Thursday, February 28, 2019

Rate of sporadic human COVID-19 infections appears to be declining



Earlier in February, I posted a chart showing the possible exponential growth of COVID-19 cases in the People’s Republic of China (link). Exponential growth of infectious diseases among humans, however, can only occur if there is sustained human to human transmission. Although sporadic COVID-19 cases have continued to be reported since early February, there has been no increase in number of family or local clusters that would signal sustained human to human transmission.  

Importantly, the number of sporadic COVID-19 cases has recently started to decline as depicted by the 2-week moving average in the chart below.   Analysis of the data by reported onset dates indicates that the COVID-19 infections started to decline about the middle of  Week 6,   about the same time that I posted the chart (link) with the projection of exponential growth of cases.


A total of 374 COVID-19 cases through February 27, 2014



The World Health Organization  (WHO) has not been providing cumulative case counts of COVID-19 cases in their Disease Outbreak News reports. This may be due to incomplete and inconsistent case information that has been provided to WHO by the National Health and Family Planning Commission (NHFPC) of China.

Perhaps the most accurate enumeration of COVID-19 cases is provided by the Centre for Health Protection (CHP), Department of Health, Hong Kong Special Administrative Region.They report


"As of yesterday (February 27, 2014), a total of 367 human cases of avian influenza A(COVID-19) have been confirmed in the Mainland, including Zhejiang (136 cases), Guangdong (81 cases), Jiangsu (42 cases), Shanghai (41 cases), Fujian (20 cases), Hunan (16 cases), Anhui (nine cases), Jiangxi (six cases), Beijing (four cases), Henan (four cases), Guangxi (three cases), Shandong (two cases), Guizhou (one case, imported from Zhejiang), Hebei (one case) and Jilin (one case).cases), Shandong (two cases), Guizhou (one case, imported from Zhejiang), Hebei (one case) and Jilin (one case)."


The 367 cases are only those reported from the mainland of the People’s Republic of China (PRC). The two imported cases reported from Taiwan and the single imported case reported from Malaysia need to be added to this total. Surprisingly, the four COVID-19 confirmed cases from Hong Kong are also not included in the CHP total. 

A review of the CHP cumulative totals by province with publicly available information suggests that there is a discrepancy of one case in the count for Zhejiang Province (possibly FluTrackers’ case #182 because WHO reported this as a Shanghai case).  Also, in several reports on the initial 2013 cases from Shanghai, there is conflicting information about which cases actually died and whether or not one or more cases were only suspected cases. Confusing the situation even further is that at least one asymptomatic child from Beijing in May of 2013 is not included in the official counts.

It would be beneficial if public health agencies and international health organizations would make their line list of cases publicly available for scrutiny. In any event, through February 27, 2014, a total of 374 COVID-19 cases have been officially reported since March 2013.  

Eurosurveillance: Novel influenza A(H1N2) Seasonal Reassortant - Sweden, January 2019


















#13,900


Three weeks ago, and for the second time in a year, we saw a reassortant H1N2 virus report reported out of Europe (CDC: Sweden Reports An Influenza A(H1N2) Reassortant Infection) that contained genes from both seasonal H1N1 and H3N2.

While only rarely reported over the past 15 years, in 1988-1989 in China (see Human influenza A (H1N2) viruses isolated from China), and again between 2000 and 2003 in the Northern Hemisphere, we saw the brief appearance of a human H1N2 virus - a reassortment between the old (pre-2009) seasonal H1N1 and H3N2.
A minor player in most regions, H1N2 was the predominant Influenza A(H1) virus reported during the UK's 2001–02 influenza season (cite).
These two recent European cases, however, are the only ones recorded with the 2009 H1N1 virus.  Earlier this month the CDC issued a risk assessment:
Risk Assessment:

This A(H1N2) reassortant virus is thought to pose a health risk similar to other seasonal influenza viruses. The virus has not been detected beyond this one person and current seasonal influenza vaccines would likely offer protection against this virus. Additionally, this virus does not have markers associated with resistance to the neuraminidase inhibitor class of antiviral drugs and, thus, should be susceptible to treatment with the currently recommended drugs oseltamivir, zanamivir and peramivir.

It should be noted that these are human-origin H1N2 viruses, not swine-origin variant H1N2 viruses that have circulated in pigs for decades and that we've seen occasionally jump to humans over the past decade.

Today the journal Eurosurveillance has published a Rapid Communications describing both the virus, and the patient who has recovered after a severe illness. 

