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Manaus COVID-19 crisis could strike across Brazil, doctors warn
The following report contains some hard data and percentages of the current P1 variant outbreak from Brazil. This is not looking good for the S. Americas.
COVID-19 infections surged by 125 percent in Manaus between January 7 and January 22, according to the National Council of Health Secretaries and Brazilian media.
Staviack said doctors have noticed an increase in the number of premature births in Manaus, as pregnant women with COVID-19 had to have caesareans due to their low oxygen levels. The threat of COVID-19 also propelled some pregnant women to take drastic steps, he said.
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Ferreira said doctors working in the area reported that the variant is spreading and this time more young people aged 30 to 50 are falling sick with more severe symptoms. “The virus will spread to other states such as Rondonia and those in the northeast of Brazil – they could suffer from a lack of oxygen as they are so poor,” Ferreira said.
He said the virus is already spreading up the Madeira River that runs through Bolivia.
“We are very, very scared about that,” said Ferreira, adding that Brazilian MP Cassio Espirito Santo recently said people from Peru and Bolivia also were coming to Tabatinga, in western Amazonas state, to be treated.
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Dr Julio Ponce, an epidemiologist who works in Sao Paulo, said last week that while deaths from the disease are under-reported, the latest data showed a seven-day daily average of 54,000 new cases and 983 deaths countrywide.
“Manaus serves as a sentinel for the rest of the country,” said Ponce, explaining that in April last year it was the first city in Brazil to experience a peak that led to the collapse of its healthcare system, followed by Para and other states in the country’s northeast.
“The same pattern will emerge this time, but with far worse outcomes,” said Ponce, who added that the new variant accounts for 42 percent of new cases in Manaus.
“All of the states and hospitals are fighting for a limited supply of oxygen. Other states besides Amazonas could run out if we don’t have a coordinated effort by the federal government. We are running out, state by state.”
But for some scientists, the most worrying variant might be the newest one. A variant called P.1, which emerged in Manaus, Brazil in early December and by mid-January, had already caused a massive resurgence in cases across the city of 2 million people.
Yesterday, officials detected the first confirmed case of P.1 in the U.S., specifically in Minnesota. The department of health picked up the case by randomly sequencing 50 nasal swabs from positive patients each week. The person infected with P.1. had previously traveled to Brazil.
"If you were to ask me right now, what's most concerning of all the things that I've heard so far, it's the fact that they are reporting a sudden increase in cases in Manaus, Brazil," virologist Jeremy Luban, at the University of Massachusetts, told NPR two weeks ago, before the variant arrived in the U.S. "Manaus already had 75% of people infected [in the spring of last year]."
The concern with P.1 is twofold: scientists don't understand why the variant has spread so explosively in Brazil, and the variant carries a particularly dangerous set of mutations.
While the variant from the U.K. took about three months to dominate the outbreak in England, P.1 took only about a month to dominate the outbreak in Manaus. In addition, Manaus had already been hit extremely hard by the virus back in April. One study estimated that the population should have reached herd immunity and the virus shouldn't be able to spread easily in the community. So why would the city see an even bigger surge 10 months later? Could P.1 be evading the antibodies made against the previous version of the virus, making reinfections easier? Could it just be significantly more contagious? Could both be true?
"While we don't *know* exactly why this variant has been so apparently successful in Brazil, none of the explanations on the table are good," epidemiologist Bill Hanage, at Harvard University, wrote on Twitter.
Reinfections are a serious concern for several reasons.
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the mutations are providing the virus with a type of invisibility cloak.
To test out this hypothesis, Moore and her colleagues took blood serum from 44 people infected with the previous version of the virus and checked to see if the antibodies in that serum still worked against the new variant from South Africa. Or did the antibodies lose their sensitivity?
"Indeed that's what we saw," she says. "In fact, it was really quite a dramatic drop-off in sensitivity. We saw that in half of the serum, the antibodies were significantly less effective against the new variant [from South Africa]." So far, scientists haven't tested out P.1 in similar neutralization experiments, but P.1 has two mutations that scientists have already shown reduce antibody binding.
And thus, now we have a game of "cat and mouse," says virologist Ravi Gupta, between the virus and the vaccine. The virus finds ways around the vaccine (and our immune system), says Gupta, and so the manufacturers have to reformulate the vaccines (or else we run the risk of getting infected twice).
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"The coronavirus is going to cause a long-term disruption."
After initially containing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), many European and Asian countries had a resurgence of COVID-19 consistent with a large proportion of the population remaining susceptible to the virus after the first epidemic wave. 1
By contrast, in Manaus, Brazil, a study of blood donors indicated that 76% (95% CI 67–98) of the population had been infected with SARS-CoV-2 by October, 2020. 2
High attack rates of SARS-CoV-2 were also estimated in population-based samples from other locations in the Amazon Basin—eg, Iquitos, Peru 70% (67–73). 3
The estimated SARS-CoV-2 attack rate in Manaus would be above the theoretical herd immunity threshold (67%), given a basic case reproduction number (R0) of 3. 4
In this context, the abrupt increase in the number of COVID-19 hospital admissions in Manaus during January, 2021 (3431 in Jan 1–19, 2021, vs 552 in Dec 1–19, 2020) is unexpected and of concern
...snip
"The only security we have is our ability to adapt."
