Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant

Abstract Background The SARS-CoV-2 variant of concern (VOC) P.1 (Gamma variant) emerged in the Amazonas State, Brazil, in November 2020. The epidemiological consequences of its mutations have not been widely studied, despite detection of P.1 in 36 countries, with local transmission in at least 5 countries. A range of mutations are seen in P.1, ten of them in the spike protein. It shares mutations with VOCs previously detected in the United Kingdom (B.1.1.7, Alpha variant) and South Africa (B.1.351, Beta variant). Methods We estimated the transmissibility and reinfection of P.1 using a model-based approach, fitting data from the national health surveillance of hospitalized individuals and frequency of the P.1 variant in Manaus from December-2020 to February-2021. Results Here we estimate that the new variant is about 2.6 times more transmissible (95% Confidence Interval: 2.4–2.8) than previous circulating variant(s). Manaus already had a high prevalence of individuals previously affected by the SARS-CoV-2 virus and our fitted model attributed 28% of Manaus cases in the period to reinfections by P.1, confirming the importance of reinfection by this variant. This value is in line with estimates from blood donors samples in Manaus city. Conclusions Our estimates rank P.1 as one of the most transmissible among the SARS-CoV-2 VOCs currently identified, and potentially as transmissible as the posteriorly detected VOC B.1.617.2 (Delta variant), posing a serious threat and requiring measures to control its global spread.

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Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant

10.1101/2021.03.03.21252706 ◽

2021 ◽

Cited By ~ 8

Author(s):

Renato Mendes Coutinho ◽

Flavia Maria Darcie Marquitti ◽

Leonardo Souto Ferreira ◽

Marcelo Eduardo Borges ◽

Rafael Lopes Paixão da Silva ◽

...

Keyword(s):

Population Level ◽

Health Surveillance ◽

Spike Protein ◽

Model Based ◽

New Variant ◽

High Prevalence ◽

Global Spread ◽

Amazonas State ◽

The City ◽

Local Transmission

The variant of concern (VOC) P.1 emerged in the Amazonas state (Brazil) in November-2020. It contains a constellation of mutations, ten of them in the spike protein. Consequences of these specific mutations at the population level have been little studied so far, despite the detection of P.1 variant in 26 countries, with local transmission in at least four other countries in the Americas and Europe. Here, we estimate P.1’s transmissibility and reinfection using a model-based approach, by fitting data from the Brazilian national health surveillance of hospitalized individuals and frequency of the P.1 variant in Manaus from December 2020 to February 2021, when the city was devastated by four times more cases than in the previous peak (April 2020). The new variant was found to be about 2.6 times more transmissible (95% Confidence Interval (CI): 2.4–2.8) than previous circulating variant(s). The city already had a high prevalence of individuals previously affected by the SARS-CoV-2 virus (estimated as 78%, CI:73–83%), and the fitted model attributed 28% of the cases during the period to reinfections by the variant P.1. Our estimates rank P.1 as the most transmissible among the current identified SARS-CoV-2 VOCs, posing a serious threat and requiring urgent measures to control its global spread.

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Isolation and characterization of the new SARS-CoV-2 variant in travellers from the United Kingdom to India: VUI-202012/01 of the B.1.1.7 lineage

Journal of Travel Medicine ◽

10.1093/jtm/taab009 ◽

2021 ◽

Vol 28 (2) ◽

Cited By ~ 1

Author(s):

Pragya D Yadav ◽

Dimpal A Nyayanit ◽

Rima R Sahay ◽

Prasad Sarkale ◽

Jayshri Pethani ◽

...

Keyword(s):

United Kingdom ◽

Severe Acute Respiratory Syndrome ◽

Surveillance System ◽

The United Kingdom ◽

Isolation And Characterization ◽

New Variant ◽

The Uk ◽

Local Transmission

We have isolated the new severe acute respiratory syndrome coronavirus-2 variant of concern 202 012/01 from the positive coronavirus disease 2019 cases that travelled from the UK to India in the month of December 2020. This emphasizes the need for the strengthened surveillance system to limit the local transmission of this new variant.

