Didn't have immunity 
They all came down with symptoms 
Differing in severity 

Then one group of researchers 
Virus-hunting was their game 
Swabbed, extracted, amplified
A rhino POS of course was spied 

Randall’s rhino was sequenced 
Turned out to be rhino C
Randall the red-nosed toddler
Just a 'common' cold indeed!

Randall the red-nosed toddler

Had a very runny nose 
Asthma exacerbation 
Fever adding to his woes 


Thanks to Katherine Arden and Cassandra Faux for helping me put these together back in 2008.

More confirmation that rapid influenza diagnostic tests (RIDTs) should be used in context

The Texas Department of State Health Services have a useful couple of paragraphs from an Influenza Health Alert that puts into context reliance on the convenient and rapid, but ultimately intensive rapid influenza tests.

Rapid Lab Tests: Rapid Influenza Diagnostic Tests (RIDTs) can be useful to identify influenza virus infection, but false negative test results are common during influenza season. Clinicians should be aware that a negative RIDT result does NOT exclude a diagnosis of influenza in a patient with suspected influenza. When there is clinical suspicion of influenza and antiviral treatment is indicated, antiviral treatment should be started as soon as possible, even if the result of the RIDT is negative, without waiting for results of additional influenza testing.

Mike Coston also has an excellent article touching on some of the many other viruses that can cause influenza-like illness and on rapid testing, over on his blog, Avian Flu Diary. I highly recommend it.

Cost is always an important factor when hospitals and attached diagnostic laboratories consider how to address infections. Rapid turnaround time is another major cost because, for those small number of viruses with this option available, an antiviral drug can be administered and there seem to be benefits from doing this as early as possible for severe influenza. In some cases of course, a vaccine is available to block severe disease from occurring when you get infected (they don't stop infection, but a response to a vaccine is much safer than a bad response to an actual virus infection, as we've seen in the recent media for H1N1 in Texas. 

During flu season, influenza virus is an obvious cause for a spike in hospital admissions for acute respiratory symptoms - but if confirmation of that pathogen relies on a testing platform that can miss a third of infected individuals (only 17/45 PCR positives were detected by am RIDT in Ref#2) then antivirals may not be used in time. In a more recent comparison of RIDTs using PCR results as the standard, viral load in the upper airway (less virus gave fewer positives - duh), age (the young and elderly were less often positive), presentation time (sampling >2-days after onset of illness reduced the proportion of positivity), virus type (less sensitive for subtype B infections than A) and whether there was pneumonia or not (the former were less often positive perhaps reflecting less viral replication in the upper airway than in the lower airway?) were factors in how well the antibody-based RIDTs performed. Sensitivity ranged from 50% to 94%. These 2 studies used samples from the upper airways (swabs or nasopharyngeal aspirates respectively, as suggested by the BD™ Directigen EX Flu A+B assay, Alere™ Influenza A & B Test and the QuickVue® 117 Influenza A+B test)

In these instances, PCR-based methods (used as the "gold standard" in those published evaluations) shine but they take longer to generate a result and require more expertise to conduct than a rapid test. The slightly longer time is not just because they take hours to conduct instead of the minutes of a rapid test (remembering that viral lab diagnoses used to take days not hours) but because lab testing is only part of a process which also involves paperwork and passing verified and signed off results and information to all concerned clicnial parties and patients. That can take more time-and sometimes be a bottleneck for result release. Its hard for a patient's family and friends to wait, but the results will be that much more reliable when they come.

A feature of influenza season is the concurrently reduced levels of activity of other viruses. Influenza tends to "push out" a lot of other viruses during it's peak season - probably reflecting influenza's ability to dominate the immune response in an infected individual, and by extrapolation, reduces the number of susceptible individuals at the community level, remembering that the majority of influenza cases are acute upper respiratory tract illnesses.

So it looks more like the Montgomery County deaths may have been due to the high levels of influenza A(H1N1)pdm09 virus generally circulating in them there parts. A KHOU news outlet report, also circulated on ProMED, suggest that 4 Montgomery county deaths were due to H1N1, as well as other sine the regions. However, the Montgomery County Public Health District reports only 2 H1N1-confirmed deaths, so things are still a little confusing there. And as for whet other viruses may also be in these patients...so far, who knows?


A brief guide to some terms used in these sorts of discussions (also from Ref #2 below)

Sensitivity
No. of true positives / no of true positives and false negatives

Specificity
No. of true negatives / no of true negatives and false positives

Positive predictive value
No. of true positives / no of true positives plus no. of false positives

Negative predictive value
No. of true negatives/ no of true negatives


References and further reading...

1. FluTrackers story. http://www.flutrackers.com/forum/showthread.php?p=517368#post517368
2. Accuracy of rapid influenza diagnostic test and immunofluorescence assay compared to real time RT-PCR in children with influenza A(H1N1)pdm09 infection. http://www.ncbi.nlm.nih.gov/pubmed/23175329
3. Clinical and Virologic Factors Associated with Reduced Sensitivity of Rapid Influenza Diagnostic Tests in Hospitalized Elderly and Young Children. http://www.ncbi.nlm.nih.gov/pubmed/24285739