Which are more infectious, and which are more resistant to vaccines?
Dr. Edsel Maurice T. Salvana
Here we go again. With the recent increase in cases to over 3,000 new COVID-19 infections daily, we cannot help but feel a sense of déjà vu. This time last year, the unprecedented rise in new COVID-19 cases culminated in a nationwide lockdown.
As part of the Technical Advisory Group (TAG) of the Department of Health and the IATF, we watched with unease as countries with strong healthcare systems such as Italy, Spain, and China buckled under the burden of exponentially growing cases that crushed their healthcare systems. Knowing that the Philippines could not possibly cope with a similar surge, we urged the government to shut down.
The three cases of COVID-19 in January 2020 were all Chinese nationals. Without any new cases in February 2020, the Philippines felt increasingly confident that our containment measures had worked. Moreover, a complete ban on flights from China was deemed sufficient to keep cases out because the bulk of cases were still concentrated on the Chinese mainland. Then cases started cropping up in Korea, Singapore, Australia, and Taiwan. All of a sudden, we were surrounded. Retrospective genomic data now shows that the January cases were indeed contained, but the March cases snuck in from countries other than China. Lineage analysis indicated Singapore or India as the source, but it could have come from anywhere in Southeast Asia. Since then, we have seen repeated introductions from different countries.
The European lineage of B.1 and B.1.1 with the more infectious D614G mutation was introduced in June 2020. D614G makes SARS-CoV-2 about three to nine times more infectious. This supercharged the July 2020 surge that was already happening due to relaxation of quarantines. The spike to 6,000 cases a day resulted in a brief return to MECQ.
Introduction of new variants is inevitable as long as people continue to come in from abroad. Even New Zealand with its suppressed epidemic saw more than 200 different introductions of SARS-CoV-2. With more than one million returning OFWs and OFs coming into our country despite travel restrictions, we can only surmise that we may have had thousands of discrete introductions.
The most recent of these were the introduction of the UK variant and the South African variant despite travel bans on incoming flights from countries reporting these variants.
Should we bother with travel restrictions then? The answer is still yes, because while travel bans cannot completely keep the variants out, these can slow down the rates of introduction of variants. Our proportion of variants of concern (UK and South African) remains about five percent of all viral genomes sequenced. In contrast, countries like Israel went from 40 percent to 80 percent UK variant in a one-month span. The virus spreads very fast and some countries are slow to report cases and variants, assuming they are doing proper surveillance.
Our first UK variant detection in a Filipino was in a returning tourist from Dubai. This was before the UAE reported their own first case of the UK variant. One of the main differences between now and last year is that we have a robust genomic surveillance system, which can detect and track the introduction of these new variants. While the June 2020 introduction of D614G took months to detect, the Dubai UK variant case was detected within two weeks, enough time to intercept his primary and secondary contacts.
Are variants driving the surge? The UK variant is about 70 percent more infectious while the South African variant is anywhere from zero to 50 percent more infectious. Since these only make up about five percent of the genomes sequenced, it is unlikely that the variants of concern are the main driver behind the current surge. Most of the sequenced viruses are not variants of concern. Variants of concern could certainly be contributing, but the most likely culprit is pandemic fatigue.
After a year of lockdowns, face masks, face shields, and physical distancing, people are pretty much fed up and are getting careless. The fact that we now have variants makes this a much more potentially dangerous situation. If the variants do become the dominant viruses in the Philippines, the higher transmissibility will result in bigger surges, which will be much more difficult to control. The genomic surveillance program has given us an early warning. Let’s not waste this advantage through fatigue and carelessness.
As if all these weren’t enough, the virus continues to surprise us. Variants of concern are continuing to come in from different countries. We have been detecting them, and we are doing our best to keep them from spreading. Unfortunately, virus mutations can happen even in our own backyard, especially when infection rates are high.
A surge of cases in Cebu showed an altogether homegrown phenomenon. Genomic surveillance in Cebu showed a cluster of cases with two worrisome mutations: N501Y, a marker for increased transmission in the UK variant; and E484K, a marker for decreased vaccine efficacy also found in the South African variant. In addition, the virus in this cluster of cases had other unique mutations. The immediate ancestor of this virus is of the Brazilian lineage B.1.1.28, which gave rise to the Brazil variant of concern P.1. We have had B.1.1.28 in the country before, it is a fairly common lineage worldwide.
We have not detected P.1. What we have is a new lineage called P.3, which is the first internationally recognized variant from the Philippines. So far, P.3 is not causing the same problems that are associated with P.1. It seems to be tapering off, thanks to enhanced public health measures by the Cebu government. So even if we went to the extreme and banned all incoming travelers, the threat of local variants emerging continues as long as community transmission is not controlled.
One theory as to why P.3 has not exploded like P.1 in Brazil is that Filipinos have been doing a good job with our public health standards. The main tools that are working to keep variant cases under control are strict quarantine of returning travelers, and the continued use of face masks, face shields, and physical distancing.
Recent studies show that while mask use is above 90 percent, face shield use is only at 30 percent. A mask only protects up to 85 percent on its own but combined with a face shield offer almost complete protection from COVID-19. With the virus and its variants levelling up, we cannot afford to slack off now. Whether it is the spread of more infectious and vaccine-resistant variants or emergence of our own homegrown viruses, the answer is the same as it has always been. The virus has no brain, no arm or legs, and is not even technically alive. It spreads because people spread it. It is also up to us to keep it contained until everyone has been vaccinated.