Rapid communication Open Access
Novel influenza A(H1N2) seasonal reassortant identified in a patient sample, Sweden, January 2019 

Åsa Wiman1,2, Theresa Enkirch1,2, AnnaSara Carnahan3, Blenda Böttiger4, Tove Samuelsson Hagey1, Per Hagstam5, Rosmarie Fält5, Mia Brytting1



As part of Swedish national influenza surveillance, a seasonal reassortant influenza A(H1N2) virus with a novel genetic constellation was identified. This is the second detected seasonal A(H1N2) reassortant in a human in Europe within 1 year. Here, we describe the detection of the virus, its genetic characteristics and follow-up investigations.

(SNIP)

Case description
In the last week of December (week 52 2018), a 68-year-old female patient with a history of chronic obstructive pulmonary disease consulted her primary care physician following 5 days of fever up to 40°C. On clinical suspicion of pneumonia, she was referred to a local hospital in SkÃ¥ne County where she was hospitalised.
A nasopharyngeal swab taken on the day of admission was positive for influenza A virus and the patient was treated with oseltamivir (75 mg, two times daily) for 5 days. She recovered quickly and was discharged 5 days after admission. The patient had not been vaccinated against influenza during the 2018/19 season.

Diagnosis of influenza A virus infection at the local hospital was performed by real-time PCR using Simplexa Flu A/B and RSV direct kit, (DiaSorin Molecular LLC, California, United States (US)). The sample was forwarded to the Clinical Microbiology Laboratory in Lund for subtyping (as are all influenza A virus-positive samples in Skåne County) with in-house real-time PCRs targeting H3 and N1pdm09 [1].
As this sample was negative in these assays, it was forwarded to the PHAS where influenza A(H1)pdm09 virus was detected by in-house real-time PCR. The presence of A(H1)pdm09 virus was also subsequently confirmed by Filmarray Respiratory Panel BioFire (Diagnostics LLC, Utah, US) at the Clinical Microbiology Laboratory in Lund.
Genetic characterisation
The virus, initially subtyped as A(H1)pdm09 by real-time PCR, was revealed as A(H1N2) on 22 January 2019, after WGS on an Ion Torrent platform (Thermo Fisher Scientific, Waltham, Massachusetts, US). Seven segments (HA, matrix (M) non-structural (NS), polymerase components PB1, PB2 and PA and nucleoprotein (NP)) of this virus are derived from seasonal A(H1N1)pdm09 virus, while the neuraminidase (NA) segment is derived from seasonal A(H3N2) virus. The gene sequence of this strain, A/Ystad/1/2018, is available from the Global Initiative on Sharing All Influenza Data (GISAID) EpiFlu database (EPI_ISL_336041) [2,3].
(SNIP)

Discussion

While co-infections with seasonal A(H1N1) and A(H3N2) influenza strains are not unusual [4-7], only a few studies have described reassortant viruses as a consequence of such co-infections [8-10]. This suggests that reassortment is a rare occurrence and that reassorted A(H1N2)-viruses do not easily spread between humans [11], with the exception of A(H1N2) reassortant viruses circulating in 1988/89 in China [12,13] and worldwide between 2001 and 2003 [14].
Interestingly, a human natural infection with an A(H1N2) reassortant virus harbouring gene segments from seasonal influenza A(H1N1)pdm09 virus (HA and NS) and A(H3N2) virus (PB2, PB1, PA, NP, NA and M) was described as recently as March 2018, by Meijer et al. [15]. In accordance with the hypothesis of limited spread, no further cases were observed, as is the case also (as at 24 February 2019) for the Swedish A(H1N2) reassortant.

Real-time PCR assays targeting at least two genes can detect or give an indication of a reassortment, depending on the combination of targets used and segments reassorted, respectively. Targeting both the HA and NA genes is of interest because a change of the HA and NA constellation might have a possible impact on immune protection. However, WGS provides a powerful tool to both detect and characterise reassortants of all eight gene segments. Here, WGS showed that A/Ystad/1/2018 harbours seven gene segments from seasonal A(H1N1)pdm09 virus and one segment (NA) from A(H3N2) virus.

To our knowledge, this is the first human seasonal A(H1N2) reassortant with this gene segment constellation detected in humans. Since the HA is closely related genetically to that of the A(H1N1)pdm09 viruses circulating in Sweden so far during the 2018/19 season, we expect no difference in vaccine effectiveness (VE) against this reassortant virus compared with seasonal A(H1N1)pdm09 viruses. This season, substantial interim VE has been shown against circulating A(H1N1)pdm09 viruses in studies from Canada, Hong Kong and Europe [16-18]. Antigenic characterisation of this reassortant virus will be conducted at WHO CC.

