All you need to know about the novel 2019 coronavirus

All you need to know about the novel 2019 coronavirus


Coronaviruses are a large family of RNA (ribonucleic acid) viruses that are known to cause illness ranging from the common cold to more severe diseases such as Middle East Respiratory Syndrome (MERS) and Severe Acute Respiratory Syndrome (SARS). They are called coronaviruses because the virus particle exhibits a characteristic ‘corona’ (crown) of spike proteins around its lipid envelope.

Coronavirus infections are common in animals and humans. Some strains of CoV are zoonotic, meaning they can be transmitted between animals and humans, but many strains are not zoonotic.

In humans, coronaviruses can cause illness ranging from the common cold to more severe diseases such as Middle East Respiratory Syndrome (caused by MERS-CoV), and Severe Acute Respiratory Syndrome (caused by SARS-CoV). Detailed investigations demonstrate that SARS-CoV was transmitted from civets to humans, and MERS-CoV from dromedary camels to humans.


The symptoms can include a cough, possibly with a fever and shortness of breath. There are some early reports of non-respiratory symptoms, such as nausea, vomiting, or diarrhea. Many people recover within a few days. However, some people — especially the very young, elderly, or people who have a weakened immune system — may develop a more serious infection, such as bronchitis or pneumonia.

What is this novel coronavirus 2019?

The new Coronavirus 2019 is a zoonotic virus, which means it is a pathogen that spreads from one species to another, however it is unclear exactly what the origin of this virus is, but the genetic sequence is already being studied (

A novel coronavirus (CoV) was identified in 2019 in Wuhan, China. This is a new coronavirus that has not been previously identified in humans.

On 31 December 2019, human cases of pneumonia of unknown etiology were reported in Wuhan City, Hubei Province of China. A coronavirus, named 2019-nCoV acute respiratory disease (2019-nCoV), was identified as the causative virus by Chinese authorities on 7 January 2020. Since then, human cases with travel history to Wuhan have been reported by several provinces in China and by a number of countries outside China.

For up to date information please consult the WHO website

How is this novel coronavirus treated?

Scientists are working hard to understand the virus, and Chinese health authorities have posted its full genome in international databases. Currently, there are no approved antivirals for this particular coronavirus, so treatment is supportive. For the sickest patients with this illness, specialized, aggressive care in an intensive care unit (ICU) can be lifesaving.

How can we combat new viruses?

Professor Eric Fevre explained the way to combat new viruses is being prepared and doing more routine and regular surveillance at places, which are a breeding ground for these viruses. “It’s very difficult to develop a drug or vaccine for something we don’t know about, so we always have to start the development process after those events have occurred,” he explained. But typically, it takes between four to five years to develop a vaccine for a new virus. Several groups are working on a vaccine right now, but there is no guarantee it will be ready before the end of the current outbreak.

What can we do to stay safe?

  • Avoiding unprotected contact with farm or wild animals.

  • People with symptoms of acute respiratory infection should practice cough etiquette (maintain distance, cover coughs and sneezes with disposable tissues or clothing, and wash hands).

  • Within healthcare facilities, enhance standard infection prevention and control practices in hospitals, especially in emergency departments

  • Based on currently available information, travel or trade restrictions are not recommended.

Are animals responsible for the 2019 novel coronavirus infections in people?

  • The source of this outbreak has yet to be confirmed but it could be any number of animal carriers from snakes to pigs.

  • Genetic sequence data reveals that 2019-nCoV is a close relative of other coronaviruses found circulating in Rhinolophus bat (Horseshoe Bat) populations.

  • There is suspicion that the 2019-nCoV may have had an animal source, but further investigations are required to confirm this.

  • Although there is suspicion that the initial introduction of 2019-nCoV to humans may have come from an animal source, the predominant route of subsequent transmission appears to be from human to human.

  • Ongoing investigations are important for identifying the animal source (including species) and establishing the potential role of an animal reservoir in this disease.

Why is One Health so important in situations involving emerging diseases such nCoV2019?

Stopping disease in humans by preventing disease in animals underpins the concept of “One Health”, an approach to public health that recognises the links between animals, people and planet. To bring this to bear and prevent similar outbreaks in the future, we need greater commitment, funding and research on these shared health threats.

