How front-line physicians have experienced two months of omicron in Brazil | AGÊNCIA FAPESP

How front-line physicians have experienced two months of omicron in Brazil Although this variant of SARS-CoV-2 is less aggressive, the explosive growth of case numbers has again driven health services to the verge of collapse. Lack of tests and a “data blackout” at the Health Ministry make an accurate assessment of the situation impossible (photo: Marcelo Camargo/Agência Brasil)

How front-line physicians have experienced two months of omicron in Brazil

February 16, 2022

By Karina Toledo  |  Agência FAPESP – When the omicron variant of SARS-CoV-2 was first identified in South Africa in late 2021, there was talk of its being a “vaccine virus”, a “Christmas present” and a “godsend”. Studies have suggested it may be less aggressive than previous variants, partly because it tends to be less efficient at invading the lungs. 

On the other hand, the speed with which it multiplies in the upper airways seems to make it as transmissible as measles, one of the most contagious pathogens ever described. According to the World Health Organization (WHO), 100 people are infected by omicron worldwide every 3 seconds.

In Brazil, this has been reflected in record numbers of new cases of COVID-19 every day. On January 29 alone, 207,316 confirmed new infections were reported by the Brazilian media consortium that compiles statistics from state departments of health. The seven-day moving average was 183,896, up 165% compared with a fortnight earlier.

According to experts interviewed by Agência FAPESP, the fact that hospitalizations and deaths from COVID-19 are not rising so fast is due more to widespread immunity via vaccination or previous infection than to the intrinsic characteristics of the virus.

“The disease can be severe in the non-vaccinated, many of whom die or sustain major internal damage. The heart of the matter is that this variant has met a great many hosts who had already been exposed to the virus,” said Paulo Saldiva, pathologist and professor at the University of São Paulo’s Medical School (FM-USP).

“Omicron is very similar to previous variants,” said Elnara Negri, a pulmonologist at São Paulo’s Syrian-Lebanese Hospital. “Brazil is fortunate to have good vaccine coverage. The only patient I’ve had to intubate so far during this wave wasn’t vaccinated. He developed SARS-CoV-2 pneumonia with classic microcirculation thrombosis. The disease hasn’t been severe in the vast majority of patients I’ve seen, and in my view, this is thanks to vaccination.”

Partnering with Saldiva and other colleagues in FM-USP’s Pathology Department, Negri was one of the first people in the world to raise the hypothesis that blood clotting disorders could be responsible for some of the most severe symptoms of COVID-19, such as respiratory failure and pulmonary fibrosis (more at: and Now she stressed that omicron can cause coagulopathy even in vaccinated patients, especially if they are elderly and have comorbidities.

“If around the sixth day of symptoms, instead of getting better, the patient starts having fever, backache, and worsening fatigue or malaise, it’s time to go to the doctor and run blood tests to check for coagulopathy,” she warned. 

According to Esper Kallás, an infectious disease consultant at FM-USP, hospitalization of COVID-19 patients has soared in areas with lower levels of vaccine coverage. An example is Brasilia and the rest of the Federal District (DF), where occupancy of intensive care beds has again reached 100%. Data from the DF’s Health Department show that 90% of patients hospitalized there for COVID-19 are unvaccinated or under-vaccinated. Intensive care occupancy is above 80% in six states (Espírito Santo, Goiás, Mato Grosso do Sul, Pernambuco, Piauí, and Rio Grande do Norte), and the situation is critical in pediatric ICUs in at least three (Mato Grosso do Sul, Maranhão, and Rio Grande do Norte).

Deaths are also trending up. The number reported nationwide on January 29 was 695, taking the total since the start of the pandemic to 626,643. The seven-day average was up 243% compared with the previous fortnight. 

Flying blind

According to the experts we interviewed for this story, a shortage of diagnostic tests and a “data blackout” at the Health Ministry allegedly due to a hacker attack on December 10 make it hard to estimate the extent of the wave caused by omicron in Brazil.

