The Principles of SARS-CoV-2 Intervariant Competition Are Exemplified in the Pre-Omicron Era of the Colombian Epidemic

Article Multidisciplinary Sciences

SARS-CoV-2 infection in free-ranging white-tailed deer

Vanessa L. Hale et al.

Summary: Research shows that free-ranging white-tailed deer in northeast Ohio, USA are highly susceptible to SARS-CoV-2 infection, potentially enabling the virus to be transmitted in wildlife, opening up new pathways for evolution.

NATURE (2022)

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Article Multidisciplinary Sciences

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Raquel Viana et al.

NATURE (2022)

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Article Multidisciplinary Sciences

Understanding the dynamics of SARS-CoV-2 variants of concern in Ontario, Canada: a modeling study

Anita T. Layton et al.

Summary: The study aims to analyze the spread of multiple variants of concern (VOC) and assess the effectiveness of vaccination and non-pharmaceutical interventions through an expanded model. The model identifies the significant role of vaccine breakthrough in the Delta variant's spread, and highlights the impact of non-pharmaceutical interventions and vaccine types on the severity of the outbreak.

SCIENTIFIC REPORTS (2022)

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Article Multidisciplinary Sciences

Epidemiological characteristics of the B.1.526 SARS-CoV-2 variant

Wan Yang et al.

Summary: Research on the B.1.526 SARS-CoV-2 variant revealed moderate increases in transmissibility, potential immunity escape, and higher infection fatality risk among older adults. The variant likely spread in the population before detection, partially offsetting previous medical advances and increasing infection severity.

SCIENCE ADVANCES (2022)

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Article Biochemistry & Molecular Biology

Safety, tolerability and viral kinetics during SARS-CoV-2 human challenge in young adults

Ben Killingley et al.

Summary: This study establishes a new SARS-CoV-2 human challenge model and investigates the viral kinetics during primary infection. The findings have implications for public health recommendations and strategies to control the transmission of SARS-CoV-2.

NATURE MEDICINE (2022)

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Article Cell Biology

Characterization of the SARS-CoV-2 B.1.621 (Mu) variant

Peter J. Halfmann et al.

Summary: The SARS-CoV-2 B.1.621 (Mu) variant, categorized as a variant of interest by the World Health Organization in August 2021, showed reduced neutralization antibody titers compared to the early isolate and another variant of concern (B.1.351). However, the immune response to the first infection still provided protection against subsequent infection with the B.1.621 variant.

SCIENCE TRANSLATIONAL MEDICINE (2022)

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Article Multidisciplinary Sciences

Cumulative SARS-CoV-2 mutations and corresponding changes in immunity in an immunocompromised patient indicate viral evolution within the host

Sissy Therese Sonnleitner et al.

Summary: This study reports the occurrence of SARS-CoV-2 immune escape mutations in an immunocompromised patient with prolonged viral shedding. The results suggest that specific mutations may confer a fitness advantage to the virus and could be potential targets for future vaccine and therapeutic development for COVID-19.

NATURE COMMUNICATIONS (2022)

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Article Microbiology

Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness

Ruian Ke et al.

Summary: This longitudinal analysis of 60 individuals during acute infection provides insights into the dynamics of SARS-CoV-2 replication and shedding. The study highlights the high inter-individual variation in infectious virus shedding and suggests the importance of individual-level heterogeneity in superspreading. The results also emphasize the potential of saliva as a superior sampling site for early detection of infection and indicate that the enhanced transmissibility of the Alpha variant cannot be explained solely by viral loads or clearance kinetics.

NATURE MICROBIOLOGY (2022)

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Article Multidisciplinary Sciences

Context-specific emergence and growth of the SARS-CoV-2 Delta variant

John T. McCrone et al.

Summary: The globally spread SARS-CoV-2 Delta variant of concern has caused resurgences of COVID-19 worldwide. In England, the Delta variant was introduced through travel and social restrictions relaxation and spread through increased human activity. Hotel quarantine for travelers helped reduce importation transmission, but the Delta transmission chains were already established before travel restrictions were implemented. Increased inter-regional travel and local population mixing were key factors in the nationwide dissemination of Delta.

NATURE (2022)

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Article Biochemistry & Molecular Biology

Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

Houriiyah Tegally et al.

