What it can and cannot do, and why it is important
CLINICAL MATTERS
Dr. Edsel Maurice T. Salvana
Ever since the horrific surge of cases in India, the world has been racing against the spread of the Delta variant. As a testament to how virulent and transmissible this variant is, it has already become the most dominant variant of concern globally in just a few months. It is currently responsible for an overwhelming majority of cases in the US, Israel, Indonesia, Thailand, and Malaysia.
Over the last few months, the Philippine Genome Center and the Research Institute of Tropical Medicine have detected many of the variants of concern in the Philippines. Alpha, also known as B.1.1.7 or the UK variant, was detected in a returning Filipino tourist from Dubai in January 2021. Retrospective detection of stored samples showed an earlier introduction in Laguna, which thankfully did not spread. Beta (B.1.351, South African Variant) was subsequently detected and has since spread to other regions. Gamma (P.1, Brazil variant) was detected in two travelers but has not been detected in the community. Delta was knocking at our door for a couple of months as shown by repeated detections in returning overseas Filipinos. It finally got through to the community ostensibly due to breaks in border control protocols. More and more cases of Delta are being detected. Delta is spreading in the Philippines, but in a linear fashion in contrast to the exponential increases in other countries.
What is genome sequencing?
Genome sequencing is the process of reading the genetic material of an organism. Genetic material is usually DNA. Some viruses, including SARS-CoV-2, use RNA as the main genetic material. If we think of the genome of an organism as a book, then the genetic sequences are like the letters and words of the book. DNA and RNA sequencing has grown by leaps and bounds in the last few decades. While early attempts at genetic sequencing could only read a few letters at a time, the technology has evolved to allow reading of the entire genetic sequence of organisms. In the case of the Human Genome Project, this consisted of reading 6,200 mega-base pairs (6.2 billion letters) that took 13 years to finish. With current scientific breakthroughs, an entire human genome can now be sequenced in a little over one hour.
With entire genomes capable of being read quickly by our machines, these genomes can be compared with one another. This is particularly useful in tracking infections from viruses and bacteria. With the proper equipment and analysis, genomic sequencing is a powerful epidemiological tool for guiding pandemic responses. It remains, however, as highly technical, expensive, and needs to be properly applied to maximize its value.
Genomic sequencing in the Philippines in past pandemics
DNA and RNA sequencing technologies were used in past pandemics in the Philippines. At the National Institutes of Health, we did partial genome sequencing of several hundred A(H1N1) influenza virus samples in 2009, which detected the first instances of local oseltamivir resistance. We have been doing whole genome sequencing of HIV at UP-NIH for the last few years. This was instrumental in detecting a shift in the dominant subtype of HIV in the Philippines from a Western subtype B to a Southeast Asian subtype CRF01-AE. This subtype shift may have contributed to the sudden increase in HIV cases in the Philippines.
Genomic sequencing in the time of COVID-19
The original Chinese virus lineages from Wuhan (lineage A and B) were first detected in the Philippines in January 2020. None of these initial viruses were able to spread to the community because of subsequent flight bans from China and the vigilance of our healthcare workers. The first local transmission of SARS-CoV-2 was detected in March 2020. It was lineage B.6, a lineage prevalent in Southeast Asia and India, which subsequently spread to other parts of the country. Sometime in June 2020, coincident with the second surge, B.1 was detected. B.1 had the D614G mutation which made the virus more transmissible. More sequencing helped identify introductions of the variants of concern, and a new variant first described in the Philippines named Theta or P.3. Theta was tagged as a variant of interest due to mutations of concern in its genome but was subsequently dropped from the list when it did not show signs of being more transmissible or being vaccine resistant.
Why does it seem genome sequencing results are late, and why don’t we sequence more?
Genomic surveillance by nature is a retrospective exercise. Alpha was detected in the UK one full month after the sample was collected. Genomic sequencing informs the public health response by monitoring the presence and the spread of variants of interest and variants of concern. In the last few years, it used to take two to four weeks to sequence whole genomes. Genome sequencing is now much faster. It gives highly reliable data.
The Philippine Genome Center (PGC) has a NovaSeq sequencer, which is on par with the best in the world. It can do 750 whole genomes of SARS-CoV-2 within three days, which is impressive for a developing country. The Philippines, through PGC, has submitted more sequences to the global repository GISAID than any other country in Southeast Asia.
Whole genome sequencing is quite expensive and takes a long time to analyze. In order to maximize each run, samples for sequencing need to be carefully selected. The specimens should have high enough levels of virus and should represent a wide range of geographic locations. Running too few samples is wasteful, and so some runs are delayed in order to gather more samples. Not all positive samples need to be run as soon as possible, since knowing the variant type for individual patients rarely changes clinical management. It is not designed to make clinical decisions in an individual patient.
One misinformed criticism against genomic sequencing is that it is often too late to make any difference in contact tracing because sequences that are released are already several weeks old. Contact tracing should be done when a person tests positive, not when genomic sequencing results come back. It shouldn’t make a difference in action points because whether the infection is a variant of concern or not, the index patient needs to be isolated and close contacts quarantined and tested.
There are two main objectives for genome sequencing: surveillance and purposive sampling. Surveillance means that proper systematic sampling is done nationwide. Sentinel sites are selected to cast as wide a net as possible and catch representative cases. Due to logistic concerns, this will usually involve samples that are weeks old. The patterns and transmission maps of each variant, called phylogenetic trees, help define the spread of variants in the country. Purposive sampling tries to grab samples from patients with specific epidemiologic characteristics such as belonging to a cluster of cases. When there is a surge of cases, purposive sampling can detect if a variant is causing an outbreak. When there are infections in people who have been vaccinated, purposive sampling can investigate if a variant of concern is becoming more prevalent. Genomic sequencing can therefore guide the wider public health response. Genomic sequencing is a “broad-strokes” intervention not meant to help manage individual patients. Sequencing more samples is desirable but resource intensive. If minimum sample sizes are already met, then there is no need to use up precious resources.
The COVID-19 pandemic is the first pandemic that has been extensively tracked by genomic sequencing. The Philippines is extremely fortunate in having state-of-the-art genomic sequencing capabilities and the needed expertise in place prior to the start of the pandemic. In order to maximize the benefits of this powerful tool, we need to understand how to apply it properly. Harnessing this new technology in the best possible way will save the most lives and will get us out of this pandemic sooner.