An In-Depth Look at COVID-19 Variants of Concern

• In today’s Recommendations for Industry, we provide an in-depth look at COVID-19 Variants of Concern and the findings of TAG’s weekly Risk Matrix Analysis. Read more below.
• Yesterday’s White House Press Briefing has highlighted and detailed the U.S. plan “to deliver booster COVID-19 shots for all fully vaccinated US adults who completed their two-dose mRNA vaccination regimen at least 8 months prior” (CIDRAP). CNN breaks down the five big takeaways from the briefing. This program will begin on September 20. However, WHO officials push back against the booster (so soon) highlighting that giving out boosters when so many in other parts of the world are unvaccinated (and have not had vaccines made available to them), can further drive more variants of COVID-19 and prevent the pandemic from ending (Reuters).
• CIDRAP reports on a recent Nature study that found, “Sending follow-up text message reminders about receiving a COVID-19 vaccination improved appointment scheduling and vaccination rates in the University of California Los Angeles (UCLA) Health system.”
• University of Washington scientists, using U.S. data throughout the pandemic, have modeled a statistical framework to characterize “the true prevalence of this disease in the United States and individual states.” This framework found that “as many as 60% of COVID-19 cases went undetected as of March 7, 2021.”
• One in five intensive care units in the U.S. have reached or exceeded capacity (NY Times). CNN further reports that ICU in Alabama have no more spaces and this was the biggest fear.

An In-Depth Look at COVID-19 Variants of Concern

In response to the many requests TAG has received for information on the various variants of COVID-19, TAG has conducted in-depth research. Following is information on those considered Variants of Concern by the CDC U.S. Centers for Disease Control (CDC) and/or the World Health Organization (WHO).

As developed by a US government SARS-CoV-2 Interagency Group (SIG), there are three classes of SARS-CoV-2 variants:

• Variant of Interest (VOI). A variant with specific genetic markers that has been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity.
• Variant of Concern (VOC). A variant for which there is evidence of an increase in transmissibility, more severe disease (e.g., increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.
• Variant of High Consequence (VOHC). A variant of high consequence has clear evidence that prevention measures or medical countermeasures (MCMs) have significantly reduced effectiveness relative to previously circulating variants.

(For more information on each, visit CDC)

The WHO has been tracking at least 24 different SARS-CoV-2 variants:

Alpha             Beta                   Gamma                Delta                Epsilon                Zeta

Eta                  Theta                 Iota                       Kappa              Lambda              Mu

Nu                  Xi                        Omicron               Pi                      Rho              Sigma

Tau                 Upsilon             Phi                         Chi                    Psi                Omega

Of these, the CDC identified four main circulating Variants of Concern, the B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and P.1 (Gamma). Additionally, within the Delta variant – the current circulating variant – there is discussion of “Delta Plus.” The WHO is also tracking four more that it has declared to be Variants of Interest: Eta (B.1.525), Iota (B.1.526), Kappa (B.1.617.1), and Lambda (C.37).

TAG has previously discussed the Alpha and Beta variants at length in our COVID-19 newsletters and Vaccine Outreach Toolkit. Additionally, the Gamma and Delta/Delta Plus variants continue to spread throughout the U.S. and deserve a look. Following is information on Gamma, Delta and Delta Plus, along with the four declared of interest by the WHO.

• First identified in India, the Gamma variant has spread throughout the globe. This variant has two different mutations, E484Q and L452R, which show similarities to other variants we have seen. E484Q shares a similar mutation to the ones identified in the Alpha and Beta variants in which the spike protein may be mutated, but its unique set of multiple spike mutations are associated with greater infectivity and transmissibility. (Source: TAG Toolkit)
• The Delta Variant, which has been discussed at length by the CDC, is currently the predominant strain in the U.S., making up the majority of current infections. It is shown to be twice as contagious as Alpha, Beta, and Gamma. An increasing number of unvaccinated individuals have been infected with Delta, with hospitalizations dominated by the unvaccinated individuals with this variant. Even those who have been vaccinated, while they may not display symptoms, have also been identified as being heavy viral load carriers.
• Delta Plus. There is now a great deal of discussion of the Delta Plus variant, which has been identified in over 10 countries. India was the first country to detect this variant, just like it was the first to find the original Delta variant. This variant of a variant seems to have spawned from the original Delta variant with a few extra mutations. It received the “Plus” designation because it’s not quite different enough from Delta to merit its own Greek alphabet letter. In fact, it’s basically the already-concerning Delta variant, plus one new addition. In one subtype, the slight variation even contains a mutation identified in the Beta variant. However, not much is known at this time about these subtypes, and there is no evidence that Delta Plus is much different than Delta. (Sources: CDC, Yale, Healthline)

