Tag Archives: pandemic

Novel Wuhan coronavirus cases leap up

Confirmed cases of the novel Wuhan coronavirus have gone from 62 detected in Wuhan (and 3 exports that we know of so far) to after a jump of 136 new cases in a single report from the Wuhan Municipal Commission of Health (WMCH). Also, and disease now includes “‘mild”‘ cases not just pneumonia. This isn’t great news.

China sits at the heart of this coronavirus outbreak.
Photo by chuttersnap on Unsplash

On January 17th Wuhan reported 17 new cases,[2] but their next report includes cases for Jan 18th – where 59 new cases have been added with 1 new death, and Jan 19th with 77 new cases.[1]

136 new cases in two days

Of the 136 new cases, 66 were male and 70 were female. This is a significant change from the male-dominated figures we’d seen to date. The youngest case was 25 years old and the oldest was 89 years old. The onset of illness continues to creep up – cases are likely to be being acquired in an ongoing fashion – from where we still don’t know. The latest natch have onset dates include up to the 18th of January.

It seems that all cases still had pneumonia but its severity has now been ranked with the 136 spread across 100 mild cases, 33 severe cases, and 3 critical cases.

A burden on hospitals

The total number of novel Wuhan coronavirus-associated pneumonia cases in Wuhan now stands at 198 (201 worldwide). 25 Wuhan cases have recovered (12.6%) and 3 been discharged (1.5%). 170 (85.8%) of cases are still in isolation in hospital so there is a very real burden to healthcare services. Of these, 126 cases (74.1% of those hospitalised) are described as mild pneumonia, 35 (20.6%) as severe, and 9 (5.3%) cases as critically ill.[1]

We are of course all assuming this is a new burden but we have no evidence yet that supports that. This may be part of a previous burden of pneumonia that went undetected because there was no seafood market to identify it as a cluster of unusual activity. Virus age remains a question.

 Contact conundrum – to watch or to test (test!)

There are now 817 close contacts in Wuhan of which 727 “medical observations have been lifted, and 90 medical observations are still underway”. This says not testing, just observing, to me. I’d love WMCH to clarify this in their next FAQ/Q&A

This is a common procedure in the early days of an emerging virus. I’ve seen it frequently, even in my short times in this field. Medical Doctors choose to watch for symptoms over testing for the virus. Test take time to develop so this is a quick way to look for obvious spread of disease. But it does not monitor the spread of the virus . Eventually, this will be done but time is lost while using a relatively incentive tool to learn about a new virus.

Tests take some time – but something highly sensitive and specific can be available within a week of having a virus’s sequence. Its sequences can be shared at that time – in this case, the first specific assays developed were by an external group in Germany and now a second group in Hong Kong; nothing from Wuhan or the Chinese CDC.

From that moment on, it would be better practice to test respiratory samples form contacts, close and otherwise. Cost is not an issue when seeking to stop the emergence of a respiratory disease and its cause because the cost that accrues after its escape will be exponentially higher. There are only excuses for not testing and old medical habits to overcome.

No related cases were found among the close contacts but as far as I can tell from these reports, they haven’t been tested with a nucleic-acid based test. An antibody detecting test – if suitably specific – is also essential. But they take longer to develop for multiple reasons. 

What will tomorrow bring? More testing I hope and with it, more answers.


  1. Wuhan Municipal Commission of Health and Health on pneumonia of new coronavirus infection |  Published: 2020-01-20 02:42:40 
  2. Wuhan Municipal Commission of Health and Health on pneumonia of new coronavirus infection |  Published: 2020-01-19 00:43:34  http://wjw.wuhan.gov.cn/front/web/showDetail/2020011909074

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Taiwan CDC Upgrades Response To nCoV-2019 Threat



In China, it is called Chūnjié. In Vietnam it is celebrated as Tết Nguyên Đán ; the Feast of the First Morning. Tết for short.  And in Korea they call it Seollal.

By whatever name, the Lunar New Year is undoubtedly the most important holiday in all of Asia, which each year sees hundreds of millions of people travel – mostly from big cities, back to their birthplace – to spend revered time with family.

Chunyun, or the Spring Festival travel season, begins about 15 days before the Lunar New Year (Jan 25th this year) and runs for about 40 days total, during which time more than 2 billion passenger journeys will be made (mostly via crowded rail and bus) across Asia.

