The earliest phase involved cases that appeared to be independent and featured viral genomes identical to those found in animal hosts, the researchers report in Science Express, the online version of the journal Science. The second phase, marked by clusters of human-to-human transmission, reveals how the virus quickly adapted to its human hosts. The third phase involved selection and stabilization, as the virus gravitated toward one common genotype that predominated through the end of the epidemic.
"What we see is the virus fine-tuning itself to enhance its access to a new host: humans," said study co-author Chung-I Wu, Ph.D., professor and chairman of ecology and evolution at the University of Chicago. "This is a disturbing process to watch, as the virus improves itself under selective pressure, learning to spread from person to person, then sticking with the version that is most effective."
In the early cases, infection rates were low, with only about three percent of those in direct contact with infected patients coming down with the disease. Within a few months that rate increased to nearly 70 percent of direct contacts.
This study, which combines a precise epidemiologic narrative of the emergence of the virus with rigorous analysis of the virus's genetic adaptations, confirms the importance of containing any new outbreaks quickly, the researchers said, before the virus becomes more difficult to control. It also points to potential targets for a vaccine aimed at the "spike" protein, involved in viral-host receptor recognition and internalization.