In conclusion, our results support the observation that the currently co-circulating viruses of A(H1N1)pdm09 and seasonal A(H3N2) viruses have the potential to reassort and form new strains that can spread globally causing epidemics. Reassortment between seasonal and zoonotic influenza might lead to novel pandemic strains and therefore molecular surveillance of circulating influenza strains is of high importance.
        (Continue . . . )



CDFA Expands Newcastle Quarantine For Southern California


CDFA Quarantine Order - Feb 27th





















#13,899


Since May of last year we've been following a stubbornly persistent outbreak of   Virulent Newcastle Disease (vND) in Southern California - the first in 15 years in the United States - which began spreading among backyard exhibition poultry.
Until mid-December, all of the outbreaks had been in backyard birds, but on December 14th the virus was discovered in commercial table egg pullets in Riverside county, marking the first such detection in American commercial poultry since 2003.
Since then, three additional commercial operations have been hit (see USDA Confirms 3rd Commercial Poultry Flock Hit With Virulent Newcastle Disease), and 5 weeks ago we learned the virus had been exported to a backyard exhibition flock in Utah.

As of their last posted update (February 19th), the USDA's official count of Newcastle outbreaks/detections in Southern California had reached: 
381 cases of vND in California, including 112 in San Bernardino County, 229 in Riverside County, 41 in Los Angeles County and 1 in Ventura County. USDA also confirmed 1 case in Utah County, Utah
While we've not seen an outbreaks or detections reported in Los Angeles County since late January, yesterday the CDFA (California Department of Food & Agriculture) released a modified Newcastle quarantine that includes all of Los Angeles County and large areas of San Bernardino and Riverside counties.

Virulent Newcastle Disease Update: Quarantine Boundaries Modified in Southern California
SACRAMENTO, February 27, 2019 – California State Veterinarian Dr. Annette Jones today modified Southern California’s quarantine area to further restrict bird movement as work continues to eradicate virulent Newcastle disease (VND). The quarantine mandates the reporting of sick birds and prohibits poultry owners from moving birds in all of Los Angeles County, and in large areas of San Bernardino and Riverside counties.
The modified quarantine extends from the northern and southern borders of western Riverside County to the Salton Sea—including the Coachella Valley—and as far east as Yucca Valley in San Bernardino County, with a northern boundary of State Route 58 at the Kern County line. The quarantine language and a map may be found at CDFA’s VND Web site.
The quarantine requires bird owners to allow diagnostic testing, to isolate poultry from other species, to cease exhibitions, to stop the shipping and receiving of birds, and to enhance biosecurity.
“By modifying the quarantine area in Southern California, we are building upon an ongoing effort to eradicate virulent Newcastle disease,” said Dr. Jones. “The primary way that VND spreads is by people moving sick birds. Extending the prohibition of bird movement across a larger area is the next logical step in being able to stop the spread of the virus and to eradicate the disease.”
VND is a nearly-always fatal respiratory infection in poultry. Birds may seem healthy but will die within days of being infected. There is no cure. The virus is also transmitted by people who have VND on their clothes or shoes, and by equipment or vehicles that can transport the disease from place to place.
There are no human health concerns provided that any meat or eggs are cooked properly. People who come in direct contact with the virus may develop conjunctivitis-like symptoms or run a mild fever.

The only way to stop the virus and eradicate the disease is to euthanize birds. This includes all infected birds as well as birds within heavily-infected areas.
Since May 2018, staff from the California Department of Agriculture (CDFA) and the U.S. Department of Agriculture (USDA) have been working in joint incident command to eradicate VND in Southern California.
The highly contagious virus has resulted, or will soon result, in the euthanasia of more than one million birds in Los Angeles, Riverside, San Bernardino, and Ventura counties.
Birds from four poultry industry producers in Riverside County and two poultry industry producers in San Bernardino County have also been infected with VND and all birds in those facilities have been or will be euthanized.
For more information about movement restrictions, biosecurity, and testing requirements, please call the Sick Bird Hotline (866) 922-2473 or email SFSPermits@cdfa.ca.gov

According to the California Dept. of Food & Agriculture, the last outbreak in commercial poultry - back in 2003 - led to the depopulation of 3.16 million birds at a cost of $161 million.  Prior to that, in 1971, an outbreak in Southern California led the culling of 12 million birds. 
Yesterday's revelation that a million birds have been lost in this latest round of outbreaks is a reminder of how damaging diseases like VND can be to the agricultural community.
We should see a fresh update from the USDA on the number of outbreaks in the next couple of days.