And while we normally monitor these mass migrations carefully – particularly during years when avian flu is prevalent in China – this year the last minute emergence of a novel coronavirus in Wuhan City, China has added yet another layer of concern. 

While the official mantra remains `no clear evidence of human-to-human transmission’, it is still very early days in this outbreak, there are obvious gaps in our knowledge and understanding of this virus (and its source), and similar coronaviruses have demonstrated varying degrees of transmissibility.

Which is why, despite the lack of `clear evidence’ of human transmission, public health entities like the WHO, CDC, Hong Kong’s CHP, and Taiwan’s CDC are all (rightfully) treating this outbreak as a credible threat. 

While none of this guarantees that this emerging coronavirus is about to embark of a world tour, the special circumstances of Chunyun make whatever public health actions that are taken over the next few weeks all the more important.  

Today Taiwan’s CDC has posted two updates.   The first upgrades – as of today – `Severe Special Infectious Pneumonia” to a Class 5 legal infectious disease.

The Department of Disease Control has listed “Severe Special Infectious Pneumonia” as a Class 5 legal infectious disease since January 15, 2020

Release Date: 2020-01-15

he Department of Disease Control has officially listed “Severe Special Infectious Pneumonia” as the fifth category of statutory infectious diseases since today, in order to strengthen the surveillance and prevention of severe special infectious pneumonia, improve the alertness of the people and medical institutions, and help Grasp the source of the epidemic and infection and related risk factors in time to stop the spread of the epidemic and reduce the risk of infection by people. In addition, in the morning (1/15) press release, two cases were tested that met the definition of “Fever Pneumonia Cases in the History of Travel in Wuhan, China.” One named H1N1 influenza virus was positive, all of them have been excluded; 9 suspected cases have been reported so far, all have been excluded.

The CDC reminds that if a suspected case meets the definition of a case when it is diagnosed by a medical institution, it must be notified to the competent health authority within 24 hours. The health unit will conduct isolation treatment, epidemic investigation, autonomous health management and contacts for the suspected case. Preventive measures such as health monitoring. Relevant definitions of disease notifications, processing procedures for suspected notification cases, methods for sample inspection and submission, and related prevention and control guidelines will be updated in a timely manner as the epidemic situation is announced and posted on the SACD Global Information Network “Severe Special Infectious Pneumonia” Epidemic Prevention Zone (http: // /www.cdc.gov.tw Home> Special Topics on Infectious Diseases and Epidemic Prevention> Infectious Diseases Introduction> Class 5 Legal Infectious Diseases> Severe Special Infectious Pneumonia). 

The CDH stated that it is now in the season of respiratory diseases such as influenza and pneumonia, and urged those who plan to visit the local area and nearby areas to avoid entering and exiting traditional public markets, hospitals and other public places, and contact with wild and livestock animals. Implement personal protective measures such as washing hands with soap and wearing a mask; if fever or flu-like symptoms occur within 14 days of returning to China, you should proactively notify the air traffic control and quarantine staff, wear masks as required, and take the initiative to inform doctors of their travel history and occupation , Contact history and cluster situation (TOCC) for timely diagnosis and notification of physicians. For related information, please refer to the CDC website (https://www.cdc.gov.tw/), or call the toll-free epidemic prevention line 1922 (or 0800-001922) for inquiries.

A second, longer statement was published today indicating that until proven otherwise, Taiwan’s CDC will prepare as if this novel coronavirus is transmissible from human-to-human. 

The Department of Disease Control has not ruled out the possibility of human-to-human transmission of the new coronavirus, and relevant control measures have been developed based on the situation that the virus may be transmitted from human to human and have been completed.
Release Date: 2020-01-15

The World Health Organization says that the new type of coronavirus may have limited human-to-human transmission in 2019; the Office of Disease Control and Administration has stated that the possibility of human-to-human transmission has not been ruled out for the virus, and that human-to-human transmission may be considered for related control measures, so people with respiratory symptoms are reminded Surgical masks should be worn, and the public is urged to avoid crowded and poorly ventilated places as much as possible. It is recommended to wear masks when going in and out of these places, but it should generally not be infected beyond 1 meter. Please don’t panic.

At present, a response team has been organized to develop guidelines for surveillance, quarantine, inspection, epidemic investigation, medical infection control, and case management. Expert meetings, county and city health bureau meetings, inter-ministerial coordination meetings, and unwarned random inspection of hospital infection control have been held. As a result, these preventive measures are developed under the condition that the virus may be transmitted from person to person, and continue to collect information about the disease and virus, consult the experts of infectious diseases, review and correct the preventive measures at any time, and supervise the implementation of various actions.

