It is said “we all live in the past.” It is probably true. If
so, how we can use the past to foresee the future could then be our task
at present.
While preparing this manuscript, SARS-CoV-2 still continues circulating
in human populations and threatening public health. This pandemic has
further stressed the importance of closely monitoring the emergence of
infectious diseases originating from animal reservoirs and transmitted
between animals and people. It is obvious that this pandemics will not
be the last; a powerful experimental evolution approach allowing us to
closely survey the dynamics of genetic mutations in a population of
circulating zoonotic viruses in the short term and possibly predict
upcoming variants is therefore pivotal to improve the scientific,
medical and societal response to future zoonoses.
Molecular barcoding has a long history in yeast
genetics[161].
And to date, it has made great progress in investigating EIDs.
Concerning RNA viruses, as mentioned in the article, molecular barcodes
have been used as a tracer to follow the consequence of individual
viruses encountering evolutionary selection forces in vivo ,
rendering us better understanding viral transmission fitness and
evolutionary dynamics. Molecular barcoding on SARS-CoV-2 are focusing on
sample multiplexing thus far; application of molecular barcodes on
coronaviruses to gain better understanding of cross-species transmission
fitness over time will be extremely important. Whereas molecular
barcodes in retroviruses (SIV and
HIV)[17,25,61,63]have been applied to identify different polymorphisms on the viral gene,
study single provirus transcriptomics and track viral rebound in animal
models. Collectively, molecular barcodes provide us a good opportunity
for virus studies in a quantitative manner.
The key to using molecular barcodes as universal identifiers for either
identifying single molecules or tracing individual viruses is to have a
very large initial collection of barcodes. Good complexity of barcodes
diminish the probability that two independent molecules harbor the same
barcodes. Several approaches used to validate the quality of barcoded
libraries, such as calculation of a minimum Levenshtein
distance[38] or establishment of a threshold for
sorting out trustable
barcodes[26]have been mentioned previously. In general, barcode duplications are
recommended to be kept at a frequency below
0.1%[60].
It is also important to note that imbalance in the representation of the
barcodes in the library has been reported; a thorough investigation into
a bias of barcode representation will be required in the future.
Eventually, the impact of molecular barcodes on viral infectivity and
replication should be always taken into account; fitness of barcoded
viruses is recommended to be verified for the usage of every new
prepared barcoded library.