COVID-19 Update: Variants, Vaccines, and Winter Illnesses 


By COL (Ret.) Zygmunt F. Dembek

Epidemiologist and biochemist COL (Ret.) Zygmunt F. Dembek gives an update on the global COVID-19 situation, emerging variants, persisting vaccine hesitancy, and the specter of seasonal illnesses threatening to exacerbate pressures on health services.

Since the COVID-19 pandemic began in 2020, we have learned a great deal about the inherent ability of the virus that causes COVID-19, SARS-CoV-2, to rapidly change genetically and to accumulate genetic changes over time. It is anticipated that new variants of the SARS-CoV-2 virus will continue to emerge. While some newly emerged SARS-CoV-2 variants will disappear from circulation, others will develop. Some of these new variants will continue to spread due to their intrinsic characteristics that enhance virus transmission. This process replaces circulating SARS-CoV-2 variants with newly emerged ones. 

The Role of Genomic Surveillance 

Genomic surveillance is an important tool used by global public health authorities to identify and track the progress of SARS-CoV-2 variants in a population. Genomic surveillance accuracy and applicability are affected by many factors, including the viral sampling method used, SARS-CoV-2 case identification, appropriate diagnostic test use, viral load, and the length of time from case identification to genome sequencing. 

It is important to recognize that the volume of sampling, analysis and surveillance has decreased from the early stages to the present endemic phase of the COVID-19 pandemic. Decreased SARS-CoV-2 viral surveillance may lead to less accurate viral prevalence predictions, and while COVID-19 home test kits indicate the presence of SARS-CoV-19 virus in an infected individual, they fail to identify a specific SARS-CoV-2 variant. Additionally, home test kit results may not be required to be reported to public health authorities, thereby creating a gap in COVID-19 surveillance.

Genomic surveillance is an important tool in tracking SARS-CoV-2 variants © U.S. CDC

Recent SARS-CoV-2 Variants in the U.S. and UK 

The World Health Organization (WHO) has identified SARS-CoV-2 variant EG.5, an Omicron descendent, as a ‘variant of interest’. Other current circulating variants of interest include XBB.1.16 and XBB.1.5. As of the end of September 2023, the new EG.5 variant now accounts for 29.4% of all COVID-19 cases in the U.S., followed by FL.1.5.1 (13.7%), HV.1 (12.9%), and XBB.1.16.6 (10.1%), along with a couple dozen more variants, all comprising less than 10% of SARS-CoV-2 cases in the U.S. There were about 3,000 COVID-19 total hospital admissions reported daily in the U.S. as of the end of September 2023, and this number is anticipated to remain constant in the coming weeks. 

Like other Omicron strains, the SARS-CoV-2 EG.5 variant infects the upper respiratory tract where it causes cold-like symptoms, including pharyngitis (sore throat) and rhinitis (runny nose). It is especially important for those aged 65 years of age and older, as well as those with a weakened immune system, to have a current vaccination booster shot as these individuals are at higher risk of severe illness from the SARS-CoV-2 virus, and a potentially lethal infection in the lower respiratory tract. 

Presently, the UK Health Security Agency has expressed concerns about the spread of SARS-CoV-2 variant BA.2.86, also called the ‘Pirola’ strain, that is being monitored globally by the WHO. Sporadic cases continue to occur in the UK without having a travel history. This indicates the presence of endemic spread of this SARS-CoV-2 variant in the UK. It is possible that the incidence of this SARS-CoV-2 variant may increase, as it appears to have a slightly greater level of escape from population immunity. However, due to the low number of cases in the UK at the time of writing, it is too early to determine this.  

As of 18 September 2023, there were 48 cases reported in England with 210 hospitalizations and no deaths, with six cases reported in Scotland, and none reported in Wales or Northern Ireland. The BA.2.86 variant has also been reported in other nations globally, including Denmark, Germany, Israel, Japan, South Africa, South Korea, the U.S., and possibly China.