The CDC has been notified by the Chinese Center for Disease Control and Prevention. As of January 15, 2020, 41 cases of pneumonia caused by new coronavirus infection have remained, including 6 severe cases and 1 death, and 7 cases have been discharged from hospital. Among the confirmed cases, a few patients denied that they had visited the South China Seafood Market and had only been exposed to similar cases. There was also a family gathering as a husband with a history of exposure and a wife without a case, but no community transmission was found; at present, a limited number of people cannot be ruled out. It is possible, but it cannot be ruled out that the family group has a common source of infection to be clarified. In addition, some environmental examinations in the South China Seafood Market detected 2019-nCoV. Lu Fang also conducted preliminary investigations in other markets, and no clues related to the source of the infection have been found. Although suspected cases have been reported from other neighbouring countries, only one case has been imported from Thailand outside of Wuhan, China.

Continuously strengthened surveillance of epidemic conditions and border control measures. Inbound fever travelers from international and small three-way ports have been asked about Wuhan’s travel history and health assessments. In addition, since December 31, 2019, the boarding and quarantine of direct flights from Wuhan started, and 25 flights have been carried out, with a total of 2,742 passengers and crew members. So far, there are 9 cases that meet the “Fever Pneumonia Cases of Wuhan Tourism History in China”, 7 of which have been ruled out, and the other 2 tests, there are currently no confirmed cases of new coronavirus in China in 2019.

The CDA once again called for the approach of the Spring Festival travel season. If fever or flu-like symptoms occur within 14 days of returning to China, you should proactively inform the aviation management and quarantine staff, wear masks according to instructions, and proactively inform physicians of their travel history, occupation, and contact. History and group situation (TOCC) for timely diagnosis and notification by physicians. For related information, please refer to the CDC website (https://www.cdc.gov.tw/), or call the toll-free epidemic prevention line 1922 (or 0800-001922) for inquiries.

Some human-to-human transmission isn’t surprising in Wuhan

A couple of people have asked me lately if they should be worried about the novel Wuhan coronavirus. Which got me to thinking. Much of what we sciencey types chat about online can quickly get – or just start off as – too technical for the general public. And sometimes that may leave them with a sense that things are more worrying than we think they are. One thing that concerns folks, is how fast this emerging virus is spreading. So I put down a few thoughts which I hope are broadly understandable. If not – ask questions below.

To say that there is *no* human-to-humsn (h2h) transmission during the very early or discovery phase of an emerging disease is to use language that is too strong. It may lead to doubt in the narrator or the story because it doesn’t feel right or might develop a false sense of security.

It makes a kind of natural sense that a virus which infected a human after exposure to an animal source, would be able to infect a human if projected from a human source. It may not do that frequently but it is quite possible that it can do that under suitable circumstances.

If the virus replicates in the lower airways rather than the upper airways like a common cold virus (think of the larynx as a boundary line), it can be less easy for us to breath, cough, drip or sneeze it out for someone else to pick up. So spread is more limited. But spread is far from impossible.

As yet, we know ZERO about where in the human body this virus replicates. We also know just as little about where it might replicate within the market animal(s) it is presumed to have been in. Or in a possible reservoir animal that the virus may naturally occur in.

Routinely, when testing for respiratory viruses, we sample from the upper airways but lower airway samples are recommended by the World Health Organization for more serious cases of illness associated with the detection of this new coronavirus. And these were the types of samples that permitted Chinese researchers to first identify the novel virus.

Some have said (perhaps a little late) that we should not be surprised to see some h2h spread. That is because of those suitable circumstances I mentioned earlier. They include close contact through caring for the sick person, picking up the virus from contaminated surfaces and items in shared environments & infection after prolonged contact

These are three things which all occur among families and this is where we can see an otherwise poorly h2h transmitting virus jump between humans. And this fits in with the a suspected family-related instance of h2h transmission of the novel Wuhan coronavirus identified thus far. The same occurs with MERS (the disease) and MERS-CoV.

We can also see h2h transmission in healthcare facilities if the healthcare workers get exposed before instituting suitably protective protocols. Nurses and doctors have close and prolonged exposure to sick patients. One reason we may not have seen this in Wuhan could be a very good use of such protocols.

