Understanding the novel coronavirus genome

By Angela Betsaida B. Laguipo, BSNMar 31 2020

The novel coronavirus emerged in December 2019 in Wuhan City, Hubei Province, in China, and since then, it has rapidly spread to over 170 countries across the globe. Our knowledge of the virus, now officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still in the early stages. However, scientists around the world are racing to better understand the virus, in the hope of shedding light on potential vaccines and therapies.

To effectively respond to an outbreak, it is crucial for health experts to study the genome of the virus, to provide a better understanding of the pathogen’s nature, how it affects the human body, what it targets, and how it is transmitted. A full understanding of genomic characterization and epidemiology of novel coronavirus will arm scientists with the tools to slow down or treat SARS-CoV-2 completely.

Genomic data

In December 2019, 27 patients out of the 41 people admitted to hospitals due to mysterious lung disease, passed through a wet market in Wuhan City. Though the origin of the virus has been traced to the market, the very first human case identified did not go to the market often. Instead, based on SARS-CoV-2 genomic sequences, the first case can be traced back to November 2019.

In a study conducted by Canadian scientists, they sequenced nearly 30,000-base genome of the SARS-associated coronavirus, called the Tor2 isolate. They found that the novel coronavirus, SARS-CoV-2, is only moderately associated with other known coronaviruses, such as the OC43 and the 229E.  

Further, the researchers found that SARS-CoV-2 belongs to the group of Betacoronaviruses, which are similar to the SARS-CoV from 2002. During that time, it was found that bats of the genus Rhinolophus were the reservoir of the virus. It was also revealed that a palm civet, a long-bodied, short-legged cat-like carnivore of the family Viverridae, was the intermediate host of the virus before it jumped to humans. In 2012, the MERS-CoV also jumped to humans through dromedary camels.

Role of pangolins remain a mystery

The novel coronavirus has shaken the world with its rapid spread out of China. On Jan. 23, due to widespread infections in Wuhan City and its neighboring provinces, the city was locked down. On Feb. 27, scientists unveiled that a virus close to SARS-CoV-2 had been found in pangolin, suggesting a new reservoir for the virus from bats.

A new review, however, noted that in analyzing genomic data from the Malaysian pangolin, there was only 90 percent of genomic concordance. The new study is hinting that pangolins may not be the reservoir for the current pandemic ravaging through countries across the globe. Still, the coronavirus extracted from pangolin is akin to 99 percent in a specific region of the S protein. The researchers concluded that the isolation of a coronavirus in the pangolin might suggest they have the potential to be an intermediate host of the novel coronavirus SARS-CoV-2.

Virus evolution and adaptation

Another analysis shows that based on next-generation sequencing of samples from bronchoalveolar lavage fluid from nine patients, eight of whom had been to the Huanan seafood market in Wuhan, where the virus first emerged. The team performed complete and partial genome sequencing to determine the evolutionary history of the infection, hinting its origin. The structural analysis of the virus shows that the SARS-CoV-2 may be able to bind with the angiotensin-converting enzyme two receptors in humans. The team also encouraged that future studies, particularly those focused on the evolution, adaptation, and spread of the virus.

In a report published on Virological.org, an online forum and data sharing website used by virologists, public health specialists, and epidemiologists, a team of scientists shared the complete genome sequence for the virus, shedding new light on how the virus is spreading across the globe.

In Italy, one of the hardest-hit countries of the COVID-19 outbreak,  the scientist haven’t yet figured out where the virus came from to arrive in Lombardy. The Italians have not yet identified their Patient 0, who would provide the answer as to whether the current outbreak came from China or somewhere else.

In Brazil, however, the team found that a case in the country closely resembles samples sequenced in Germany on Jan. 28. The genome is also different from that sequenced in Wuhan City. The team also showed that the virus mutates slowly and relatively little, about once a month. Upon studying the whole genome of the virus isolated from the second patient in the country, they found that there are differences between those from the first and the second patients.

The global sharing of COVID-19 data may soon provide a way for experts to develop potential vaccines and diagnostic tests.

Not man-made

During the peak of the epidemic in China, several theories have emerged that the coronavirus may be man-made. In a recent report, however, the researchers reviewed the origin of SARS-CoV-2 from comparative analyses of genomic data. They found that the virus is not a laboratory construct or a purposefully manipulated virus.