By identifying disease threats and spread as early as possible, health authorities can take pre-emptive action, such as tighter biosecurity controls on farms or at food markets, or public awareness campaigns. By developing and using new and better treatments for animal disease, we can help stop their spread both among animal populations and among people.

Where and how are new diseases likely to emerge?

Our team lead, Eric Fevre, a professor of infectious diseases at the University of Liverpool, while speaking with ITV, outline that new diseases are likely to spring up in urban environments where humans have created very densely packed human populations, alongside a population of bats, rodents, birds, pets and other things living organisms. This creates an intense interaction and opportunities for pathogens to move from species to species. Other such environments, which are created as part of the economy or the way we live are slaughterhouses where individuals who work there are in intense contact not just with animals but with the different parts of the insides of animals or wet markets. Similarly, where animals are sold, cut up and cleaned and where there are a lot of people interacting with those individuals.

David Quammen, the author of “Spillover: Animal Infections and the Next Human Pandemic, in an opinion piece in the New York Times, “When people invade tropical forests and other wild landscapes, which harbor so many species of animals and plants — and within those creatures, there are so many unknown viruses. We cut the trees; we kill the animals or cage them and send them to markets. We disrupt ecosystems, and we shake viruses loose from their natural hosts. When that happens, they need a new host. Often, we are it.”

Other ways that disease emerge are current circumstances which include a perilous trade in wildlife for food, with supply chains stretching through Asia, Africa and to a lesser extent, the United States and elsewhere. That trade has now been outlawed in China, on a temporary basis; but it was outlawed also during SARS, then allowed to resume — with bats, civets, porcupines, turtles, bamboo rats, many kinds of birds and other animals piled together in markets such as the one in Wuhan. And one consequence of that abundance in human population, that power, and the consequent ecological disturbances is increasing viral exchanges — first from animal to human, then from human to human, sometimes on a pandemic scale.

What is the key take home message: Do not panic!

Given the current spread of this virus and the pace and complexity of international travel, the number of cases and deaths will likely to continue to climb. We should not panic, even though we are dealing with a serious and novel pathogen. Public health teams are assembling. Lessons learned from other serious viruses, such as SARS and MERS, will help. As more information becomes available, public health organizations like the World Health Organization (WHO) will be sharing key information and strategies worldwide.

Are there any precautions to take with live animals or animal products?

In accordance with advice offered by the World Health Organisation, as a general precaution, when visiting live animal markets, wet markets or animal product markets, general hygiene measures should be applied, including regular hand washing with soap and potable water after touching animals and animal products, avoiding touching eyes, nose or mouth with hands, and avoiding contact with sick animals or spoiled animal products. Any contact with other animals possibly living in the market (e.g., stray cats and dogs, rodents, birds, bats) should be strictly avoided. Attention should also be taken to avoid contact with potentially contaminated animal waste or fluids on the soil or structures of shops and market facilities.

Standard recommendations issued by the World Health Organisation to prevent infection spread include regular hand washing, covering mouth and nose when coughing and sneezing, and thoroughly cooking meat and eggs. Avoid close contact with anyone showing symptoms of respiratory illness such as coughing and sneezing.  Raw meat, milk or animal organs should be handled with care, to avoid cross-contamination with uncooked foods, as per good food safety practices. Further recommendations from WHO can be consulted here:

What are the Veterinary Authority’s international responsibilities in this event?

The detection of 2019-nCoV in animals meets the criteria for reporting to the OIE through WAHIS, in accordance with the OIE Terrestrial Animal Health Code as an emerging disease. Therefore, any detection of 2019-nCoV in an animal (including information about the species, diagnostic tests, and relevant epidemiological information) should be reported to the OIE.

It is important for Veterinary Authorities to remain informed and maintain close liaison with public health authorities and those responsible for wildlife, to ensure coherent and appropriate risk communication messages and risk management.

Effective biosecurity risk management and cooperation with inspection authorities should be maintained at borders.

What are key lessons we have learnt?