Infection by close contact or contact with contaminated surfaces is pretty self-explanatory. Prolonged exposure may occur through repeated exposure to small doses of a virus such that our immune system cannot contain the virus and an infection takes hold, becoming ill.

So should you be worried if you live somewhere other than Wuhan and visit a market containing live or freshly killed animals of all shapes and sizes or their component parts? Not at this stage based on the info we have to hand.

That isn’t a lot of info though and things may change.

What we know is that the virus isn’t causing widespread pneumonia. What little h2h transmission there has been, is not continuous. Could the virus be causing milder respiratory illnesses? It doesn’t seem like it is based on observations of the 760 contacts in Wuhan, China. 187 of them have already been released from quarantine without showing any symptoms for two weeks. That’s good news.

It seems like something delivered the virus to human airways probably from animals at the Huanan seafood (and other animals) market. That animal may be at one more other markets but remains unfound. The recently reported case in a traveller from Wuhan who arrived in Thailand had not visited the Huanan seafood market. This suggests the suspected animal source may have been sold at more than one market. There seems to be limited h2h transmission, even associated with close contact so the other option, h2h transmission in the community, seems less likely.

So now we wait for more information. That info will take time to get together. So more patience is required. But to be clear, China has put these findings together and reported on them in record time. Faster than I think most other countries would have.

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EID Journal: High Pathogenicity of Nipah Virus from Pteropus lylei Fruit Bats, Cambodia

Really bad news.

Credit CDC


Nipah emerged as a recognizable zoonotic threat in Malaysia in 1998 when it spread from bat to pigs – and then from pigs to humans – eventually infecting at least 265 people, and killing 105 (see Lessons from the Nipah virus outbreak in Malaysia).

Since then, we’ve seen a few dozen outbreaks in India, Pakistan, and most commonly, Bangladesh, but it is likely that additional individual infections and/or outbreaks have gone undetected. 

As the CDC map above indicates, the range of fruit bats of the Pteropodidae family – the natural host of Henipaviruses (Nipah & Hendra) – extends from Australia, to China, and across the Indian Ocean to Africa. 


While old world fruit bats have been pegged as the natural host for Nipah (and for its less well known Australian cousin Hendra), that family encompasses scores of species, and other types of bats may also be carriers.

In addition to bats and humans – other mammals have been infected in the wild (horses, pigs, and dogs) – and many others have been experimentally infected in the lab (including guinea pigs, hamsters, ferrets, squirrel monkeys, and African green monkeys).

In the 2013 paper The pandemic potential of Nipah virus by Stephen P. Luby, the author wrote (bolding mine):

Characteristics of Nipah virus that increase its risk of becoming a global pandemic include: humans are already susceptible; many strains are capable of limited person-to-person transmission; as an RNA virus, it has an exceptionally high rate of mutation: and that if a human-adapted strain were to infect communities in South Asia, high population densities and global interconnectedness would rapidly spread the infection.

All of which means that the more we can learn about the host range, ecology, and pathogenicity of these Henipaviruses, the more likely we are to be able to prevent, or at least contain, larger outbreaks in the future.

To this end, the January 2020 issue of the CDC’s EID Journal provides us with detailed look at Nipah Virus (NiV) isolate collected in 2003 from Cambodia; a country that has yet to report human infection.

This is a lengthy, detailed, report and so I’ve only post the abstract and some excerpts from the discussion.  Follow the link to read it in its entirety.  I’ll have a postscript when you return.


High Pathogenicity of Nipah Virus from Pteropus lylei Fruit Bats, Cambodia
Maria Gaudino, Noémie Aurine, Claire Dumont, Julien Fouret, Marion Ferren, Cyrille Mathieu, Olivier Reynard, Viktor E. Volchkov, Catherine Legras-Lachuer, Marie-Claude Georges-Courbot, and Branka Horvat


We conducted an in-depth characterization of the Nipah virus (NiV) isolate previously obtained from a Pteropus lylei bat in Cambodia in 2003 (CSUR381). We performed full-genome sequencing and phylogenetic analyses and confirmed CSUR381 is part of the NiV-Malaysia genotype. 

In vitro studies revealed similar cell permissiveness and replication of CSUR381 (compared with 2 other NiV isolates) in both bat and human cell lines. Sequence alignments indicated conservation of the ephrin-B2 and ephrin-B3 receptor binding sites, the glycosylation site on the G attachment protein, as well as the editing site in phosphoprotein, suggesting production of nonstructural proteins V and W, known to counteract the host innate immunity. In the hamster animal model, CSUR381 induced lethal infections. 

