Epidemiologist Sergios-Orestis Kolokotronis, PhD, and scientists from Taiwan, Munich, Berkeley and Madison are examining genome data from every confirmed case of 2019-nCoV to unearth insights into viral emergence

Twice each day, SUNY Downstate School of Public Health evolutionary epidemiologist Sergios-Orestis Kolokotronis, PhD, joins a global group of scientists in reviewing a worldwide database of the latest genomic information about the Wuhan strain of novel coronavirus (2019-nCoV) that so far has infected more than 28,000 people, including more than 250 outside of China, and resulted in at least 560 deaths. By comparison, 349 people died in China during the outbreak of severe acute respiratory syndrome (SARS) in 2002-2003.

Dr. Kolokotronis is one of 6 researchers at 5 different institutions that have formed an international ad-hoc collaboration initiative to uncover clues as to the evolutionary trajectory of this form of coronavirus by untangling the virus’ genetic evolution over time and space.

Dr. Kolokotronis likens he and his colleagues to scientific detectives. They look at the genetic profile of the virus as it presents in each patient within the larger context of coronavirus diversity. Other variables that may be considered as the transmission continues are when certain patients began showing symptoms, where they have been, who they have been with, whether it had been transmitted to them by someone else or someone else has contracted it from them, and a host of other clues in an unending effort to uncover important insights.

“For instance, we can look at one of the confirmed cases in California and tell you for certain that the virus in that person has mutated very few times since right before it presented in the first patient,” said Dr. Kolokotronis. “Additionally, we can also use this data, and genomic data from other patients and animals, to determine whether the virus jumped from animals to humans, what we call a spillover, or emerged in humans altogether sometime in November or early December, even though the first cases were not reported until later in December. Genomic surveillance, empowered with computational modeling, allows us to do a deep dive into a pathogen’s history, evolutionary potential and interactions with its environment. The natural history of pathogen emergence and spread is usually a puzzle, where pieces get put together every day as more data points are generated and analyzed.”

Dr. Kolokotronis emphasizes that the group is not looking to develop a treatment, a vaccine, or a cure for Wuhan coronavirus, but rather to put the pieces together for those that will.

“Our job is to examine the genotype of the virus in its various mutations and connect the dots as to how the virus is behaving genomically, the speed and manner in which it mutates and spreads, and by doing so over time, provide insights that will be foundational to any public health effort to combat and mitigate this deadly strain of coronavirus, including:

• Decisions about whether it is appropriate to institute quarantines or otherwise isolating infected patients
• Determining the most appropriate and effective treatment of infected patients
• Implementing protocols to protect police officers, first responders, EMS, healthcare workers and others whose occupations may bring them in contact with infected patients
• Developing effective antiviral therapies and vaccines to treat, slow or stop the spread of the virus

“The work of Dr. Kolokotronis and his collaborators to better understand this emerging epidemic exemplifies the importance of the work done by our researchers at the School of Public Health, and the role they play in both improving public health and addressing emerging threats,” said Kitaw Demissie, M.D., MPH, Dean of the SUNY Downstate School of Public Health.

Other institutions in the collaboration include Academia Sinica in Taiwan, Technical University of Munich, Germany, The University of California, Berkeley, and the University of Wisconsin, Madison.

Dr. Kolokotronis says the group considers its work to be open research, and will use public and social media, as well as direct communication with public health officials and the media to share and report their key findings as the epidemic spreads, eventually publishing their findings in academic journals.

“We are very, very early in this outbreak, and we are fortunate that, so far, the mortality rate, of just approximately 2 % of patients is small when compared to the previous outbreaks of SARS (11% mortality) and MERS (Middle East Respiratory Virus), in which more than one-third of patients died,” added Dr. Kolokotronis. “But there is nothing to say that over time this virus couldn’t mutate into something even more deadly, or like SARS, simply die off. This is why our work is so important, and why we need to be vigilant to the data as it changes day by day. What we learn can inform effective public health efforts and the actions of coordinated global health networks.”