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Screening blood donors for hereditary hemochromatosis: Decision analysis model based on a 30-year database

Gastroenterology ◽

10.1016/0016-5085(95)90283-x ◽

1995 ◽

Vol 109 (1) ◽

pp. 177-188 ◽

Cited By ~ 86

Author(s):

Paul C. Adams ◽

James C. Gregor ◽

Ann E. Kertesz ◽

Leslie S. Valberg

Keyword(s):

Decision Analysis ◽

Blood Donors ◽

Hereditary Hemochromatosis ◽

Decision Analysis Model ◽

Analysis Model ◽

Model Based

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Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant

10.1101/2021.01.24.427991 ◽

2021 ◽

Cited By ~ 2

Author(s):

Ann-Kathrin Reuschl ◽

Lucy G. Thorne ◽

Lorena Zuliani-Alvarez ◽

Mehdi Bouhaddou ◽

Kirsten Obernier ◽

...

Keyword(s):

Elongation Factor ◽

Therapy Resistance ◽

P38 Map Kinase ◽

Therapeutic Interventions ◽

Health Concern ◽

The United Kingdom ◽

Map Kinase Cascade ◽

New Variant ◽

Order Of Magnitude ◽

Kinase Cascade

AbstractCoronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths worldwide and massive societal and economic burden. Recently, a new variant of SARS-CoV-2, known as B.1.1.7, was first detected in the United Kingdom and is spreading in several other countries, heightening public health concern and raising questions as to the resulting effectiveness of vaccines and therapeutic interventions. We and others previously identified host-directed therapies with antiviral efficacy against SARS-CoV-2 infection. Less prone to the development of therapy resistance, host-directed drugs represent promising therapeutic options to combat emerging viral variants as host genes possess a lower propensity to mutate compared to viral genes. Here, in the first study of the full-length B.1.1.7 variant virus, we find two host-directed drugs, plitidepsin (aplidin; inhibits translation elongation factor eEF1A) and ralimetinib (inhibits p38 MAP kinase cascade), as well as remdesivir, to possess similar antiviral activity against both the early-lineage SARS-CoV-2 and the B.1.1.7 variant, evaluated in both human gastrointestinal and lung epithelial cell lines. We find that plitidepsin is over an order of magnitude more potent than remdesivir against both viruses. These results highlight the importance of continued development of host-directed therapeutics to combat current and future coronavirus variant outbreaks.

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Effect of Delta variant on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK

Nature Medicine ◽

10.1038/s41591-021-01548-7 ◽

2021 ◽

Author(s):

Koen B. Pouwels ◽

Emma Pritchard ◽

Philippa C. Matthews ◽

Nicole Stoesser ◽

David W. Eyre ◽

...

Keyword(s):

Natural Infection ◽

Absolute Difference ◽

Community Based ◽

Symptomatic Infection ◽

The United Kingdom ◽

Viral Burden ◽

Alpha Variant ◽

The Uk ◽

Prior Infection ◽

Similar Peak

AbstractThe effectiveness of the BNT162b2 and ChAdOx1 vaccines against new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections requires continuous re-evaluation, given the increasingly dominant B.1.617.2 (Delta) variant. In this study, we investigated the effectiveness of these vaccines in a large, community-based survey of randomly selected households across the United Kingdom. We found that the effectiveness of BNT162b2 and ChAdOx1 against infections (new polymerase chain reaction (PCR)-positive cases) with symptoms or high viral burden is reduced with the B.1.617.2 variant (absolute difference of 10–13% for BNT162b2 and 16% for ChAdOx1) compared to the B.1.1.7 (Alpha) variant. The effectiveness of two doses remains at least as great as protection afforded by prior natural infection. The dynamics of immunity after second doses differed significantly between BNT162b2 and ChAdOx1, with greater initial effectiveness against new PCR-positive cases but faster declines in protection against high viral burden and symptomatic infection with BNT162b2. There was no evidence that effectiveness varied by dosing interval, but protection was higher in vaccinated individuals after a prior infection and in younger adults. With B.1.617.2, infections occurring after two vaccinations had similar peak viral burden as those in unvaccinated individuals. SARS-CoV-2 vaccination still reduces new infections, but effectiveness and attenuation of peak viral burden are reduced with B.1.617.2.

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