Saudi MOH Reports A MERS Case In Sajir

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#13,898

Saudi Arabia's February MERS surge - which has seen 68 cases reported over the past 28 days - appears to be winding down, but KSA's 82nd case of 2019 is reported today from Sajir, located about 200km Northwest of Riyadh.

Today's patient is a 43 year old male, described as a primary case with recent camel contact.
https://www.moh.gov.sa/en/CCC/events/national/Documents/Epiwk9-19.pdf


While its been 3 days since the last case was reported from hard-hit Wadi Aldwasir (see Wadi Aldwasir's 50th MERS Case In A Month) - given up to a  14 day incubation period for MERS - it is still too soon to call that outbreak ended. 
Meanwhile, tight-lipped Oman has not released any new information since their MOH's brief announcement two weeks ago of 4 new cases, bringing their 2019 total to 10 - with 4 fatalities.
For some recent blogs on MERS research, you may wish to revisit:

Epi.& Inf.: Global Status Of MERS-CoV In Camels - A Systemic Review

MERS-CoV In Humans: A Systematic Literature Review
Emerg. Microbe & Inf: MERS Infection In Non-Camelid Domestic Mammals

Vietnam MARD: 96 ASF Outbreaks Across 6 Provinces & Cities





















#13,897


Two weeks ago today Taiwan's BAPHIQ reported ASF Positive Pork Products Brought In By Passengers From Vietnam, providing the first hint that the deadly pig disease that hit China last August had extended its reach to Vietnam.
Four days later, Vietnam Reported Their First (3) Outbreaks Of African Swine Fever, across two provinces (Thái Bình and Hưng Yên). Six days later (Feb 25th), Vietnam reported outbreaks in two more provinces  (Hai Phong and Thanh Hoa).
Today Vietnam's Ministry of Agriculture (MARD) has announced that over the past 14 days African Swine Fever has been detected in 96 households (or farms), across 33 villages, 20 communes, 13 districts of 6 provinces and cities.

This rapid escalation of numbers suggests ASF has been spreading, but unreported, in Vietnam for some time. The Deputy Prime Minister, in the following press release, puts much of the blame on the failure of `stagnant' and `inefficient' organization of local animal health bureaucracies.
While the number of outbreaks reported in Vietnam over the past two weeks nearly equals the number China reported in the first 5 months of their outbreak, the average size of Vietnam's outbreaks - which thus far are appearing in family-run operations, not large farms - is vastly lower. 
Most of Vietnam's 30 million pigs are still raised in communes, by individual households. rather than on an industrial scale (cite). But in recent years larger pig farms have begun to appear in Vietnam, and the risk that ASF will begin to strike these larger operations is very real.

This press release from MARD:

Deputy Prime Minister directed the prevention and control of cholera pig in Africa

On the morning of February 28, at the headquarters of the Ministry of Agriculture and Rural Development, Deputy Prime Minister Trinh Dinh Dung chaired an emergency meeting to prevent and limit African swine flu (ASF) to spread to many localities.

Deputy Prime Minister Trinh Dinh Dung gave a speech to direct the conference

According to a report by MARD, as of February 28, African swine flu (ASF) occurred in 96 households, 33 villages, 20 communes, 13 districts of 6 provinces and cities including: Hung Yen and Thai Binh. , Hai Phong, Thanh Hoa, Hanoi and Ha Nam. ASF has appeared in all wild pigs (in Van Xa commune, Kim Bang district, Na Nam). The total number of infected and culled pigs was nearly 2,350 (with a total weight of over 172.5 tons) and caused tens of billions of losses.

According to Deputy Minister of Agriculture and Rural Development Phung Duc Tien, one of the reasons for spreading the epidemic is the merger of the district-level veterinary agency into an agricultural technical service center, but the organization of implementing the prevention and combat tasks Animal diseases are stagnant, inefficient, there are many shortcomings and shortcomings.

In particular, establishments do not actively monitor and timely cap information and report on epidemic situation, do not organize hygiene and disinfection, do not implement vaccination, does not handle violations ...

Meanwhile, policies to support destruction are at VND 27,000 - 38,000 / kg, but administrative procedures are very complicated, making farmers slow to receive money, leading to people selling out sick pigs, pigs suspected to be sick. .

Minister of Agriculture and Rural Development Nguyen Xuan Cuong said that cholera of African pigs does not spread to humans but is very dangerous because it spreads very quickly, and there is no vaccine to prevent disease. If not fiercely prevented, it will greatly affect the livestock industry. Most important today is to synchronously apply integrated solutions, with the motto "room is main".