It may seem counter-intuitive, then, but with six out of 10 infectious diseases being zoonotic, one of the best ways to protect people from diseases like coronavirus is to first protect the health of animals. But recent novel cases of human coronavirus are just the latest reminder that we are too often missing the opportunity to act before new diseases emerge in people.

As David Quammen puts it, “We are faced with two mortal challenges, in the short term and the long term. Short term: We must do everything we can, with intelligence, calm and a full commitment of resources, to contain and extinguish this nCoV-2019 outbreak before it becomes, as it could, a devastating global pandemic. Long term: We must remember, when the dust settles, that nCoV-2019 was not a novel event or a misfortune that befell us. It was — it is — part of a pattern of choices that we humans are making.”

Further resources and references

More resources on the novel coronavirus 2019

Do livestock have a role in the emergence of disease in urban cities?

Do livestock have a role in the emergence of disease in urban cities?

One of the primary objectives of the Urban Zoo project is to quantify and understand microbial diversity in an urban setting and to try and link that to urban livestock keeping. In so doing we aim to elucidate the possible role of livestock as a risk factor in the emergence of disease in cities.

To give us a handle on microbial diversity we have chosen commensal Escherichia coli as an indicator species, which we have isolated from samples taken from a diversity of sources across the city of Nairobi. These comprise people and their living spaces, including the food they eat; their immediate environments, including water sources, waste and wildlife; and the livestock that they keep either for their own consumption or for sale. From these samples we isolate and culture E. coli, extract their DNA, and perform whole genome sequencing, enabling us to compare isolates from different compartments and to determine how closely related they are, and thus how microorganisms might pass from one to another.

The collection of these samples has been guided by a highly structured sampling frame, which I described in Urban Zoo newsletter number 7. Essentially, we have selected 33 sub-locations in Nairobi representing a range of social strata and, within each, have chosen 3 households to sample: one with no livestock; one with only monogastric species (pigs or chickens); and one with ruminant livestock (sheep, goats or cattle); You can view the spatial maps at our earlier post by clicking here .

The collection of such comprehensive data from these 99 households was an enormous undertaking and has been a considerable logistical feat of coordination between the field and the laboratory. The good news is that the sampling is now complete, thanks to the heroic efforts of the field team, led by Judy Bettridge and James Akoko, and of our colleagues in the laboratories.

Overall, 2,351 samples have been collected and we managed to culture E. coli from 80% of these (1,850). Once the last few have been done this will give us 1,809 whole genome sequences to analyse. 327 of these are from people; 58 from the places where they prepare food; 64 from animal source foods (milk meat and eggs); 644 from 12 different species of livestock; 239 from the environment around the home-stead including water sources; and 477 from a wide diversity of wildlife in the vicinity of the household.

But it is not over yet. We will very soon have finalised the sequencing and now comes the equally challenging task of deciphering all of this genetic data to unveil the pattern of microbial diversity across Nairobi. Over to you Melissa!

On that note, I would like once again to congratulate the field and laboratory teams, and to wish everyone a great year ahead, 2017.

This article was authored by Dr. Timothy Robinson who is a co-principal investigator in the Urban Zoo project and also a principal scientist with ILRI’s Livestock Systems and Environment research group.

Endemic infectious diseases: the next 15 years

Endemic infectious diseases: the next 15 years

I have recently returned from the International AIDS Conference in Durban, South Africa. It was, as many have noted, a landmark event: a chance to celebrate the remarkable success of the HIV response over the past 15 years.

But it was also a stark wake-up call. Despite the tangible results – which include millions of lives saved – it is increasingly clear that to achieve the goal of ending the AIDS epidemic as a public health threat by 2030, the world needs to take the fight several steps further.

Accelerating progress across all infectious diseases

Dr Ren Minghui, Assistant Director-General for HIV/AIDS, Tuberculosis, Malaria and Neglected Tropical Diseases WHO

Dr Ren Minghui, Assistant Director-General for HIV/AIDS, Tuberculosis, Malaria and Neglected Tropical Diseases

The Sustainable Development Goals (SDGs), agreed last September at the United Nations in New York, offer an ample opportunity to accelerate progress across all infectious diseases. The focus on equity, health systems strengthening, universal health coverage, and multi-sectoral action will transform the way we tackle these diseases.

