Ebola virus: wild and domestic animals, plants and insects...

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-Ian

Publishing on 'ebola' is a booming pastime...

One of my jobs since October last year has been to keep up on the literature for Ebola virus and Ebola virus disease. 

At this stage I have a lot of reading to catch up on.


There were 1,858 publications during the 37 years including 1977 to 2013. In 2014 and 2015 (so far), there have been 1,485 publications. 

Click on image to enlarge.

According to a basic search of PubMed using the term 'ebola' - there have been over 1,500 publications - and those are the ones captured by PubMed - to be found using that search term.

Camels and MERS: links to peer-reviewed scientific literature...[UPDATE #2]

Add caption
Camels at the centre, aerosol all around...

I thought this might be a useful page for anyone who would like to know just how much data has been generated that supports a link between camels and MERS-CoV, and studies that have shown near identical viral genomes from camels, and the humans in contact with them. 

Its also worth nothing only 1 ~180nt PCR fragment from 1 bat in 1 study has had a MERS-CoV sequence detected in it and yet they are still considered the most likely ancestor of the MERS-CoV because bats seem to be the ancestral source of many CoVs. 

No studies have found MERS-CoV or infection-blocking (neutralizing) antibodies to MERS-CoV in any non-human or non-dromedary camel animal despite investigation of:

• horses
• llamas
• alpacas
• bactrian camels
• guanaco
• goats
• sheep
• water buffalo
• cows
• birds
• pigs
• chickens

While rats and mice have not been tested in the wild, deliberately inoculated lab mice and Syrian hamsters do not support growth of MERS-CoV and 2 rat cell lines (Chan et al. J Infect Dis. 2013;207:p1743-52) did not support viral transcription or growth. Not the end of the small animal story of course and more testing of small animals is a good thing, but neither has the camel story been completed yet (finding infectious virus in milk, urine and meat and some air sampling and testing from around camels would be nice). However, the camel story does already have some very solid chapters suggesting humans could be coming into sporadic contact with the virus. 

So a few quick thoughts to put camels in context with sporadic infections that are not traceable to contact with a known human case. 

1. I don't think any scientist has ever suggested every camel is carrying/shedding MERS-CoV all the time. Nothing supports that. 
2. Most MERS-CoV cases have been from spread between humans and most of those are now linked with hospital-based settings (thanks Jeddah outbreak!). Whether community spread is ongoing is completely unknown until someone tests the community, post-Jeddah outbreak, and not people linked to hospitalized confirmed cases (they only bias the results). 
3. As we saw in 2nd and 3rd US MERS-CoV detections, 2 face-to-face business meetings, 1 with at least 40-min of face time, and a handshake, was sufficient to pass along MERS-CoV between humans when the index case was not all that ill. 
• I hope the R0 guys can build this sort of event into their predictive models and 
• I think this has real and major implications for what "contact" with a camel actually means. I have serious doubts that people who are RT-rtPCR positive and being interviewed and asked about their exposure to camels would think of being near a camel as contact with camels. Is that how they are being asked?
  THIS RESULT WAS RETRACTED 28-May-2014 FOLLOWING A NEGATIVE NEUTRALIZING ANTIBODY TESTING.

Better understanding the proximity-possibility needs experimental testing but in the meantime it is also very important for those who are asking infected people about their animal exposures and contacts to understand that respiratory viruses don't just spread by physical contact. I am unaware of what is being asked and in how much detail - this may already be well understood. 

If people being asked about past contact with camels are thinking "hey, yeah, I was walking between camel pens for 20 minutes, but no I didn't kiss one or lick its nose or feed it or anything touchy-feely" (I'm 100% certain those would be exactly the words in their heads) - then they may well say "no contact". To my mind, that level of proximity in that example, especially if 1 or 2 of those camels was symptomatic, would be contact.

Anyway, do let me know if I've missed any papers below - or if new references come out.

Camels in the literature...