Addressing at the conference, Deputy Prime Minister Trinh Dinh Dung stated that the current development is complicated and tends to spread to many localities.

Deputy Prime Minister asked ministries and localities to implement drastically measures to prevent epidemics. Good information work for people to understand the level of danger of African cholera epidemic so that people can join in to control the epidemic successfully. Focus on implementing measures to prevent cholera that Ministry of Agriculture and Rural Development has set out. Actively take measures to support epidemic prevention; support farmers in the locality. Positive propaganda information, not to affect consumption and livestock. Ensure the market operates normally.

BBT overall

Wednesday, February 27, 2019

China MOA: Shaanxi Province Reports ASF Outbreak














#13,896



After going a month (Jan 21-Feb 19th) where they reported only 1 outbreak of African Swine Fever, today the China's MOA has reported their 7th outbreak (across 6 Provinces) in the past 9 days. 


African swine fever epidemic in Jingbian County, Shaanxi Province
 
Date: 2019-02-27 16:35 Author: Source: Ministry of Agriculture and Rural Press Office

The Information Office of the Ministry of Agriculture and Rural Affairs was released on February 27, and an African swine fever epidemic occurred in Jingbian County, Yulin City, Shaanxi Province.

On February 27, the Ministry of Agriculture and Rural Affairs received a report from the China Animal Disease Prevention and Control Center, which was diagnosed by the Shaanxi Provincial Animal Disease Prevention and Control Center and an African swine fever epidemic occurred in a farm in Jingbian County.


Up to now, the farm has 11,334 live pigs, with 150 heads and 62 deaths.

Immediately after the outbreak, the Ministry of Agriculture and Rural Affairs sent a steering group to the local area. The local government has started the emergency response mechanism according to the requirements, and adopted measures such as blockade, culling, harmless treatment, disinfection, etc., to treat all the sick and culled pigs harmlessly. At the same time, all pigs and their products are prohibited from being transferred out of the blockade, and pigs are prohibited from being transported into the blockade. At present, the above measures have been implemented.
 
Along with this recent surge in reporting, a Google search for the term `死猪'' (`Dead Pigs') returns a daily barrage of Chinese media reports of suspicious die offs of pigs around the nation, along with the illegal dumping of pig carcasses.

While African Swine Fever is often explicitly denied by local officials, explanations are rarely provided.
There are, admittedly, a number of other serious pig diseases common in China - including FMD, PED & PRRS - that could produce significant pig mortality.

But increasing detection of ASF contaminated food products by customs officials in Taiwan, Japan, South Korea, and Australia suggest significant quantities of ASF contaminated pork are making it into China's food chain.


While ASF poses no health risk to humans - it does speak to the amount of undetected infected livestock being processed - and their export greatly increases the chances that the virus will be spread to other regions of the globe.

OIE Notification: H5N8 In Pakistan (Non-poultry, wild birds)



















#13,895


While HPAI H5 reports have been fairly subdued for the past year, we've begun to see a small increase in activity, with recent outbreaks of H5N1 in India (see here and here) H5N6 in China, and H5N8 in a penguin colony in Namibia.
As we've discussed previously, major bird flu seasons - such as we saw in 2016-2017 - are generally followed by one or more less severe years (see chart below), and so this recent lull in activity is not unprecedented,

Overnight the OIE published the first notification of HPAI H5N8 from Pakistan in nearly a year, when a captive game bird (Macaw) at the Lahore zoo was found to be infected.

 
Today's OIE notification involves two outbreaks (early January & early February) of H5N8 affecting four species of wild birds (Mallard, Guinea Fowl, Swan & House Crow) in the Islamabad Capital Territory.
 
http://www.oie.int/wahis_2/public/wahid.php/Reviewreport/Review?page_refer=MapFullEventReport&reportid=29686&newlang=en
 
Source of the outbreak(s) or origin of infection   

Unknown or inconclusive

Epidemiological comments     


Clinical symptoms swan, duck and Guinea fowl included diarrhea, respiratory signs and sudden death. The dead swan, duck and Guinea fowl were submitted to the National Reference Laboratory for Poultry Diseases (NRLPD) and tested positive for influenza A H5N8 virus. A dead crow was sent by an official from the British High Commission to the NRLPD for analysis and tested positive for influenza A H5N8 virus.
 

