Tracking the Evolution of a ‘Variant of Concern’ in Brazil
Posted on by Dr. Francis Collins
By last October, about three out of every four residents of Manaus, Brazil already had been infected with SARS-CoV-2, the virus that causes COVID-19 . And yet, despite hopes of achieving “herd immunity” in this city of 2.2 million in the Amazon region, the virus came roaring back in late 2020 and early 2021 to cause a second wave of illness and death . How is this possible?
The answer offers a lesson in viral evolution, especially when an infectious virus such as SARS-CoV-2 replicates and spreads through a population largely unchecked. In a recent study in the journal Science, researchers tied the city’s resurgence of SARS-CoV-2 to the emergence and rapid spread of a new SARS-CoV-2 “variant of concern” known as P.1 . This variant carries a unique constellation of mutations that allow it not only to sneak past the human immune system and re-infect people, but also to be about twice as transmissible as earlier variants.
To understand how this is possible, consider that each time the coronavirus SARS-CoV-2 makes copies of itself in an infected person, there’s a chance a mistake will be made. Each mistake can produce a new variant that may go on to make more copies of itself. In most cases, those random errors are of little to no consequence. This is evolution in action.
But sometimes a spelling change can occur that benefits the virus. In the special case of patients with suppressed immune systems, the virus can have ample opportunity to accrue an unusually high number of mutations. Variants carrying beneficial mutations can make more copies of themselves than other variants, allowing them to build their numbers and spread to cause more infection.
At this advanced stage of the COVID-19 pandemic, such rapidly spreading new variants remain cause for serious concern. That includes variants such as B.1.351, which originated in South Africa; B.1.1.7 which emerged in the United Kingdom; and now P.1 from Manaus, Brazil.
In the new study, Nuno Faria and Samir Bhatt, Imperial College London, U.K., and Ester Cerdeira Sabino, Universidade de Sao Paulo, Brazil, and their colleagues sequenced SARS-CoV-2 genomes from 184 patient samples collected in Manaus in November and December 2020. The research was conducted under the auspices of the Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE), a project focused on viral genomics and epidemiology for public health.
Those genomic data revealed the P.1 variant had acquired 17 new mutations. Ten were in the spike protein, which is the segment of the virus that binds onto human cells and the target of current COVID-19 vaccines. In fact, the new work reveals that three of these spike protein mutations make it easier for the P.1 spike to bind the human ACE2 receptor, which is SARS-CoV-2’s preferred entry point.
The first P.1 variant case was detected by genomic surveillance on December 6, 2020, after which it spread rapidly. Through further evolutionary analysis, the team estimates that P.1 must have emerged, undetected for a brief time, in mid-November 2020.
To understand better how the P.1 variant led to such an explosion of new COVID-19 cases, the researchers developed a mathematical model that integrated the genomic data with mortality data. The model suggests that P.1 may be 1.7 to 2.4 times more transmissible than earlier variants. They also estimate that a person previously infected with a variant other than P.1 will have only 54 percent to 79 percent protection against a subsequent infection with P.1.
The researchers also observed an increase in mortality following the emergence of the P.1 variant. However, it’s not yet clear if that’s an indication P.1 is inherently more deadly than earlier variants. It’s possible the increased mortality is related primarily to the extra stress on the healthcare system in Manaus from treating so many people with COVID-19.
These findings are yet another reminder of the importance of genomic surveillance and international data sharing for detecting and characterizing emerging SARS-CoV-2 variants quickly. It’s worth noting that at about the same time this variant was detected in Brazil, it also was reported in four individuals who had traveled to Brazil from Japan. The P.1 variant continues to spread rapidly across Brazil. It has also been detected in more than 37 countries , including the United States, where it now accounts for more than 1 percent of new cases .
No doubt you are wondering what this means for vaccines, such as the Pfizer and Moderna mRNA vaccines, that have been used to immunize (at least one dose) over 140 million people in the United States. Here the news is encouraging. Serum from individuals who received the Pfizer vaccine had titers of neutralizing antibodies that were only slightly reduced for P.1 compared to the original SARS-CoV-2 virus . Therefore, the vaccine is predicted to be highly protective. This is another example of a vaccine providing more protection than a natural infection.
The United States has made truly remarkable progress in combating COVID-19, but we must heed this lesson from Manaus: this terrible pandemic isn’t over just yet. While the P.1 variant remains at low levels here for now, the “U.K. variant” B.1.1.7 continues to spread rapidly and now is the most prevalent variant circulating in the U.S., accounting for 44 percent of new cases . Fortunately, the mRNA vaccines also work well against B.1.1.7.