Summary: The genomic characterization of the SARS-CoV-2 Omicron lineages BA.4 and BA.5, responsible for the fifth wave of the COVID-19 pandemic in South Africa, reveals their continued viral diversification and sheds light on the potential mechanisms that allow these new lineages to outcompete their predecessors. These new lineages, BA.4 and BA.5, share identical spike proteins with BA.2 but have certain differences such as the presence of the 69-70 deletion, L452R, F486V, and the wild-type amino acid at Q493. They can be identified by the S-gene target failure, a proxy marker associated with the 69-70 deletion. BA.4 and BA.5 have rapidly replaced BA.2 and have become the dominant lineages in South Africa.

NATURE MEDICINE (2022)

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Letter Medicine, General & Internal

Duration of Shedding of Culturable Virus in SARS-CoV-2 Omicron (BA.1) Infection

Julie Boucau et al.

Summary: The shedding of the culturable SARS-CoV-2 omicron (BA.1) variant could be detected within a median of 8 days after symptom onset or the initial positive test in outpatients with Covid-19, as revealed by frequent PCR and viral-culture assessments.

NEW ENGLAND JOURNAL OF MEDICINE (2022)

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Article Multidisciplinary Sciences

Modelling the interplay of SARS-CoV-2 variants in the United Kingdom

N. L. Barreiro et al.

Summary: Many COVID-19 vaccines have proven to be highly effective in preventing severe disease and reducing infections. However, the uneven distribution of vaccines favors the emergence of new variants, such as the highly transmissible Delta variant, which particularly affects unvaccinated individuals. It is crucial to develop reliable models to analyze the spread of different variants, taking into account vaccination effects and other measures like social behavior. This study presents a stochastic geographical model that fulfills these requirements, allowing for the study of the emergence and dynamics of COVID-19 variants. The model separates disease-related parameters from social behavior and mobility restrictions. Applied to the UK, computer simulations describe the appearance of periodic waves and provide predictions for future vaccination boosters. The model can be applied to other countries as well.

SCIENTIFIC REPORTS (2022)

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Article Immunology

Forecasted Trends of the New COVID-19 Epidemic Due to the Omicron Variant in Thailand, 2022

Rapeepong Suphanchaimat et al.

Summary: This study aimed to forecast the trends in COVID-19 cases and deaths from the Omicron variant in Thailand using different scenarios. The most pessimistic scenario predicted a peak in cases and deaths, while the most optimistic scenario showed a lower peak in cases. Thailand may face a new wave of the COVID-19 epidemic due to the Omicron variant, but the death toll is expected to be proportionately lower. Vaccination campaigns for booster doses should be expedited to prevent severe illnesses and deaths.

VACCINES (2022)

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Article Cell Biology

Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA

Rebecca Earnest et al.

Summary: The Delta variant of SARS-CoV-2 has shown higher transmissibility and faster emergence compared to the Alpha variant, with variations observed across different regions.

CELL REPORTS MEDICINE (2022)

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Article Immunology

Duration of Infectious Virus Shedding by SARS-CoV-2 Omicron Variant-Infected Vaccinees

Kenichiro Takahashi et al.

Summary: In order to determine the duration of virus shedding, clinical samples were collected from the upper respiratory tracts of individuals infected with the Omicron variant of severe acute respiratory syndrome coronavirus 2 in Japan between November 29 and December 18, 2021. It was found that vaccinees with mild or asymptomatic infection continued to shed infectious virus for 6-9 days after the onset or diagnosis, even after the resolution of symptoms.

EMERGING INFECTIOUS DISEASES (2022)

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Article Multidisciplinary Sciences

Multi-scale modelling reveals that early super-spreader events are a likely contributor to novel variant predominance

Ashish Goyal et al.

Summary: The emergence of new SARS-CoV-2 variants of concern has hindered global efforts to control the COVID-19 pandemic. These variants are characterized by higher transmissibility, worse infection outcomes, and evasion of immunity. They are believed to have originated from animal reservoirs, communities with low surveillance, or individuals with poor immune control. The factors that determine the predominance of these variants are not fully understood. A multi-scale model of SARS-CoV-2 dynamics suggests that stochasticity plays a significant role in determining predominance. Variants with higher infectiousness, early super-spreader events, and the decline of the current dominant variant are more likely to become predominant. Furthermore, most highly infectious variants that infect only a few individuals do not persist in the population. Therefore, reducing super-spreading events can delay or mitigate the emergence of variants of concern.

JOURNAL OF THE ROYAL SOCIETY INTERFACE (2022)

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Article Virology

Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic

Marta Giovanetti et al.