A coronavirus variant from Manaus in northern Brazil, first detected in Japan in January, is now the dominant form of the virus in the hard-hit city, a local researcher told AFP on Wednesday.
The variant's quick spread confirms fears that it is more contagious than the original form of the virus, said Felipe Naveca, who studies coronavirus mutations in northern Amazonas state.
The variant which was first detected early this month in people arriving in Japan from Brazil "is already dominant in Manaus," he said.
"The only security we have is our ability to adapt."
Colombia reports two infections of Brazilian coronavirus variant
JANUARY 31, 20218:52 PM. UPDATED 26 MINUTES AGO
By Reuters Staff
BOGOTA (Reuters) - Two Colombian citizens in Leticia, capital of the country’s Amazonas province, have been infected with the Brazilian variant of coronavirus, the National Health Institute (INS) said on Sunday.
“The National Health Institute confirmed yesterday afternoon infections in a man and a woman - both with Colombian nationality - with the Brazilian P1 strain,” the INS said in a statement.
The woman, aged 39, is a resident of Leticia. She presented symptoms on Jan. 10 and was diagnosed as positive for coronavirus five days later, the INS said.
The second case was confirmed in an indigenous man, aged 79, who was hospitalized on Jan. 7 with an acute respiratory infection caused by COVID-19, the statement added.
Since December 2020, the Minnesota Department of Health (MDH) Public Health Laboratory has been receiving 100 specimens per week (50 from each of two clinical partners) with low cycle threshold (Ct) values for routine surveillance for SARS-CoV-2, the virus that causes COVID-19. On January 25, 2021, MDH identified the SARS-CoV-2 variant P.1 in one specimen through this surveillance system using whole genome sequencing, representing the first identified case of this variant in the United States. The P.1 variant was first identified in travelers from Brazil during routine airport screening in Tokyo, Japan, in early January 2021 (1). This variant has been associated with increased transmissibility (2), and there are concerns that mutations in the spike protein receptor-binding domain might disrupt both vaccine-induced and natural immunity (3,4). As of February 28, 2021, a total of 10 P.1 cases had been identified in the United States, including the two cases described in this report, followed by one case each in Alaska, Florida, Maryland, and Oklahoma (5).
The first Minnesota P.1 variant case was identified in a person who became symptomatic in early January and was hospitalized for 9 days. During the case investigation, the person reported having traveled to southeastern Brazil within the 14 days before symptom onset. The patient’s travel partner, who lived in the same household, also had symptoms of COVID-19 and received a positive SARS-CoV-2 test result after returning. The diagnostic specimen from this household contact was obtained for whole genome sequencing and confirmed to be the P.1 variant. The sequences from both patients were identical and had 15 of the 17 mutations associated with the P.1 variant, including the 10 S-gene mutations (2). The Minnesota patients were reinterviewed to obtain information on exposures and close contacts.† This activity was reviewed by CDC and conducted consistent with applicable federal law and policy.?
The hospitalized Minnesota patient had interacted with four Minnesota health care facilities. Risk assessments were conducted for 111 health care personnel who provided care, and they were offered testing. No high-risk exposures? were identified among these health care personnel; 22 (20%) submitted specimens for testing, and no positive test results were reported. The CDC Minneapolis Quarantine Station was notified of potential travel-associated COVID-19 exposures on the arriving international flight and a domestic flight to Minnesota. Because 19 days had passed since the flights, CDC did not initiate a full aircraft contact investigation; however, CDC did obtain information for potentially exposed passengers and notified health departments in their states of residence. In addition to health care personnel, 42 persons in Minnesota who might have had close contact with the patients were notified and offered testing; 20 were tested, and all received negative test results.
The two travel-associated cases of the SARS-CoV-2 variant P.1 in Minnesota represent the first identified occurrences of this variant in the United States. Initial identification of the P.1 variant in Brazilian travelers in Japan and its introduction into Minnesota were identified through routine sequencing, demonstrating the importance of genomic surveillance at state and federal levels to identify variants of concern and to track and prevent their spread (6). Genomic surveillance using whole genome sequencing of SARS-CoV-2 specimens is an important public health tool for identifying mutations and monitoring variants of concern (7). Identification of the P.1 variant in the United States underscores the importance of community prevention strategies to slow transmission of SARS-CoV-2, including use of well-fitting masks, physical distancing, washing hands, quarantine, testing of persons who have had contact with a person with laboratory-confirmed COVID-19, isolating persons with symptoms of COVID-19 or with diagnosed COVID-19, and adhering to CDC recommendations to delay travel.** In addition, testing should be considered one component of a comprehensive travel risk management strategy. Properly timed testing, both before and after travel, together with self-monitoring for symptoms, a period of self-quarantine after travel, hand hygiene, and physical distancing, are critical elements of this strategy (8).††
Patients described in this report; Minnesota Public Health Laboratory; Minnesota Molecular Surveillance of SARS-CoV-2 clinical laboratory partners; University of Minnesota Infectious Diseases Diagnostic Laboratory; University of Minnesota Advanced Research and Diagnostic Laboratory; Infinity BiologiX; Carmen Bernu; Jennifer Plum, Special Case Investigator Team.
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