We must continue to do absolutely everything possible, individually and collectively, to prevent these new SARS-CoV-2 variants from slowing or even canceling the progress made over the last year. We need to remain vigilant for just a while longer, while encouraging our friends, neighbors, and loved ones to get vaccinated.
 Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic. Buss, L. F., C. A. Prete, Jr., C. M. M. Abrahim, A. C. Dye, V. H. Nascimento, N. R. Faria and E. C. Sabino et al. (2021). Science 371(6526): 288-292.
 Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. Sabino EC, Buss LF, Carvalho MPS, Prete Jr CCA, Crispim MAE, Fraiji NA, Pereira RHM, Paraga KV, Peixoto PS, Kraemer MUG, Oikawa MJ, Salomon T, Cucunuba ZM, Castro MC, Santos AAAS, Nascimento VH, Pereira HS, Ferguson NM, Pybus OG, Kucharski A, Busch MP, Dye C, Faria NR Lancet. 2021 Feb 6;397(10273):452-455.
 Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Faria NR, Mellan TA, Whittaker C, Claro IM, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC et al. Science. 2021 Apr 14:eabh2644.
 GRINCH Global Report Investigating novel coronavirus haplotypes. PANGO Lineages.
 COVID Data Tracker. Variant Proportions. Centers for Disease Control and Prevention.
 Antibody evasion by the P.1 strain of SARS-CoV-2. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR, et al. Cell. 2021 Mar 30:S0092-8674(21)00428-1.
COVID-19 Research (NIH)
Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE)
Nuno Faria (Imperial College, London, U.K.)
Samir Bhatt (Imperial College)
Ester Cerdeira Sabino (Universidade de Sao Paulo, Brazil)
NIH Support: National Institute of Allergy and Infectious Diseases
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Posted In: News
Tags: ACE2, B.1.1.7, B.1.351, Brazil, CADDE, coronavirus, COVID-19, COVID-19 infections, COVID-19 variants, evolution, genomic epidemiology, genomic surveillance, genomics, herd immunity, Manaus, Moderna, mRNA vaccine, novel coronavirus, P.1, pandemic, Pfizer/BioNTech vaccine, public health, SARS-CoV-2, South Africa, spike protein, U.K. variant, vaccines, variant of concern, viral evolution
What kind of protection does the Janssen vaccine provide against the P.1 variant?
Pat Statwick – please let us know if you find some data, I have tried very hard to get hard data on the US’ vaccines efficacies against variants and could not find much.
I do not mean to disrespect or assume anything about any part of medicine but some serious questions come to my mind:
1. Since apparently, recognition of a serious new threat came about in November, I have to wonder why some vaccines were not sent to Manaus by some time in December – to do a study, admittedly with far fewer participants than normal and under adverse conditions, but to see as best I can if our vaccines worked on that variant before a massive vaccination program which, had we been unlucky, would have not prevented a P1 surge which could have been taking place right now.
2. The data on the Pfizer vaccine is certainly reassuring, but even now, actual field data would be nice. To be honest, that goes over my head, but the politicized disputes about continued use of masks seems to indicate our authorities do not feel certain our vaccines stop all the variants. Dr. Fauci sort of admitted that after being forced to. I respect Dr. Fauci but I think he should be saying this rather definitively, without being pushed. And I know, as the bearer of possible bad news, he will get castigated by ignorant and immature people for it, but the rest of us need to know.
3. I am upset, if the variant was identified so far back, and certainly they knew something bad was going on by late November, that we were not told to avoid travel to Brazil. I understand this may be PARTLY the responsibility of the former President- but considering that he lost the election and Dr. Fauci was a prominent public figure by that point, I believe he should have told people unambiguously, travel to Brazil was too risky.
IF that had been done, perhaps we would have fewer cases of P1 in the US now – maybe it will not matter, but before the encouraging data from Pfizer, this should have been done as a precaution IMO.
If this was remiss, it appears to be an omission other countries are also guilty of, but perhaps no one is being adequately proactive?
I am concerned that we did not send vaccines to Manaus to test if our vaccines – not yet even having EUA but it was certainly contemplated – would be effective against the variant, before we started a massive vaccination campaign which might have had limited effectiveness. It seems like a very big oversight.
In 4 months, I’ll be ready to take the third dose of the Pfizer vaccine. It would be interesting if Dr. Collins could update us on the progress hopefully being made by the drug manufacturing companies on researching and developing a third dose that can stop the 8 most-talked about variants.
All right, that’s an opportunity once in a lifetime . . .
Interesting post, thanks for sharing.