Summary: The COVID-19 epidemic in Brazil was initially driven by the Gamma variant, but was later replaced by the Delta variant. Unlike in other countries, the rapid spread of Delta in Brazil did not lead to a significant increase in cases and deaths, which may be attributed to the combination of early vaccination campaign and natural immunity from prior infection with the Gamma variant. The study highlights the importance of strengthening genomic monitoring on a national level to detect the emergence and spread of other variants of concern.

VIRUS EVOLUTION (2022)

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Article Virology

The early SARS-CoV-2 epidemic in Senegal was driven by the local emergence of B.1.416 and the introduction of B.1.1.420 from Europe

Lester J. Perez et al.

Summary: Molecular surveillance of SARS-CoV-2 in Senegal reveals two waves of infection, with the B.1.416 lineage originating in Senegal and spreading mainly to Europe, and the B.1.1.420 lineage introduced from Italy and gaining fitness in Senegal before spreading globally. These lineages carry selected mutations that may explain their local dominance, emphasizing the importance of monitoring their mutation profiles. Molecular surveillance in Africa will play a vital role in controlling the spread of the pandemic.

VIRUS EVOLUTION (2022)

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Article Mathematics, Applied

Modeling the impact of SARS-CoV-2 variants and vaccines on the spread of COVID-19

A. M. Ramos et al.

Summary: The continuous mutation of SARS-CoV-2 may lead to new variants, and the impact of these variants and vaccines on the spread of COVID-19 is a major concern. Mathematical models can help evaluate different future scenarios, providing valuable insights for decision makers.

COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION (2021)

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Article Multidisciplinary Sciences

Immunological characteristics govern the transition of COVID-19 to endemicity

Jennie S. Lavine et al.

Summary: The study suggests that infection-blocking immunity to SARS-CoV-2 wanes rapidly while disease-reducing immunity is long-lived. The model predicts that once reaching endemic phase, SARS-CoV-2 may become no more virulent than the common cold. However, a different outcome is predicted for an emergent coronavirus causing severe disease in children.

SCIENCE (2021)

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Article Biology

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e

Kathryn E. Kistler et al.

Summary: Seasonal coronaviruses, including OC43 and 229E, are undergoing adaptive evolution in regions of the viral spike protein exposed to human immune response, potentially leading to reinfection. This adaptive change may require continual vaccine updates for effective protection against these viruses.

ELIFE (2021)

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Article Immunology

Persistent SARS-CoV-2 RNA Shedding Without Evidence of Infectiousness: A Cohort Study of Individuals With COVID-19

Daniel Owusu et al.

Summary: The study found that most COVID-19 patients remained positive for SARS-CoV-2 for >= 10 days after symptom onset, but individuals with mild to moderate COVID-19 are unlikely to be infectious >= 10 days after symptom onset. Participants under 18 had shorter shedding resolution times, while those over 50 had longer shedding resolution times compared to those aged 18-49.

JOURNAL OF INFECTIOUS DISEASES (2021)

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Article Biochemistry & Molecular Biology

Relax, Keep Walking - A Practical Guide to Continuous Phylogeographic Inference with BEAST

Simon Dellicour et al.

Summary: Spatially explicit phylogeographic analyses can be conducted using a framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This approach, introduced 10 years ago, has provided new opportunities in the field of phylodynamics for mapping and analyzing the spatial dissemination of rapidly evolving pathogens. The authors provide a detailed guide on setting up, running, and interpreting continuous phylogeographic analyses using specific programs.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

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News Item Multidisciplinary Sciences

HOW TO REDESIGN COVID VACCINES SO THEY PROTECT AGAINST VARIANTS

Ewen Callaway et al.

NATURE (2021)

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Article Multidisciplinary Sciences

Detection of a SARS-CoV-2 variant of concern in South Africa

Houriiyah Tegally et al.

Summary: The article describes a newly emerged lineage of SARS-CoV-2, 501Y.V2, characterized by eight mutations in the spike protein, which may result in increased transmissibility or immune escape. This lineage originated in South Africa and quickly became dominant in Eastern Cape, Western Cape, and KwaZuluNatal provinces within weeks.

NATURE (2021)

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Article Multidisciplinary Sciences

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Eduan Wilkinson et al.

Summary: The progression of the SARS-CoV-2 pandemic in Africa has shown heterogeneous patterns, with many countries experiencing epidemics initiated mainly by imports from Europe. The implementation of early travel restrictions helped reduce this trend. However, ongoing transmission and increasing mobility within Africa have led to the emergence and spread of various concerning variants. This highlights the importance of not neglecting Africa in the global pandemic response to prevent it from becoming a source of new variants.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

Nicholas G. Davies et al.