1. Reusken CB, Haagmans BL, Muller MA, Gutierrez C, Godeke GJ, Meyer B et al. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study. Lancet InfectDis 2013 October;13(10):859-66.
2. Perera RA, Wang P, Gomaa MR, El-Shesheny R, Kandeil A, Bagato O et al. Seroepidemiology for MERS coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in Egypt, June 2013. Euro Surveill 2013;18(36):ii.
3. Hemida MG, Perera RA, Wang P, Alhammadi MA, Siu LY, Li M et al. Middle East Respiratory Syndrome (MERS) coronavirus seroprevalence in domestic livestock in Saudi Arabia, 2010 to 2013. Euro Surveill 2013;18(50):20659.
4. Reusken CB, Ababneh M, Raj VS, Meyer B, Eljarah A, Abutarbush S et al. Middle East Respiratory Syndrome coronavirus (MERS-CoV) serology in major livestock species in an affected region in Jordan, June to September 2013. EuroSurveill 2013;18(50):20662.
5. Haagmans BL, Al Dhahiry SH, Reusken CB, Raj VS, Galiano M, Myers R et al. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation. Lancet Infect Dis 2014 February;14(2):140-5.
6. Alexandersen S, Kobinger GP, Soule G, Wernery U. Middle East respiratory syndrome coronavirus antibody reactors among camels in Dubai, United Arab Emirates, in 2005. Transbound Emerg Dis 2014 April;61(2):105-8.
7. Alagaili AN, Briese T, Mishra N, Kapoor V, Sameroff SC, Burbelo PD et al. Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia. MBio 2014;5(2):e00884-14.
8. Meyer B, Muller MA, Corman VM, Reusken CB, Ritz D, Godeke GJ et al. Antibodies against MERS coronavirus in dromedary camels, United Arab Emirates, 2003 and 2013. Emerg Infect Dis 2014 April;20(4):552-9.
9. Hemida MG, Chu DKW, Poon LLM, Perera RAPM, Alhammadi MA, Ng H-Y et al. MERS Coronavirus in dromedary camel herd, Saudi Arabia. Emerg Inf Dis2014;20(7).
10. Nowotny N, Kolodziejek J. Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels, Oman, 2013. Euro Surveill2014;19(16).
11. Raj VS, Farag EABA, Reusken CBEM, Lamers MM, Pas SD, Voermans J et al. Isolation of MERS Coronavirus form a Dromedary Camel, Qatar, 2014. Emerg Inf Dis 2014;20(8).
12. Corman VM, Jores J, Meyer B, Younan M, Liljander A, Said MY et al. Antibodies against MERS Coronavirus in Dromedary Camels,Kenya, 1992-2013. EmergInf Dis 2014;20(8).
13. Chu DKW, Poon LLM, Gomaa MR, Shehata MM, Perera RAPM, Zeid DA et al. MERS coronaviruses in dromedary camels, Egypt. Emerg Infect Dis 2014;20(6).
14. Ziad A. Memish, Matthew Cotten, Benjamin Meyer, Simon J. Watson, Abdullah J. Alsahafi, Abdullah A. Al Rabeeah, Victor Max Corman, Andrea Sieberg, Hatem Q. Makhdoom, Abdullah Assiri, Malaki Al Masri, Souhaib Aldabbagh, Berend-Jan Bosch, Martin Beer, Marcel A. Müller, Paul Kellam, and Christian Drosten. Human Infection with MERS Coronavirus after Exposure to Infected Camels, Saudi Arabia, 2013. Emerg Inf Dis 20(6) (online May 16). 
15. Esam I. Azhar, Ph.D., Sherif A. El-Kafrawy, Ph.D., Suha A. Farraj, M.Sc., Ahmed M. Hassan, M.Sc., Muneera S. Al-Saeed, B.Sc.,Anwar M. Hashem, Ph.D., and Tariq A. Madani, M.D. Evidence for Camel-to-Human Transmission of MERS Coronavirus
NEJM June 4.
NB. This study is the same human case and camel herd tested in #14. Sampling times differ subtly.

Camels and MERS: links to peer-reviewed scientific literature...[UPDATE #1]

Add caption
Camels at the centre, aerosol all around...

I thought this might be a useful page for anyone who would like to know just how much data has been generated that supports a link between camels and MERS-CoV, and studies that have shown near identical viral genomes from camels, and the humans in contact with them. 

Its also worth nothing only 1 ~180nt PCR fragment from 1 bat in 1 study has had a MERS-CoV sequence detected in it and yet they are still considered the most likely ancestor of the MERS-CoV because bats seem to be the ancestral source of many CoVs. 

No studies have found MERS-CoV or infection-blocking (neutralizing) antibodies to MERS-CoV in any non-human or non-dromedary camel animal despite investigation of:

• horses
• llamas
• alpacas
• bactrian camels
• guanaco
• goats
• sheep
• water buffalo
• cows
• birds
• pigs
• chickens

While rats and mice have not been tested in the wild, deliberately inoculated lab mice and Syrian hamsters do not support growth of MERS-CoV and 2 rat cell lines (Chan et al. J Infect Dis. 2013;207:p1743-52) did not support viral transcription or growth. Not the end of the small animal story of course and more testing of small animals is a good thing, but neither has the camel story been completed yet (finding infectious virus in milk, urine and meat and some air sampling and testing from around camels would be nice). However, the camel story does already have some very solid chapters suggesting humans could be coming into sporadic contact with the virus. 