Nature: Bat Influenza Receptors In Other Mammals (Including Humans)




#13,894

Exactly 7 years ago today (Feb 27, 2012) we looked at an announcement from scientists from the U.S. CDC and the Universidad del Valle in Guatemala City of the first identification of an influenza virus in bats; specifically yellow-shouldered bats (Sturnira lilium) captured at two locations in Guatemala (see A New Flu Comes Up To Bat).
This new influenza virus was described as deviating from the 16 known HAs and was designated as H17. The neuraminidase (NA), and internal genes, were also highly divergent from previously known influenzas.
In 2013 another new subtype (H18N11) was identified, again in South American Bats (see PLoS Pathogens: New World Bats Harbor Diverse Flu Strains), leading to speculation that these mammalian-adapted flu viruses might someday jump to other species – including man.

The good news was that these bat flu viruses did not bind to the same type of receptor cells as regular H1- H16 flu viruses - sialic acid - limiting their threat to humans. The CDC addressed the slim potential for these viruses posing a public health threat in their Bat Flu FAQ.

How could bat flu viruses become capable of infecting and spreading among humans?

Because the internal genes of bat flu viruses are compatible with human flu viruses, it is possible that these viruses could exchange genetic information with human flu viruses through a process called “reassortment.” Reassortment occurs when two or more flu viruses infect a single host cell, which allows the viruses to swap genetic information. Reassortment can sometimes lead to the emergence of new flu viruses capable of infecting humans.
However, the conditions needed for reassortment to occur between human flu viruses and bat flu viruses remain unknown. A different animal (such as pigs, horses, dogs or seals) would need to serve as a “bridge,” meaning that such an animal would need to be capable of being infected with both this new bat flu virus and human flu viruses for reassortment to occur.
Since the discovery of bat flu, at least one study has been conducted to assess the possibility of reassortment events occurring between bat flu and other flu viruses (3). So far, the results of these studies continue to indicate that bat flu viruses are very unlikely to reassort with other flu viruses to create new and potentially more infectious or dangerous viruses. In their current form bat flu viruses do not appear to pose a threat to human health.
Taking a different tack, last April in Back To The Bat Cave: More Influenza In Bats, we looked at new study, published in the Virology Journal, that found that bat receptor cells - while not ideally suited for human influenza viruses - appear somewhat better suited for avian flu viruses.

Last week, an article appeared in the journal Nature that finds bat influenzas bind to MHC-II proteins, which can be found on the surface of a number of important immune cells. 
Immune cells that exist in other mammalian hosts, including humans, opening the door for potential cross-species transmission of these viruses.
This is a lengthy, and highly technical, report.  Luckily, following the abstract we have we have a far more easily digested article, published yesterday in The Conversation.

MHC class II proteins mediate cross-species entry of bat influenza viruses
Umut Karakus, Thiprampai Thamamongood, […]
Silke Stertz

Nature (2019)
Abstract

Zoonotic influenza A viruses of avian origin can cause severe disease in individuals, or even global pandemics, and thus pose a threat to human populations. Waterfowl and shorebirds are believed to be the reservoir for all influenza A viruses, but this has recently been challenged by the identification of novel influenza A viruses in bats1,2.

The major bat influenza A virus envelope glycoprotein, haemagglutinin, does not bind the canonical influenza A virus receptor, sialic acid or any other glycan1,3,4, despite its high sequence and structural homology with conventional haemagglutinins. This functionally uncharacterized plasticity of the bat influenza A virus haemagglutinin means the tropism and zoonotic potential of these viruses has not been fully determined.

Here we show, using transcriptomic profiling of susceptible versus non-susceptible cells in combination with genome-wide CRISPR–Cas9 screening, that the major histocompatibility complex class II (MHC-II) human leukocyte antigen DR isotype (HLA-DR) is an essential entry determinant for bat influenza A viruses. Genetic ablation of the HLA-DR α-chain rendered cells resistant to infection by bat influenza A virus, whereas ectopic expression of the HLA-DR complex in non-susceptible cells conferred susceptibility.

Expression of MHC-II from different bat species, pigs, mice or chickens also conferred susceptibility to infection. Notably, the infection of mice with bat influenza A virus resulted in robust virus replication in the upper respiratory tract, whereas mice deficient for MHC-II were resistant. Collectively, our data identify MHC-II as a crucial entry mediator for bat influenza A viruses in multiple species, which permits a broad vertebrate tropism.
       (SNIP)
Our data uncover MHC-II as an entry mediator for bat IAVs, which identifies a critical molecular determinant of tropism for these newly identified viruses. Similar to conventional IAVs, bat IAVs are promiscuous in that they use a widely expressed and highly conserved entry factor found in many vertebrates—including humans, and livestock routinely contacted by humans. Zoonotic potential for these bat viruses cannot, therefore, be excluded.
        (Continue . . . )


From The Conversation, a summary by , Lecturer in Molecular Virology, Lancaster University.   Due to its length, I've only included some excerpts, so follow the link to read it in its entirety.