The SDGs build on the momentum generated during the Millennium Development Goals era, and on lessons learned during the first 15 years of this century. And they recognize that while the global response has significantly reduced the infectious disease burden and saved over 50 million lives, much more needs to be done.

In 2000, who would have thought that by 2015 the world could get 17 million people in low- and middle-income countries on antiretroviral treatment, reduce malaria mortality rates by 60% and cut tuberculosis (TB) deaths by 47%? Who would have predicted that, within the space of 15 years, it could bring down the number of guinea worm infections from over 75 000 to just 22? But it did.

What we have to do now is maintain our resolve and further intensify our efforts.

“More than anything, the next 5 years should be about creating solid foundations for ending the infectious disease epidemics everywhere. This is not a moment to lift our foot off the accelerator. These diseases are known for returning with a vengeance, if we ever slow down.”

Dr Ren Minghui, WHO Assistant Director-General for HIV/AIDS, Tuberculosis, Malaria and Neglected Tropical Diseases

Infectious diseases continue to have far-reaching impacts on people’s lives. In some of the poorest countries of the world, they continue to devastate economies and cripple health systems. Progress remains uneven and millions are not being reached with prevention measures and treatment.

From the outset, the fight against infectious diseases has been dogged by social, legal and economic barriers, and funding gaps have been significant. These are a major reason why HIV, TB, malaria, viral hepatitis and neglected tropical diseases (NTDs) still kill more than 4 million people every year.

Globally, 480 000 people develop multi-drug resistant TB each year, and drug resistance is starting to complicate the fight against HIV and malaria, as well. A coordinated effort to tackle this challenge – under the umbrella of the WHO global action plan on antimicrobial resistance – will be critical to success.

Global strategies on infectious diseases

To help countries deliver on their pledge to ‘end the epidemics’ by 2030, the World Health Assembly has adopted global strategies on HIV, TB, and malaria. This year, it passed the world’s first-ever global hepatitis strategy and set the first global hepatitis targets. Since 2012, a WHO roadmap has been available to guide global efforts on NTDs which affect over a billion people.

The strategies are backed up by a set of evidence-based guidance documents to help countries design and implement their own plans. They emphasize opportunities to maximize the impact of prevention, treatment and care services, and to mitigate the impact of biological challenges, such as drug and insecticide resistance, and climate change.

At the same time, WHO is working to help countries move closer to universal health coverage, by ensuring that all people have access to the health services they need, without being thrown into poverty as a result.

As well as establishing robust health financing systems, this means building up a qualified workforce and investing in efforts to improve the quality of treatments, diagnostics and prevention tools. It means assuring adequate supplies of affordable, safe and effective health products and putting an end to stock-outs. And it means joining up the dots: a greater integration of services, as we are already seeing in many places.

More than anything, the next 5 years should be about creating solid foundations for ending the infectious disease epidemics everywhere. This is not a moment to lift our foot off the accelerator. These diseases are known for returning with a vengeance, if we ever slow down.

This post was authored by Dr. Ren Mingui (WHO Assistant Director-General for HIV/AIDS, Tuberculosis, Malaria and Neglected Tropical Diseases) originally appeared as a commentary on the World Health Organisation website on 17th August 2016. Available at:

Human, Food and Environmental data collection

Human, Food and Environmental data collection

WhatsApp-Image-20160607Human, food and environmental data are among the wide range of data collected within the 99 households. The data are often collected by Clinical Officers. Human sampling involves among others, individual consenting to participate, questionnaire interviews administration, general physical examination and anthropometric measurements, biological data collection and offering feedback and health education on the outcome of the laboratory based investigations. Two sets of structured questionnaires are administered; a general household and individual participant questionnaires. Biological data that is collected includes fecal samples and nasal swabs. Fecal samples are assessed for E. coli and campylobacter bacteria while nasal swabs are assessed for antimicrobial resistance. Collection and transportation of human samples from the field to laboratories involves sterile techniques.

