Bats, snakes, civets … where did the new coronavirus come from?

By Manuel Peinado Lorca, Alcalá University

The emergence in China of an outbreak of pneumonia caused by a coronavirus (2019-nCoV) is a challenge for virologists, who have embarked on a time trial race to obtain more data on the genetic sequence, epidemiology and spread of the pathogen.

The most urgent question is to determine how it spreads. The real-time monitoring of the speed at which the new cases appear, together with when the symptoms began for each of them, are the signals that indicate to the experts the ease with which the virus can circulate among humans and if the Outbreak has the potential to persist.

Each virus has a different method of transmission. Among these are transmission vectors, which are other organisms that transmit them between carriers. Animal viruses are usually spread from vertebrate to vertebrate by hematophagous insects.

Coronaviruses are a family of 39 viruses. Some cause diseases in people, while others infect animals such as camelids (MERS), felines and bats (SARS).

In rare cases, animal coronaviruses can evolve to infect people and then spread to each other by airborne transmission (sneezing or coughing). They can also be transmitted by recently contaminated objects or substances, such as the influenza virus and the MERS, whose route of infection was probably the intake of fresh milk from freshly milked camelids.

Although many details of 2019-nCoV are still unknown, a WHO statement suggests that an animal is the primary source of this new outbreak. Despite this, the National Health Commission of China has confirmed that some cases have been caused by direct transmission between humans (as happened with its two predecessors), but it is still unclear if that is the norm.

Where does the virus come from?

Experts are working with the hypothesis that the virus originated from an unidentified animal or animals, and then spread to humans in a large food market in Wuhan.

In that food market, now closed, wild animals are sold for consumption as snakes. In an article published by Chinese virologists on January 22, the first animals designated as primary sources have been precisely those reptiles.

The study analyzed the genetic sequence of the new virus and compared it with the genetic sequences of more than two hundred other coronaviruses around the world that infect several animals. They considered several potential hosts such as marmots, hedgehog pangolins, bats, birds, humans and snakes.

They concluded that the 2019-nCoV was able to use two common snakes as a resident in southeastern China, the krait pluribanda (Bungarus multicinctus) or the Chinese cobra Naja atra, both commercialized in the supply market of Wujan.

Chinese cobra, one of the first species suspected of being a carrier of the new coronavirus. Thomas Brown, CC BY

However, this theory seems discarded today. Other scientists say there is no evidence that these coronaviruses can infect species other than mammals. The background supports them.

At the end of 2002, cases of a pneumonia-like disease began to appear in Guangdong, in southeast China. The disease, called SARS, triggered a worldwide emergency as it spread throughout the world in 2003. Thousands of people were infected.

Chinese scientists identified a coronavirus strain as a possible culprit and found genetically similar viruses in palm civets (Paguma larvata), some mammals similar to our ginets that were sold in the supply markets of Guangdong.

Paguma, a species of civet carrying the SARS virus. Rushenb, CC BY

Later, exploring inside caves, virus hunters found a large number of coronaviruses related to SARS in horseshoe bats Rhinolophus sinicus, which suggested that the strain probably originated in these mammals and then passed to the civets before reaching humans.

That is why the virologists of the Pasteur Institute in Shanghai who in 2017 identified SARS-related viruses in grotto bats are clear. The SARS and 2019-nCoV viruses are part of a subgroup of four viruses known as betacoronavirus. Field work carried out following the outbreak of SARS 2002–03 by these and other virologists has only detected this type of virus in mammals.

What does the virus genome tell us?

The genetic sequencing of Wuhan's coronavirus offers clues about its origins and spread. A phylogenetic analysis of eleven of these strains published on January 20 showed little genetic diversity among them. This suggests that the common ancestor of the different strains of 2019-nCoV found in humans arose in November or December (when the first cases appeared) and has spread rapidly, without suffering many alterations. However, genomes do not yet indicate whether rapid virus expansion occurred in humans or in an intermediate animal reservoir.

The available data do not allow to determine if the most common recent ancestor of the sampled cases was in a human or an animal. For the moment, phylogenetic data suggests that the jump from animals occurred shortly before the first cases identified in humans. If multiple zoonotic jumps occurred, they did not come from a genetically diverse virus reservoir.

This suggests that the virus had recently been established at the non-human source or that the initial human patients had been exposed to an animal source whose virus population was genetically limited. This could be the case if one or more infected animals had been taken to Wuhan from another location.

With more viral sequences it would be possible to find out if most cases are caused by repeated spread of the virus from animals to humans, with limited transmission from person to person; or if, on the contrary, the virus spread to a small number of humans and most cases are being caused by a direct secondary transmission from human to human.

Finding out is the great epidemiological objective in these confusing moments in which the globalization of communications paddles in favor of a possible direct and widespread human transmission.

Manuel Peinado Lorca, University Professor. Department of Life Sciences and Researcher of the Franklin Institute of American Studies, Universidad de Alcalá

This article was originally published in The Conversation. Read the original.