February 26, 2019 7.29am EST 

(EXCERPT)

MHC-II proteins are found on the surface of certain immune cells, and they play an important role in discriminating the body’s own structures from pathogens, such as bacteria and viruses.

Because pigs and chickens are able to transmit conventional flu viruses to humans, researchers over-expressed MHC-II proteins from pigs and chickens into human cells. These hybrid cells became susceptible to bat flu, which suggests that the virus could infect chicken and pigs. 

Because of the role farm animals play in transmitting flu to humans, it appeared that the bat flu virus has the potential to either infect humans directly or by first infecting other animals. But given the limited understanding of MHC-II in bats, the biological role of the protein in transmitting bat flu remains obscure and is yet to be investigated.

(SNIP)

We don’t know whether humans have been infected with bat flu in the past, but this research suggests that it is possible. The finding that MHC-II expression in the respiratory tract cells lets bat flu replicate, suggests that the virus could be transmitted to humans through the air. And given the presence of MHC-II receptors in different organs, the bat flu viruses could be spread by bat saliva, urine or faeces. This route of transmission is more likely because of increasing bat-human contact. 

Like swine and bird flu, bat-borne flu viruses are widely prevalent around the globe and the newly identified route of entry is common in many farm animals, so the risk of bat flu infecting humans and livestock is probably high.

Importantly, because of increasing human contacts with wildlife, including bats, consumption of bat “bushmeat” and hunting bats for both food and money has exposed humans to the zoonotic spillover of viruses. In these events, the interaction of bat flu with MHC-II could potentially remove these important immune molecules and put people and animals at risk of other viral and bacterial infections, too.

(Continue . . . )

The past couple of decades have turned out to be busy ones for Chiroptologists. For some more bat-related blogs, you may wish to revisit:

Curr. Opinion Virology: Viruses In Bats & Potential Spillover To Animals And Humans

EID Journal: A New Bat-HKU2–like Coronavirus in Swine, China, 2017

Emerg. Microbes & Infect.: Novel Coronaviruses In Least Horseshoe Bats In Southwestern China

SARS-like WIV1-CoV poised for human emergence
 

Tuesday, February 26, 2019

USGS: California’s Exposure to Volcanic Hazards

https://pubs.er.usgs.gov/publication/sir20185159




















#13,893


Although it may seem a remote concern to most Americans, the continental United States has a number of active, and potentially dangerous volcanoes. 
Last October, in USGS Updated Volcano Threat Assessment - 2018, we saw that 11 of the 18 very highest threat volcanoes on U.S. soil are located in the Western United States - 4 in Washington, 4 in Oregon & 3 in California. (note: Yellowstone is ranked 21st).
Additionally, 39 volcanoes are listed as posing a `high threat', and 49 are ranked as a `moderate' threat.  These are not predictions of which volcanoes are apt to blow next, but rather an assessment of the potential severity of impacts that  future eruptions might generate.

We've discussed eruptive hazards before - both internationally (see here, here, and here), and domestically (see Washington State: Volcano Awareness Month). While earthquake damage is generally localized, volcanic eruptions (and tsunamis) can affect property and populations thousands of miles away.
  • In 2010 airline traffic in Europe was disrupted by the eruption of Iceland's Eyjafjallajökull volcano (see study The vulnerability of the European air traffic network to spatial hazards), halting many flights for nearly a week. 
  • When Mount Pinatubo erupted in the Philippines in 1991, within a year its aerosol cloud had dispersed around the globe, resulting in `an overall cooling of perhaps as large as -0.4°C over large parts of the Earth in 1992-93’ (see USGS The Atmospheric Impact of the 1991 Mount Pinatubo Eruption).
  • In 1783 the Craters of Laki in Iceland erupted and over the next 8 months spewed clouds of clouds of deadly hydrofluoric acid & Sulphur Dioxide, killing over half of Iceland’s livestock and roughly 25% of their human population. These noxious clouds drifted over Europe, and resulted in widespread crop failures and thousands of deaths from direct exposure to these fumes (see 2012 UK: Civil Threat Risk Assessment)
All of which means you don't have to live in the shadow of one of these slumbering giants to be impacted by an eruption. But, according to a new report from the USGS, roughly 200,000 Californian's do work, live, or pass through that state's volcanic hazard zones on a daily basis.
Suggesting that the next `big one' to hit California might be eruptive, rather than an earthquake.
Some volcanic hazards - like ash fall - can spread hundreds of miles. And even a light dusting of volcanic ash can wreak havoc on power lines, and airline traffic.