Other variants declared of interest by the WHO:

• The Eta Variant shares similar mutations found in the Beta and Gamma variants. First identified in the UK in December 2020, it has traveled to Denmark, Nigeria, and India. At this time, not enough is known as to whether the variant has higher transmissibility or severity. (Sources: The News Minute, Times of India, Wikipedia)
• First identified in New York City in November 2020, the Iota Variant has been detected throughout the U.S. and in 27 countries. A recent study conducted with the New York City Department of Health and Mental Hygiene and Columbia University also identified that the Iota Variant “has considerably higher transmissibility and immune escape potential than previously circulating variants and that it can increase the infection fatality rate by 62% – 82% among older adults.” It is being watched for “reduced susceptibility to the combination of bamlanivimab and etesevimab monoclonal antibody treatment, though it’s not clear what impact that would have as alternative monoclonal antibody treatments are available.” In the second U.S. pandemic wave, there was a rapid increase in the Iota Variant throughout New York City, as it quickly became the dominant strain. There is also increasing concern that some monoclonal antibody treatments may not be as effective against it. The study found that the Iota Variant had increased fatality rates in individuals >75 years old.
• While little has been published on the Kappa Variant, it is seen as a sibling variant of Delta. However, it is not as prevalent or as important right now that we are able to identify.
• We are hearing some increasing information on the Lambda Variant. Based on a current pre-print study, the spike protein (the protein that triggers infectivity) in Lambda is greater than the original, Alpha, or the Gamma variants. In that, it seems that Lambda may have increased infectivity while being able to evade the immune system and whatever antibodies are in the body to seek and destroy them (i.e., it may be more resistant to vaccine-induced antibodies). Due to this and its slight global increase, the WHO has labeled it as a VOI. First identified in Peru, this variant has now been found in over 20 countries including the U.S., Chile, Ecuador, and Argentina. In the U.S., Lambda has been identified in at least California and Georgia. By June 2021, this new variant had been reported in more than 20 countries with most of the available sequences coming from the previously cited South American countries. However, at this time, CDC states that there is no need to worry about the Lambda variant. (Sources: Savannahnow, LA Times, CalMatters)

Risk Matrix

Following are the most recent findings from TAG’s weekly 50-State Risk Matrix Analysis:

Table 1.

Figure 1.

Table 2.

Table 3.

