been a lot of time for evolution, which suggests the original virus was
introduced a while ago. These methods are now commonly used in
public health. Recall how in earlier chapters, we looked at the arrival
of Zika into Latin America and into North America. In both cases,
teams used genetic data to estimate the timing of the virus’s
introduction. Researchers have also applied these same ideas to
other infections, from pandemic influenza to hospital superbugs like
MRSA.[7]
With access to genetic data, we can also work out whether an
outbreak started with a single case or multiple introductions. When
our team analysed Zika viruses isolated in Fiji during 2015 and 2016,
we found two distinct groups of viruses in the phylogenetic tree.
Based on the rate of evolution, one group of viruses had arrived into
the capital Suva in 2013–14, spreading at low levels for the
subsequent year or two, while a separate outbreak had later started
in the west of the country.[8] I didn’t realise it at the time, but some of
the mosquitoes I swatted away during my 2015 visit had probably
been infected with Zika.
Another benefit of phylogenetic analysis is that we can track
transmission in the final stages of an outbreak. In March 2016, a new
cluster of Ebola cases appeared in Guinea, three months after
had declared the West Africa epidemic over. Perhaps the virus had
been spreading undetected in humans all along? When
epidemiologist Boubacar Diallo and his collaborators sequenced
viruses from the new cluster of cases, they hit upon an alternative
explanation. The new viruses were closely related to an Ebola virus
found in the semen of a local man who’d recovered from the disease
back in 2014. The virus had persisted in his body for almost a year-
and-a-half, before spreading to a sexual partner and sparking a new
outbreak.[9]
Sequence data is becoming an important part of outbreak
analysis, but the idea of evolving viruses can sometimes lead to
alarmist coverage. During the Ebola and Zika epidemics, several
media reports played up the fact that the viruses were evolving.[10]
But this isn’t necessarily as bad as it sounds: all viruses evolve, in