Like human sampling, sterile steps are also observed during food and environmental data collection. Only livestock sourced foods are collected in the study. A sample of meat, milk and a wipe of egg shells if available, are collected. Sterile wipes of kitchen working surfaces such as chopping boards as well as kitchen door knobs are also collected. Environmental samples are collected using sterile boot socks. Normal saline-wet boot socks are worn and environmental samples collected by walking around the area surrounding the household as well as surfaces within livestock pens if available. Whirl pack bags are used in transportation of environmental samples. Water samples from water puddles, boreholes or storage water tanks are also collected as environmental samples. Subsamples of food and environmental samples are marked with a red dot to identify those going for whole genome sequencing and a blue dot on those being analyzed for campylobacter. All collected data are de-identified using barcode numbers to enhance participant and sample anonymity.

On completion of data collection, participants in the household are either given Albendazole or Mebendazole anthelminthic depending on age. Anyone found to be clinically ill is offered a prescription. If they are seriously ill a written referral letter to the nearest and most preferred health facility for further management is offered. Laboratory outcomes are communicated back to individual participants within two to three weeks of data collection. This is accompanied by health education with emphasis on how to maintain proper hygiene as well as interaction with livestock. Like many other community studies, our study is not devoid of challenges. Some of the challenges encountered involve heavy traffic. As investigators, we have to sometimes anticipate early morning starts. Participants which means rescheduling the day to collect data. Others include withdrawal from participation and inability to access household heads especially in high income settings.

Laureen AlumasaFredrick Amanya

 Article by Lorren Alumasa & Amanya Fredrick

This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.

Update: 99 Household study update

Update: 99 Household study update

Well, time has flown since we sampled the first household in the 99 households study. On 7th June we visited our 66th household, meaning that after 8 months we are now two thirds of the way through. The project is taking us to all parts of Nairobi, as the maps illustrate. The field teams normally spend Monday to Wednesday collecting data, then use Thursdays and Fridays to recruit new households to the study, meet with local chiefs and county officials, give feedback to participants and keep on top of all the other jobs, such as vehicle maintenance, stock-keeping, accounting and paperwork. The wildlife team regularly go out on evenings and weekends to set and check traps for rodents and bats (who inconveniently refuse to venture out during normal working hours!) In some areas it has occasionally been necessary to conduct the study interviews in the evening, when participants return from work. Having to be flexible to fit around our human and animal participants’ needs, plus the perennial problem of Nairobi traffic, means early starts and long days.

The laboratory teams also come in for their share of hard work. Even with motorbike couriers, samples normally do not arrive at the labs until the afternoon, especially when large households are sampled. To process all these samples takes time. Each sample is first incubated in an enrichment broth, then undergoes two rounds of purification on a special type of agar which selects for E. coli, before being cultured on a more general agar prior to freezing the bacteria for storage. As you may imagine, this is several days’ work – each step takes at least 24 hours – and of course the bacteria don’t stop growing at weekends! Timing of steps is crucial, to ensure that pure colonies can be selected for storage. Later on, batches of isolates are revived and a number of biochemical tests are performed, to check that the bacteria we send to the UK for sequencing really are the E. coli that we are interested in. Once we are reasonably sure that what we have is an E. coli, they have to be regrown once more so that they can be sent to ILRI, where the DNA is extracted to send to the sequencing facility at Oxford.

So as you might imagine, it is extremely gratifying to finally start to see some of the results of all this hard work. Dr. Melissa Ward recently visited the teams in Nairobi and brought with her some of the first outputs of the sequencing to show us. In return, we took her along to see the sampling in action, in one of the slum sites. Melissa said, “It really brings the project to life, to see exactly how all the data and the samples are collected. Now, when I sit at my computer, I can really understand where it’s all coming from.” For us, it was equally exciting to get some tantalising glimpses of what the final dataset might look like and what kind of patterns we may be able to identify from the phylogenetic structure and genomic data. We’re not giving anything away at this stage – but we can tell you that we definitely have E. coli – and lots of it!

Judy_BettridgeArticle by Judy Bettridge

This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.

Click to view enlarged maps

Map ruminants
Map poultry
Map monogastrics

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