• In Tuesday’s Recommendations for Industry, we discussed why developed countries, including the U.S., need to see Nigeria’s cholera outbreak as a cautionary warning. Read more here.
• Sources: US to recommend COVID vaccine boosters at 8 months – U.S. health experts are expected to recommend COVID-19 vaccine boosters for all Americans, regardless of age, eight months after they received their second dose of the shot, to ensure lasting protection against the coronavirus as the delta variant spreads across the country. Doses would only begin to be administered widely once the Food and Drug Administration formally approves the vaccines. That action is expected for the Pfizer shot in the coming weeks.
• S. Department of Labor issues updated guidance on protecting unvaccinated and other at-risk workers from the coronavirus – OSHA issued updated guidanceto help employers protect workers from the coronavirus. The updated guidance reflects developments in science and data, including CDC’s updated COVID-19 guidance issued July 27. The guidance:
  • Recommends that fully vaccinated workers in areas of substantial or high community transmission wear masks in order to protect unvaccinated workers;
  • Recommends that fully vaccinated workers who have close contacts with people with coronavirus wear masks for up to 14 days unless they have a negative coronavirus test at least 3-5 days after such contact;
  • Clarifies recommendations to protect unvaccinated workers and other at-risk workers in manufacturing, meat and poultry processing, seafood processing and agricultural processing; and
  • Links to the latest guidance on K-12 schools and CDC statements on public transit
• Direct Financial Support, Access to Male-Dominated Jobs, and Investing in Child Care Can Increase Women’s Participation in Post-COVID Workforce, Says New Expert Consultation – The COVID-19 pandemic and resulting economic recession have led to major changes in women’s lives and employment, ranging from lost jobs to reduced working hours and increased caregiving responsibilities at home. Over the course of the pandemic, 2.5 million women left the job market, compared with 1.8 million men. Short-term Strategies to Address the Impact of the COVID-19 Pandemic on Women’s Workforce Participationoutlines key actions for decision-makers to consider including short-term recovery efforts to mitigate harm to women and increase women’s employment:
• US COVID-19 cases back to pre-vaccination levels – For the first time since February, the United States reported more than 900,000 COVID-19 cases last week—with the country representing 20% of global cases—a sign the pandemic surge caused by the Delta (B1617.2) variant has stalled the progress made by an aggressive vaccine rollout that dampened cases this spring and summer. The number of children hospitalized in this country is now also at a new pandemic high, with confirmed and suspected pediatric hospitalizations at 1,902 on Aug 14, according to Department of Health and Human Services data, Reuters reports. Though children currently make up about 2.4% of hospitalizations, that percent is expected to climb as people 12 years and older are increasingly vaccinated, leaving younger children vulnerable to Delta.
• Young kids more likely than older kids to spread COVID-19 to household – a Canadian studypublished today in JAMA Pediatrics suggests that while younger children are less likely than older children to be the index COVID-19 patient in their home, they are more likely to spread it to household members. Children of all ages most often spread SARS-CoV-2 to household members 20 years or younger or 30 to 50 years old. When analyzing data on just older children, however, the authors found that they tend to transmit infection to older adults in those age-groups. Kids were more likely to spread the coronavirus amid COVID-19 testing delays (OR for 1-day delay, 1.24 vs 2.98 for 5 or more days). Larger family size also increased the chances of transmission (OR, 1.63 per person increase).
• WHO: $7.7 billion needed for COVID variant detection, oxygen – The $7.7 billion appeal—needed over the next 4 months—is part of the ACT Accelerator’s 2021 budget and would go toward increased testing and surveillance, oxygen supplies, and personal protective equipment. The funding would also support other tools to battle the pandemic, such as diagnostics and treatments, and include research and development to ensure that they remain effective.
• US wildfires associated with excess COVID-19 – US wildfires were associated with excess COVID-19 cases and deaths from mid-August to mid-October 2020, according to a study published late last week in Science Advances. The researchers looked at 92 counties in California, Oregon, and Washington—the states most affected by 2020 US wildfires—creating a distributed lag model from synthesized county- and daily-level data on fine particulate air pollution, wildfire days, and COVID-19 cases and deaths. After accounting for weather, population size, and physical distancing data, they say that an average daily increase of 10 micrograms of particulates per cubic meters each day for 28 days was tied with an 11.7% increase in COVID-19 cases and an 8.4% increase in deaths. In absolute numbers, the data projected that US wildfires were associated with 19,700 more cases and 750 more deaths from Aug 15 to Oct 15, 2020.

Food Safety & Public Health News:

• OSHA: Safe + Sound is a year-round campaign to encourage every workplace to have a safety and health program. – Safe + Sound Week(August 9-15, 2021) is a nationwide event held each August that recognizes the successes of workplace health and safety programs and offers information and ideas on how to keep America’s workers safe.
• Source of Ivory Coast Ebola case probed – An investigation is under way into the source of an Ebola infection in a traveler from Guinea whose infection was detected in the Ivory Coast’s major urban center of Abidjan, marking the country’s first case since 1994. In an Aug 14 statement, the World Health Organization (WHO) said there is no indication that the Ivory Coast case is linked to an earlier outbreak in Guinea. However, further investigation—including genetic sequencing—is under way to see if the two events are connected.
• The new reality of USDA catfish regulation – Domestic catfish farmers wanted USDA inspection as a strategy against their foreign competitors. But domestic catfish prices and production have not improved with the change. And catfish imports to the United States increased by 65,000 additional tons in 2019 compared to 2015, the year after the Memorandum of Understanding was signed. The FDA no longer inspects, samples, or analyzes catfish or Siluriformes products but exercises regulatory oversight over all other fish and fish products. FSIS has jurisdiction over all wild-caught and farm-raised Siluriformes fish that are harvested and sold for human food in the United States. This includes Siluriformes fish and fish products that are imported into the United States.
• Studies shine light on Irish E. coli infections, parasites in Peru – Researchers have looked at patterns in sporadic Shiga toxin–producing E. coli (STEC) infections in Ireland. The Republic of Ireland often reports the highest annual incidence rates of STEC in the European Union. There is a high proportion of sporadic STEC infections and they are often associated with environmental exposures. The most frequently confirmed serogroups associated with infection were E. coli O26 and E. coli O157. Of the remaining serogroups, STEC O145, O103, and O146 were the only ones associated with more than 50 confirmed infections.