CDC: Omicron Breakthrough Infections in Fully Vaccinated, Boosted

December 14th, 2021

By Gary Evans, Medical Writer

While the emerging Omicron variant of COVID-19 is “blowing through” previously infected and vaccinated people in South Africa, there are early indications that the highly mutated virus will cause less severe disease. Of the first 43 cases in the United States, one was hospitalized for two days and none died, the Centers for Disease Control and Prevention (CDC) reported.

A troubling finding in the same report suggests, as reported in South Africa, that the new variant will cause breakthrough infections in those fully vaccinated. Among the 43 cases, 34 (79%) occurred in those who had completed a primary series of COVID-19 vaccine. Fourteen of those 34 received an additional booster dose, although five had just recently received it and likely had not gained its immune benefits. Removing those, that means nine (21%) of the first 43 cases in the United States were fully immunized and boosted individuals. In addition, six people infected had a documented previous SARS-CoV-2 infection.

The most commonly reported symptoms were cough, fatigue, and congestion or runny nose, the CDC reported. The breakthrough infections are a concern, and the CDC report included this ominous note: “Even if most infections are mild, a highly transmissible variant could result in enough cases to overwhelm health systems.”

The evidence emerging from South Africa certainly suggests that the “highly transmissible” criteria are being met there, as estimates are that Omicron is spreading roughly twice as fast as the Delta variant.

The Omicron outbreak in the Tshwane District of the Gauteng Province in South Africa is increasing rapidly. With the new variant first identified in the region in mid-November, investigators reported some 42,000 cases in the province as of Dec. 3, 2021. Overall, the average number of daily cases in South Africa has increased from 350 on Nov. 1 to 13,500 on Dec. 8, with Omicron suspected as the main reason. Despite the surge, the perception that this is a milder version of the virus is reinforced by early reports from South Africa, which it should be emphasized represent only the first two weeks of the outbreak.

“The main observation that we have made over the last two weeks is that the majority of patients in the COVID wards have not been oxygen dependent,” the researchers reported. “SARS-CoV-2 has been an incidental finding in patients that were admitted to the hospital for another medical, surgical or obstetric reasons.”

In the United Kingdom, where public health officials project Omicron will overtake Delta as the predominant SARS-CoV-2 variant (> 50%) by the by mid-December 2021, there was also this finding: “[Omicron] continues to grow rapidly in all regions of England. … None of the cases to date is known to have been hospitalized or died.”

While the unfolding level of transmission has heightened concerns, the reports of mild cases have given rise to the speculative hope that SARS-CoV-2 virus has evolved to a less severe form that will supplant the Delta variant globally, causing less serious infections and fewer deaths.

Roger Shapiro, MD, MPH, a professor of immunology and infectious diseases at Harvard University, tempered these expectations, while conceding that the scenario is a familiar evolutionary pattern in viruses. Shapiro has conducted extensive research in Africa as chair of the Botswana–Harvard AIDS Institute Partnership (BHP).

“It is possible for viruses to mutate in a way that either makes them more severe or less severe,” he said at a Dec. 3, 2021 Harvard press conference. “It’s very often the case that viruses adapt to become less severe over time, but it is not always the case. Over this short term, it is really hard to predict what direction will be most beneficial to the virus survival, which is really all the virus is concerned about: surviving and replicating. It is certainly tempting to think that a more transmissible but less severe virus would be advantageous, but there are other ways this can go. We can’t hang too much on that optimism.”

When the outbreak began in South Africa, approximately 30% of people had been fully vaccinated and some 40% had prior clinical COVID-19 infection, he said.

“There is evidence emerging that people who either had prior COVID or have been vaccinated can get this new Omicron variant fairly easily,” Shapiro said. “It is blowing right through prior exposure and reinfecting people. Prior variants have not shown that [ability] as much as this variant, and that is one of the most worrisome features. It really seems to be transmitting despite evidence in people of prior COVID or vaccination.”

This new variant was first detected on Nov. 11, 2021 by Sikhulile Moyo, PhD, MPH, director of the BHP laboratory in Gaborone, Botswana. The level of mutation was so unusual that Moyo immediately reran all lab procedures to see if an error was made, he said at the press conference. It was not.

Noting that Omicron has now spread to dozens of countries — making travel bans by the United States and other nations moot and counterproductive — Moyo said we are a “global village“ and we must mount a “global response” to this new variant.

Indeed, infectious disease clinicians and researchers in South Africa warn that the scarcity of COVID-19 vaccine in Africa and a large population of immune-compromised HIV patients — 8 million of whom are not receiving antiretroviral treatment to fend off full-blown AIDS — sets the stage for continued mutation and global spread of SARS-CoV-2.

It should be emphasized that it has not been definitively determined how the highly mutated Omicron variant arose, but the prevailing theory among many scientists is it arose after prolonged mutation in an immunocompromised patient.

“Immunocompromised people with COVID promote the mutation and amplification of the virus,” says Pei-Yong Shi, PhD, a distinguished professor of molecular biology at the University of Texas Health Science Center in Galveston. “That is the opportunity for the virus to change — it is like some sort of incubator or a petri dish. The virus can grow easily without much pushback from immune protections.”

In that regard, the aforementioned South African researchers described a case in their country in which SARS‑CoV-2 persisted more than six months in patient with uncontrolled, advanced HIV.

It would be of great global benefit if richer nations helped Africa prevent and treat COVID-19 and HIV simultaneously, they emphasized. A top priority in such an endeavor would be to “vaccinate Africa” for COVID-19.

“Over and above the ethical arguments to address vaccine nationalism and reduce deaths globally, the available data strongly indicate that vaccinating people in Africa will help to reduce transmission rates globally, limit the emergence of new variants, and accelerate global control of the pandemic,” they said.

Gary Evans, BA, MA, has written numerous articles on infectious disease threats to both patients and healthcare workers. These include stories on HIV, SARS, SARS-CoV-2, pandemic influenza, MERS, and Ebola. He has been honored for excellence in analytical reporting five times by the National Press Club in Washington, DC.