Summary: A new variant of SARS-CoV-2 has emerged in England, with a higher reproduction number and potential for large resurgences of COVID-19 cases. Without stringent control measures, it is projected that COVID-19 hospitalizations and deaths in England for the first 6 months of 2021 will exceed those in 2020. The variant has spread globally and exhibited similar transmission increases in Denmark, Switzerland, and the United States.

SCIENCE (2021)

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Article Multidisciplinary Sciences

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Nuno R. Faria et al.

Summary: A new variant of concern, P.1, with 17 mutations including three spike protein mutations associated with increased binding to human ACE2 receptors, emerged in Manaus, Brazil between November 2020 and January 2021. Molecular analysis suggests P.1 may be 1.7- to 2.4-fold more transmissible and that previous infection may provide 54 to 79% protection against P.1 infection compared to other lineages. Enhanced global genomic surveillance of such variants is crucial for pandemic response.

SCIENCE (2021)

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Review Microbiology

Mink, SARS-CoV-2, and the Human-Animal Interface

Florence Fenollar et al.

Summary: Mink, small carnivores of the Mustelidae family, have been widely bred for their fur. Outbreaks of SARS-CoV-2 have been reported in mink farms in multiple countries, raising concerns about their potential role in the pandemic and the impact of mutant viruses on various aspects of the disease.

FRONTIERS IN MICROBIOLOGY (2021)

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Article Multidisciplinary Sciences

Untangling introductions and persistence in COVID-19 resurgence in Europe

Philippe Lemey et al.

Summary: In late summer 2020, more than half of the SARS-CoV-2 lineages circulating in many European countries resulted from new introductions, and the success in onward transmission of these newly introduced lineages was negatively associated with the local incidence of COVID-19. The widespread dissemination of variants in summer 2020 highlights the threat of viral spread when restrictions are lifted.

NATURE (2021)

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Article Multidisciplinary Sciences

Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization

Delphine Planas et al.

Summary: The SARS-CoV-2 B.1.617 Delta variant, first identified in India in 2020, has become dominant in some regions and is spreading to many countries. This variant shows resistance to certain monoclonal antibodies and antibodies in convalescent sera, as well as reduced neutralization by some COVID-19 vaccines. Administration of two doses of the vaccine is needed for a neutralizing response against the Delta variant.

NATURE (2021)

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Article Biochemistry & Molecular Biology

COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

Felipe Gomes Naveca et al.

Summary: Analysis of circulating SARS-CoV-2 viruses during the first and second waves of COVID-19 in Amazonas, Brazil, shows successive lineage replacements led to predominance of the variant of concern P.1 and are associated with variable levels of social distancing.

NATURE MEDICINE (2021)

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Editorial Material Medicine, General & Internal

SARS-CoV-2 Variants in Patients with Immunosuppression

Lawrence Corey et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

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Article Multidisciplinary Sciences

Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

Moritz U. G. Kraemer et al.

Summary: Understanding the spatial invasion dynamics of the B.1.1.7 lineage, researchers found a multistage process with early growth rates linked to human mobility and asymmetric lineage export from dominant source locations. Additionally, they explored how the spread of B.1.1.7 was influenced by nonpharmaceutical interventions and spatial variation in previous attack rates. The study emphasizes the importance of considering behavioral and epidemiological contexts in accurately interpreting the growth rates of emerging variants of concern.

SCIENCE (2021)

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Article Virology

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

Aine O'Toole et al.

Summary: The global virus genomics community has responded unprecedentedly to the SARS-CoV-2 pandemic, leading to significant advances in 'real-time' generation and sharing of genomic data. The development of new analytical methods, such as pangolin, has been necessary to handle the rapid growth in virus genome data production. Pangolin has processed nearly two million virus genomes, aiding in SARS-CoV-2 genomic epidemiology and providing researchers with valuable information about the pandemic's transmission lineages.

VIRUS EVOLUTION (2021)

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Article Biochemistry & Molecular Biology

A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages

Simon Dellicour et al.

Summary: Researchers have developed a rapid analytical pipeline to study the spatiotemporal dispersal history and dynamics of SARS-CoV-2 lineages, focusing on the high density of available genetic data in Belgium. This methodology can be quickly applied to other countries or regions to complement epidemiological analyses and assess the impact of intervention measures on the pandemic.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

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Article Biochemistry & Molecular Biology