So a few quick thoughts to put camels in context with sporadic infections that are not traceable to contact with a known human case. 

1. I don't think any scientist has ever suggested every camel is carrying/shedding MERS-CoV all the time. Nothing supports that. 
2. Most MERS-CoV cases have been from spread between humans and most of those are now linked with hospital-based settings (thanks Jeddah outbreak!). Whether community spread is ongoing is completely unknown until someone tests the community, post-Jeddah outbreak, and not people linked to hospitalized confirmed cases (they only bias the results). 
3. As we saw in 2nd and 3rd US MERS-CoV detections, 2 face-to-face business meetings, 1 with at least 40-min of face time, and a handshake, was sufficient to pass along MERS-CoV between humans when the index case was not all that ill. 
• I hope the R0 guys can build this sort of event into their predictive models and 
• I think this has real and major implications for what "contact" with a camel actually means. I have serious doubts that people who are RT-rtPCR positive and being interviewed and asked about their exposure to camels would think of being near a camel as contact with camels. Is that how they are being asked?
  THIS RESULT WAS RETRACTED 28-May-2014 FOLLOWING A NEGATIVE NEUTRALIZING ANTIBODY TESTING.

Better understanding the proximity-possibility needs experimental testing but in the meantime it is also very important for those who are asking infected people about their animal exposures and contacts to understand that respiratory viruses don't just spread by physical contact. I am unaware of what is being asked and in how much detail - this may already be well understood. 

If people being asked about past contact with camels are thinking "hey, yeah, I was walking between camel pens for 20 minutes, but no I didn't kiss one or lick its nose or feed it or anything touchy-feely" (I'm 100% certain those would be exactly the words in their heads) - then they may well say "no contact". To my mind, that level of proximity in that example, especially if 1 or 2 of those camels was symptomatic, would be contact.

Anyway, do let me know if I've missed any papers below - or if new references come out.

Camels in the literature...

1. Reusken CB, Haagmans BL, Muller MA, Gutierrez C, Godeke GJ, Meyer B et al. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study. Lancet InfectDis 2013 October;13(10):859-66.
2. Perera RA, Wang P, Gomaa MR, El-Shesheny R, Kandeil A, Bagato O et al. Seroepidemiology for MERS coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in Egypt, June 2013. Euro Surveill 2013;18(36):ii.
3. Hemida MG, Perera RA, Wang P, Alhammadi MA, Siu LY, Li M et al. Middle East Respiratory Syndrome (MERS) coronavirus seroprevalence in domestic livestock in Saudi Arabia, 2010 to 2013. Euro Surveill 2013;18(50):20659.
4. Reusken CB, Ababneh M, Raj VS, Meyer B, Eljarah A, Abutarbush S et al. Middle East Respiratory Syndrome coronavirus (MERS-CoV) serology in major livestock species in an affected region in Jordan, June to September 2013. EuroSurveill 2013;18(50):20662.
5. Haagmans BL, Al Dhahiry SH, Reusken CB, Raj VS, Galiano M, Myers R et al. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation. Lancet Infect Dis 2014 February;14(2):140-5.
6. Alexandersen S, Kobinger GP, Soule G, Wernery U. Middle East respiratory syndrome coronavirus antibody reactors among camels in Dubai, United Arab Emirates, in 2005. Transbound Emerg Dis 2014 April;61(2):105-8.
7. Alagaili AN, Briese T, Mishra N, Kapoor V, Sameroff SC, Burbelo PD et al. Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia. MBio 2014;5(2):e00884-14.
8. Meyer B, Muller MA, Corman VM, Reusken CB, Ritz D, Godeke GJ et al. Antibodies against MERS coronavirus in dromedary camels, United Arab Emirates, 2003 and 2013. Emerg Infect Dis 2014 April;20(4):552-9.
9. Hemida MG, Chu DKW, Poon LLM, Perera RAPM, Alhammadi MA, Ng H-Y et al. MERS Coronavirus in dromedary camel herd, Saudi Arabia. Emerg Inf Dis2014;20(7).
10. Nowotny N, Kolodziejek J. Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels, Oman, 2013. Euro Surveill2014;19(16).
11. Raj VS, Farag EABA, Reusken CBEM, Lamers MM, Pas SD, Voermans J et al. Isolation of MERS Coronavirus form a Dromedary Camel, Qatar, 2014. EmergInf Dis 2014;20(8).
12. Corman VM, Jores J, Meyer B, Younan M, Liljander A, Said MY et al. Antibodies against MERS Coronavirus in Dromedary Camels,Kenya, 1992-2013. EmergInf Dis 2014;20(8).
13. Chu DKW, Poon LLM, Gomaa MR, Shehata MM, Perera RAPM, Zeid DA et al. MERS coronaviruses in dromedary camels, Egypt. Emerg Infect Dis 2014;20(6).