© U.S. CBC

Persisting Vaccine Hesitancy

Existing COVID-19 tests and medications used to treat COVID-19 appear to be effective in detecting COVID-19 infections with the BA.2.86 variant. Of concern is that the U.S. Centers for Disease Control and Prevention (CDC) initially stated that BA.2.86 may be more capable of causing infection in people who have previously had COVID-19 or who have received COVID-19 vaccines. They have since modified that observation to now state that new data suggests that circulating antibodies from previous COVID-19 vaccines and COVID-19 infection do provide protection against the BA.2.86 variant. Updated COVID-19 vaccines are also expected to provide similar protection as for other circulating variants.

There have been controversies surrounding COVID-19 vaccines, and a recent U.S. survey indicated that 25% of adults would definitely receive their COVID-19 vaccine, while 33% definitely would not, and another 19% state that they probably would not get vaccinated. This suggests that just under half of US adults could be persuaded to get the new COVID-19 vaccine. This could present a problem should a severe outbreak of COVID-19 occur in the U.S., with over half the population at risk due to not being recently immunized.

Notably, a recent U.S. study of vaccinated and unvaccinated incarcerated individuals found that while the bivalent COVID-19 vaccine offers protection against severe outcomes, it does not significantly reduce the risk of infections entirely. It must also be noted that vaccination continues to be the best available protection against the most severe outcomes of COVID-19, including hospitalization and death, as well as reducing the chance of having “Long COVID”, or long-lasting effects from COVID-19 infection. The vaccine is recommended to all eligible to receive it, and especially those at greatest risk of severe illness, especially all adults over 65 years of age.

COVID-19 vaccination is recommended to all eligible to receive it © U.S. CDC

RSV and Influenza 

Importantly, public health authorities are concerned not only about COVID-19 circulating this coming winter season, but also about circulating respiratory syncytial virus (RSV) coupled with the annual circulating strain of influenza virus. RSV can be fatal for those at risk, including infants and older adults. The good news is that there are effective vaccines available for all three diseases, with a new COVID-19 booster shot available for this year. Those at risk of illness should avail themselves of all three of these vaccines. 

In the UK, RSV accounts for 29,000 hospitalizations and 83 deaths annually in children, mostly in infants. In the U.S., there are 58,000-80,000 hospitalizations from RSV in children under 5 years of age, and 60,000-160,000 hospitalizations in those 65 years of age and older. There are between 100-300 deaths from RSV annually in those under 5 years of age, and 6,000-10,000 deaths in those over 65 years of age. 

In the UK, annual RSV epidemics usually begin in October and last for 4-5 months, with a peak in December. In the U.S., RSV activity usually starts in the fall and peaks in the winter. That U.S. pattern was disrupted last year by COVID-19 prevention measures, and RSV activity began in the summer, peaked in October and November, and declined in the winter. 

While RSV causes mild illness in most individuals, the very young and the elderly are at highest risk of severe illness, especially infants under 6 months of age. RSV causes cold-like symptoms, including runny nose, sneezing, nasal congestion, and sometimes fever. Ear infection and croup (an upper airway infection that causes a severe barking cough) can occur in children. No specific treatment exists for RSV, other than supportive care and symptom relief. The antiviral medication Ribavirin may be used for cases of severe illness. 

Influenza illness levels and spread of the virus currently remain low in both the UK and U.S. According to the U.S. CDC, quadrivalent influenza vaccines to be used for the 2023-2024 flu season contain HA (hemagglutinin) derived from an influenza A H1N1-like virus, an influenza A H3N2-like virus, and 2 influenza B-like viruses. The UK has similar quadrivalent influenza vaccines available, with varying formulations and vaccine manufacturers for use in different age groups.

To sum up, while there is a ‘triple threat’ of newly emerged SARS-CoV-2 variants along with circulating RSV and influenza viruses coming during the winter months, the good news is that there are protective vaccines available for all, and that immune protection is better achieved through vaccination than surviving the viral illness.

COL (Ret) Zygmunt F. Dembek is an epidemiologist and biochemist. He has written extensively on biodefence and has conducted pandemic preparedness exercises worldwide. 

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