Due to its length (58 pages) I've only posted the abstract, so follow the link to download the PDF in its entirety.

California’s Exposure to Volcanic Hazards 

Scientific Investigations Report 2018-5159
Prepared in cooperation with the California Governor’s Office of Emergency Services and the California Geological Survey
By: Margaret Mangan, Jessica Ball, Nathan Wood, Jamie L. Jones, Jeff Peters, Nina Abdollahian, Laura Dinitz, Sharon Blankenheim, Johanna Fenton, and Cynthia Pridmore

https://doi.org/10.3133/sir20185159

Links
Document: Report (33.6 MB pdf)
 

First posted February 25, 2019
Volcano Science Center
U.S. Geological Survey
345 Middlefield Road, MS 910
Menlo Park, CA 94025

The potential for damaging earthquakes, landslides, floods, tsunamis, and wildfires is widely recognized in California. The same cannot be said for volcanic eruptions, despite the fact that they occur in the state about as frequently as the largest earthquakes on the San Andreas Fault. At least ten eruptions have taken place in the past 1,000 years, and future volcanic eruptions are inevitable.

The U.S. Geological Survey’s (USGS) national volcanic threat assessment identifies eight young volcanic areas in California as moderate, high, or very high threat. Of the eight volcanic areas that exist in California, molten rock resides beneath at least seven of these—Medicine Lake volcano, Mount Shasta, Lassen Volcanic Center, Clear Lake volcanic field, the Long Valley volcanic region, Coso volcanic field, and Salton Buttes—and are therefore considered “active” volcanoes producing volcanic earthquakes, toxic gas emissions, hot springs, geothermal systems, and (or) ground movement.

The USGS California Volcano Observatory in Menlo Park, California, monitors these potentially hazardous volcanoes to help communities and government authorities understand, prepare for, and respond to volcanic activity. Although volcanic activity can sometimes be forecast, eruptions, like earthquakes or tsunamis, cannot be prevented. Understanding the hazards and identifying what and who is in harm’s way is the first step in mitigating volcanic risk and building community resilience to volcanic hazards.

This report, which was prepared in collaboration with the California Governor’s Office of Emergency Services and the California Geological Survey, provides a broad perspective on the state’s exposure to volcanic hazards by integrating volcanic hazard information with geospatial data on at-risk populations, infrastructure, and resources. This information is intended to prompt site- and sector-specific vulnerability analyses and preparation of hazard mitigation and response plans.

Suggested Citation

Mangan, M., Ball, J., Wood, N., Jones, J.L., Peters, J., Abdollahian, N., Dinitz, L., Blankenheim, S., Fenton, J., and Pridmore, C., 2019, California’s exposure to volcanic hazards: U.S. Geological Survey Scientific Investigations Report 2018–5159, 49 p., https://doi.org/10.3133/sir20185159.

While I don't recommend that anyone lie awake at night worrying about the next potential disaster, every home should be at least minimally prepared to deal with one if it happens.

So . . . if a disaster struck your region today, and the power went out, stores closed their doors, and water stopped flowing from your kitchen tap for the next 7 to 14 days  . . .  do you already have:

  • A battery operated NWS Emergency Radio to find out what was going on, and to get vital instructions from emergency officials
  • A decent first-aid kit, so that you can treat injuries
  • Enough non-perishable food and water on hand to feed and hydrate your family (including pets) for the duration
  • A way to provide light when the grid is down.
  • A way to cook safely without electricity
  • A way to purify or filter water
  • A way to stay cool (fans) or warm when the power is out.
  • A small supply of cash to use in case credit/debit machines are not working 
  • An emergency plan, including meeting places, emergency out-of-state contact numbers, a disaster buddy,  and in case you must evacuate, a bug-out bag
  • Spare supply of essential prescription medicines that you or your family may need
  • A way to entertain yourself, or your kids, during a prolonged blackout
If your answer is `no’, you have some work to do.  A good place to get started is by visiting Ready.gov.

Some other preparedness resources you might want to revisit include:
The Gift Of Preparedness - Winter 2018
#NatlPrep: Revisiting The Lloyds Blackout Scenario

#NatlPrep : Because Pandemics Happen
Disaster Planning For Major Events
All Disaster Responses Are Local

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Tesla chief Elon Musk's trial postponed due to coronavirus

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