Viral genome sequencing may provide clues as to why different people respond very differently to infection, which could be important for more accurate identification and protection of those at greatest risk of severe disease
By Edsel Maurice T. Salvana, MD, DTM&H, FPCP, FIDSA
The great thing about being an infectious diseases doctor and a molecular biologist is that I can take different aspects of my fields of expertise and use them to complement each other. When dealing with an outbreak, molecular biologists can use molecular techniques as a sort of high-tech magnifying glass to answer questions about the origin and spread of a disease.
Infectious diseases doctors study the clinical behavior of infections, particularly how epidemics and pandemics evolve. Prior to the discovery of nucleic acid—DNA and RNA—sequencing, there were limits to proving what we intuitively knew was happening. With new and powerful genomic tools, we can now obtain hard evidence to support our clinical data.
For instance, the recent announcement of the first ever documented case of reinfection of Covid-19 made headlines and not a few people panicked. Some speculated that this had occurred multiple times in anecdotal cases they heard from friends or online. There was the doctor who got sick again and died, then both the senator and the general tested positive for Covid-19 twice.
Many of these cases of “reinfection” can be explained by the persistence of viral genetic material in the body for a long time, even after the patient has recovered and the virus is no longer transmissible. It may still be detected by RT-PCR but can no longer infect others. Another explanation would be a “false positive” occurrence where either the first or the second RT-PCR result was spurious due to a contaminated specimen.
The threshold for proving a case is a true reinfection is very stringent. It should satisfy clinical, immunologic, and genomic criteria. Clinical criteria are characterized by the presence or absence of symptoms. Immunologic criteria are evidenced by generation of an immune response such as antibodies. Genomic criteria are satisfied when two different viral genomic sequences are isolated from the same person at different times.
The Hong Kong case seems to have satisfied at least some of these requirements, although the full scientific paper is still for publication. We do not know if this is a common occurrence, nor do we know what implication this has for upcoming vaccines. There is no need to panic, and we need to closely listen to what the science is telling us.
Genomic data is particularly useful for figuring out epidemic timelines and gauging responses. If we look at the evolution of the Covid-19 outbreak in the Philippines, there was an initial cluster of three cases at the end of January 2020, followed by a whole month without detected cases. In epidemiology, a period of two long incubation periods is needed to say that an epidemic is contained. Covid-19 has an average incubation period of five days, and a long incubation period of about 14 days. At the end of February 2020, after four weeks without a new case, WHO commended the Philippines for controlling its outbreak.
At the beginning of March, two new cases were detected. The fourth overall case had a history of travel to Japan and was clearly imported. The fifth case was much more concerning. Patient number five had no travel history and no close contact with a known case. We knew this might represent ongoing community transmission and might be just the tip of the iceberg. If he was a first-generation contact, then there were probably at least two others whom the original undetected case had infected. If he was a second-generation contact, at least six people would have been infected, and so on. Time was of the essence. The cases diagnosed in March were unlikely to have been related to the first three Chinese cases in January since the government had already banned travel from China, and four weeks had passed. There was no genomic data, however, to prove it at that time, so the possibility of a link could not be ruled out.
A few days later, we had 10 cases. Those of us on the Technical Advisory Group of the Department of Health, a panel made up of infectious diseases and public health experts from academe, were getting antsy. We looked at what was going on in Italy and Spain and we were very worried that our healthcare system might be overwhelmed. Since Italy and Spain were highly developed countries with strong medical infrastructures, their predicament set off alarm bells. The usual threshold to declare widespread lockdowns in response to community transmission had come too late for them to mitigate a catastrophic surge of cases. If thousands of people were dying in those countries and they no longer had enough hospital beds to admit everyone, what would happen to the Philippines, where we have much fewer beds and a much lower healthcare capacity? The only blueprint that had worked had been the drastic lockdown in Wuhan, and this approach was affirmed by WHO in its report on the Covid-19 outbreak in China.
On March 12, at only 52 confirmed Covid-19 cases, based on our reading of the science, we recommended to the IATF that community quarantine be declared in Metro Manila. This was affirmed and transmitted to President Duterte who acted on it. This was to be one of the earliest lockdowns in the world, and the first in the capital of a developing country. Given the exponential growth of infectious diseases, a few days can translate into a difference of tens of thousands of deaths and millions of cases, and so an early lockdown was essential.
In April and May, cases began to stabilize, and deaths were relatively low. The government began relaxing quarantine measures to revive its battered economy. Unfortunately, a second epicenter started to emerge in Cebu, which reverted to ECQ. In Metro Manila, cases also started to surge as measures were relaxed. There was emerging evidence of a more transmissible form of SARS-CoV-2, a mutation termed D614G giving rise to a variant (G614), which was replacing the original SARS-CoV-2 D614 viruses worldwide. Some estimates put G614 at three to 10 times more transmissible than D614. Fortunately, there is no evidence that G614 is deadlier.
As cases continue to rise, genomic data has been slowly but surely gathered to help us make sense of our epidemic. A new study of the Research Institute of Tropical Medicine now shows multiple introductions of different Covid-19 lineages to the Philippines.
The first three cases in January (patients one to three) are genetically distinct (lineage A and B) from the March samples (patients four and beyond, lineage B.6). The June samples are also genetically distinct since some are G614 variants (lineage B.1 and B.1.1).
This shows that the Philippines was able to contain the first three cases of Covid-19 in January 2020. There is no molecular evidence of undetected community transmission that links those first three Chinese cases to the subsequent March cases.
The March cases are lineage B.6, which are distinct from the January lineages. Only two of the March cases had a history of travel, neither of them from China. This supports at least one separate introduction in March distinct from the first three cases in January. Lineage B.6 has been found in India, Singapore, Gambia, and other countries. More introductions occurred after March as shown by the introduction of the G614 variant. Since tourism was limited during the lockdown, these variants are most likely from returning OFWs, more than 100,000 of whom have been repatriated since the start of the lockdowns.
With this genomic data, we can make the following reasonable conclusions and proposed actions. First, the original introductions in January were controlled by banning travel from China and doing quarantine and contact tracing for those with a pertinent travel history. Early containment measures worked. Second, the next wave of cases in March came from other countries apart from China. This means that we should have moved
faster in banning travel from other countries with ongoing community transmission. Finally, the continued introduction of new variants can only have come from returning travelers. This means we need to be more stringent with quarantine for everyone entering the country from abroad. Due to the limitations of testing, a blanket 14-day quarantine would probably be more effective since this will completely shut down transmission from false negative asymptomatic carriers.
Genomic data is a new and extremely potent weapon in the fight against disease. With institutions like the Philippine Genome Center and the National Institutes of Health, we will be better poised to deal with the pandemic and subsequent infectious diseases that can threaten the lives of Filipinos.