Ways in which seasonal and pandemic influenza infections differ

In commenting on another article in the American Journal of Pathology but Gao et al, Kevin Hartshorn nicely summarizes some of the possible reasons why a pandemic influenza kills otherwise healthy young adults more often than a seasonal influenza does. 

The answer is as complex as the milieu of interactions between viral proteins and nucleic acids and our innate and adaptive immune systems, our health, genetic factors, environmental factors and our prior exposure to different influenza viruses - and that's pretty complex!

Hartshorn categorizes the differences between seasonal and emerging influenza impact in young adults using 3 sections:

1. Differences in their ability to cause disease (pathogenicity).
• pandemic influenza generally kill more young adults whereas seasonal influenza kills mostly the elderly and the young
• This is also apparent in ferret animal models
• The viral haemagglutin (HA) protein is key to pathogenesis, playing a central role in pathology due to immune responses and inflammation whereas increases in viral replication are due to the viral replication complex (including PB1, PB2 and PA). Glycosylation of HA is a key pathogenicity determinant because a lack of apical glycosylation allows viral escape from a major non-specific defence; the action of surfacant protein D.
2. Differences in the way the infected host responds to them.
• Pregnant mice and humans show increased severity of disease. This may relate to a reduced innate immune response to pandemic influenza. Bypassing innate immunity may also allow the virus to bypass a key regulatory process, leading to a more over-reactive inflammation.
3. Differences in past history of influenza virus exposures
• Possibly, even with a strong immune cell response, the absence of any prior exposure to a related influenza results in the absence of any cross-protective neutralizing antibodies - the type that can moderate disease - in younger adults compared to older adults. The elderly may have such antibodies from exposures to other H1N1 strains between 1918 and 1957. 

Prof Ziad A Memish: principal author of MERS-CoV data

Since the human cases of MERS-CoV started in 2012, the majority of publications describing signs and symptoms of disease, incubation periods, sites and routes of transmission clusters of infections have come from the Kingdom of Saudi Arabia, and most of those have involved co-authorship, usually as senior author, by Prof Memish. He also commented on the initial ProMED posting from Prof Ali Mohamed Zaki, which announced the MERS-CoV to the world. I wrote something about that back in May.

According to a WHO biography, Prof Memish is a senior infectious diseases consultant at King Fahad Medical City, Professor at Alfaisal University and King Saud University, President of the Saudi Association of Public Health, Adjunct Professor at Emory University. He is also the KSA Ministry of Health's Assistant Deputy Minister of Health for Preventative Medicine in the Kingdom of Saudi Arabia (KSA).

I've briefly compiled some (its not exhaustive) of Prof Memish's MERS-CoV-related literature,  looking at the points he has found interesting and/or lacking in data and  requiring more research. As someone at the current hotzone, these should be points worthy of addressing. I have ordered the papers in time - starting each with the number of known MERS-CoV cases listed by the paper:

1. 3 Cases. In the article in the Saudi Medical Journal, Oct 2012, AlBarrak and colleagues noted:
• The need for a validated serological test from international colleagues; 
• 1/3 cases had farm animal exposure, but all cases had been exposed to dust storms through the summer, possibly aerosolized virus also
• Investigations of potential animal reservoirs are in progress
2. 9 Cases. In an article in the International Journal of Infectious Diseases, Dec 2012, Pollack and colleagues noted:
• 5/9 cases had a history of prior animal exposure
• They asked what the animals were and whether there had been any animal, including bat, studies?
3. 9 Cases. In an article in Clinical Microbiology and Infection, Feb 2013, Gautret and colleagues noted:
• Their study was not based on case selection using symptoms, but was a (first?) prospective screening study without regard for symptoms.
• MERS-CoV was absent from departing or returning French Hajj pilgrims using a slightly adapted (different cycler, same primers) RT-PCR assay based on that of Corman et al.
• 2012 French Hajj pilgrims had a lower flu vaccination rate than did a 2009 cohort
• Limited data to support human-to-human transmission, suggesting zoonotic transmission is likely
4. 15 cases. In an article in the Lancet Infectious Diseases, May 2013, McCloskey and colleagues noted:
• The importance of rapid genetic sequencing as was shown during the SARS-CoV outbreak
• Knowledge gaps include those pertaining to the source, mode of transmission, epidemiology  geographic distribution, predisposing factors for infection and disease, incubation period, immunopathogenesis, range of clinical manifestations and epidemic potential
• Focus on the Middle East may be missing international MERS-CoV cases
• Available molecular tests are experimental and their sensitivity and specificity require definition
• Serological test are urgently needed for epidemiology and investigations of global distribution 
5. 90 cases. In the Lancet Infectious Diseases, July 2013, Assiri and colleagues describe the largest case study so far noting:
• MERS-CoV cases present with a wide range of clinical manifestations, with greatest impact in those with underlying comorbidities
• Knowledge gaps (43 key gaps and priorities listed) include those pertaining to epidemiology, community prevalence, transmission, clinical course, diagnostics, patient management and infection control
6. ? Cases. In the Eastern Mediterranean Health Journal, July 2013, Alwan and colleagues noted:
• Priority to monitor for sustained human-to-human transmission
• The global public health community must attempt to understand the public health risks posed by MERS-CoV
• Knowledge gaps include those pertaining to source, how it emerged in humans, how widespread it is
• WHO and the global community have benefited from willingness of countries in the region to share viruses and information immediately, allowing rapid development of diagnostic tests
7. ? Cases. In the Eastern Mediterranean Health Journal, July 2013, Joseph and colleagues noted:
• Knowledge gaps include those pertaining to spectrum of disease, changes in MERS incidence, case definition, source of infection.
• There are global high expectations that everything is being done to detect and control an emerging disease threat; global preparation is needed due to uncertainties
• Need to train laboratory staff for MERS-CoV testing, identify where capacity building is required and liase with animal research group to strengthen collaborative studies
8. 90 cases. In the International Journal of Infectious Diseases, Aug 2013, Omrani and colleagues noted:
• Nosocomial transmission may be occurring via undetected or asymptomatic healthcare workers
• Knowledge gaps include those pertaining to source, intermediate host, pathogenesis, infectivity and risk factors
• Diagnostic assays need optimizing
• Therapeutic options need to be identified
9. 94 cases. In the New England Journal of Medicine, Aug 2013, Memish and colleagues noted: 
• Health care workers should be reminded of infection prevention and control measures
• The KSA routinely screens all close contacts of MERS-CoV patients and this screening has identified 7 HCWs positive for MERS-CoV
• How great a risk is posed to healthcare workers by MERS-CoV patient body fluids, excreta, bodily fluids, samples and surfaces contaminated by such

So, there is a consistent thread among these expert publications highlighting a need to find the animal host and requests for improved diagnostic tests, although I'm not sure what is wrong with the WHO-recommended assays. 

There is a similar need for antibody-detection (serological) tests. I believe these already exist, but are lacking in validation (proof they are as good at detecting negatives as positives, and not picking up too many false negatives or false positives). This will need a suitably large panel of known positive sera, best obtained from the most numerous source of cases, the KSA. Hopefully that is being assembled now, even if it requires contacting former patients, symptomatic or asymptomatic, to retrospectively ask for a blood sample. This is a one-off validation that would be invaluable to the world since there are multiple sources of MERS-CoV or virus proteins to make the assay, but sources of known positive sera are limited. 

As noted by Prof Memish, an antibody test would allow each country to see if MERS-CoV was was/had been active there and could be used to determine what level of mild or asymptomatic illness there is, if any, worldwide.

What Prof Memish and his co-authors and the world's scientist want to know seems to have been largely made clear back in 2012 when MERS emerged. What's unclear is what is being done to address the list (Ref 7 has a good example) and who is doing what?

New summary of H7N9 events.

The US CDC publish a wrap-up in an early release issue of Morbidity and Mortality Weekly Report.

Study supports poor H7N9 transmission - from anything!

A new paper in by J. Han et al. Emerging Microbes and Infection concludes that neither 2 vendors in an H7N9-positive poultry market visited by the H7N9-positive patient (our Case#10, also studied in recent Lancet article) nor his close contacts, were WHO RT-rtPCR positive. 

So picking up H7N9 is certainly not a frequent thing. Also supported by the few cases that have been identified considering the population in these areas that move through and interact with birds and the markets. 

Also, once you have it, transmitting H7N9 it seems to be an infrequent event.