Altogether, these data suggest that the Cambodia bat-derived NiV isolate has high pathogenic potential and, thus, provide insight for further studies and better risk assessment for future NiV outbreaks in Southeast Asia.


Although NiV has been shown to circulate in Cambodia (20,21), Thailand (39), and Vietnam (40), transmission to humans or domestic animals has not been reported in these countries. According to our results, the absence of detected outbreaks in this region cannot be attributed to lower pathogenicity of the circulating NiVs; our results suggest that other factors probably contribute. However, the NiV isolate presented in this report has been the only live NiV isolated in this region, and the existence of other NiVs with different pathogenic potentials cannot be excluded.

In Cambodia, P. lylei bats were found to often forage in residential areas and visit palm trees used in the region as a source of date palm sap; thus, opportunities abound for bats to interaction with humans and livestock in this country (41). Bat colony migration toward urban sites is further enhanced by the presence of hunters in rural areas (42) and deforestation (causing consequent damage to roosting trees and food sources) (43). Contamination of palm sap, which is consumed raw by persons in the region, with bat urine, saliva, or feces was found to be a major route of NiV transmission to humans during annual outbreaks in Bangladesh (10).

Diverse agricultural practices in Southeast Asia could also play a role in NiV regional ecodynamics, potentially favoring easier NiV spillover in some countries over others. High intensity pig farming was recognized as a major risk factor for outbreaks in Malaysia during 1998–1999; because of the low-scale pig production ongoing in Cambodia (44), the risk for NiV transmission from Pteropus spp. to domestic animals and humans in this country might be reduced.

Unrecognized NiV outbreaks might have occurred in Cambodia and neighboring countries; hospital-based surveillance in Bangladesh was shown to have missed nearly half of the NiV outbreaks in that country since the first reported virus emergence (45). Interdisciplinary approaches are certainly required to identify these outbreaks and the drivers of NiV emergence (46), and regular testing of patients with encephalitis in Cambodia and neighboring countries could provide additional insight.

Our study contributes to the assessment of the risk for NiV outbreaks in Asia. Our findings can be used to help target adequate preventive measures, which could ultimately help reduce the risk for NiV emergence.

(Continue . . . )

While novel influenza remains the world’s biggest pandemic threat, over the past couple of decades Nipah, SARS, MERS-CoV, and other suspected bat-borne viruses have become increasingly viewed as having some pandemic potential.

  • In Steven Soderbergh’s 2011 pandemic thriller `Contagion’, technical advisor Ian Lipkin – director of Columbia University’s Center for Infection and Immunity in New York – painstakingly created a fictional MEV-1 pandemic virus based on a mutated Nipah virus.
  • In May of 2018, in the Johns Hopkins Clade X exercise, a genetically altered Nipah virus (spliced onto a parainfluenza backbone) was the cause of their fictional pandemic.

In 2017 EcoHealth Alliance published a letter in Nature (Host and viral traits predict zoonotic spillover from mammals) providing the first comprehensive analysis of viruses known to infect mammals.

From their website summary:

The study shows that bats carry a significantly higher proportion of viruses able to infect people than any other group of mammals; and it identifies the species and geographic regions on the planet with the highest number of yet-to-be discovered, or ‘missing’, viruses likely to infect people. This work provides a new way to predict where and how we should work to identify and pre-empt the next potential viral pandemic before it emerges.

Bats are the most abundant and geographically dispersed vertebrates on earth. Their ability to carry and vector dangerous diseases without ill-effect (i.e. Rabies, Nipah, Hendra, etc.) is increasingly viewed as a potential public health threat.

None of this is meant to demonize bats, as they are an important part of our environment, but it does make them very much worth studying. 

Some other bat-related blog posts include:

PLoS NTDS: Prioritizing Surveillance of Nipah Virus in India

Potential For Zoonotic Emergence Of Coronavirus In Latin America

Nature: Fatal Swine Acute Diarrhoea Syndrome Caused By An HKU2-related Coronavirus Of Bat Origin

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

PNAS: SARS-like WIV1-CoV Poised For Human Emergence

Sci Rpts: Avian & Human Influenza Compatible Receptor Cells In Little Brown Bats