“We’re at a loss as far as the death rate is concerned, for example. That’s a crucial metric. It can persuade people to get vaccinated,” Saldiva said.

The problem is also a reflection of underinvestment in epidemiological surveillance by state governments. “At the height of the pandemic, the human resources gap was filled here in the state of São Paulo by the academic community working on a voluntary basis, but the teams have now stood down,” he said.

In the third week of January, the Brazilian effective reproduction number calculated by Imperial College London in the UK was 1.78, the highest since July 2020. This is Reff, a measure of how many people will catch the disease from a single infected person on average. ICL stopped calculating Reff for Brazil in December because of the Health Ministry’s “data blackout”.

What has changed

Loss of smell and taste was considered one of the main signs that a person had contracted the virus in 2020, during the first wave of the pandemic. This symptom is no longer observed, according to Negri, whereas sore throat is much more frequently reported. “Fever and cough are still common. Some patients have diarrhea,” she said.

For Ana Escobar, Professor of Preventive and Social Pediatrics at FM-USP, a similar trend can be seen among children, most of whom have not yet been vaccinated. “The first symptom is usually a sore throat, followed by fever, which can reach 39 °C and last two or three days, as well as headache and muscle aches. Children typically get well on or around the fourth day. They may continue coughing until day ten,” she said.

Whereas in children the symptoms of omicron differ very little from those of previous variants, case numbers have risen significantly. “Hospitalization has increased as well, especially among children with pre-existing illnesses such as cancer, chronic lung disease or rheumatic disease,” she added.

Like previous variants, omicron can cause pediatric multisystem inflammatory syndrome (PMIS), a condition characterized by persistent fever and inflammation of several organs, including the heart, intestines and lungs, noted Werther Brunow de Carvalho, coordinator of pediatric and neonatal ICUs at the Children’s Institute of Hospital das Clínicas, the hospital complex run by FM-USP.

“The percentage of children who develop the syndrome is smaller with omicron, but it can happen, so there’s no questioning the need to vaccinate children,” he said. 

At another hospital in São Paulo where he also works (Hospital Santa Catarina), the number of children seeking treatment for respiratory infections doubled in January compared with the previous month. “As well as SARS-CoV-2, there are cases of flu, rhinovirus, parainfluenza, and respiratory syncytial virus,” he said.

Pregnant women and women with newborns continue to be at high risk for the severe forms of COVID-19, according to obstetrician Rossana Pulcineli, a professor at FM-USP and a member of the Brazilian Obstetric Observatory (OOBr). Unvaccinated pregnant women were 526% more likely to die of the disease than fully immunized pregnant women before the advent of omicron, according to data published by the group in 2021.

“The death rate among unvaccinated pregnant women hospitalized for COVID-19 was 15%. Among those who had been vaccinated with one dose and two doses, it was 9% and 3% respectively,” she said.

Although cases of the disease caused by omicron tend to be milder among pregnant women, especially if they are vaccinated, hospitalizations for treatment of influenza syndrome have increased sharply, rising from 147 in November to 1,643 in January, according to the Health Ministry’s flu surveillance system (SIVEP-Gripe). A large proportion of those hospitalized (45.3%) had a confirmed diagnosis of COVID-19, while 4.8% had influenza A subtype H3N2. No cause was reported for 51.6%, reflecting the shortage of diagnostic tests.

“It’s well-known that pregnant women respond badly to flu, and there was no monitoring at all when the cases began to rise. We were bereft of updated statistics for weeks in this critical period,” said Pulcineli, who also stressed the importance of two doses plus a booster for pregnant women.

Regarding treatments with proven effectiveness, Kallás noted that the antiviral medication remdesivir and monoclonal antibodies have been approved by the regulator in Brazil. “However, they’re expensive and the government has done nothing to make them accessible to more people,” he said.




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