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Article
Multidisciplinary Sciences
Delphine Planas et al.
Summary: The Omicron variant of SARS-CoV-2, identified in November 2021, has spread rapidly worldwide and shows resistance to most therapeutic monoclonal antibodies and vaccine-elicited antibodies. However, it can be neutralized by antibodies generated by a booster vaccine dose.
Article
Multidisciplinary Sciences
Baisheng Li et al.
Summary: This article reports the first local transmission of the Delta variant in mainland China. Compared to A/B lineage infections during the first wave in China in early 2020, Delta infections had viral loads that were on average about 1000 times greater when they first tested positive, suggesting potentially faster viral replication and greater infectiousness during early infection. The transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in most donor-recipient transmission pairs. However, transmission of minor intra-host variants resulted in at least 3 of the 34 substitutions identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Lennard Y. W. Lee et al.
Summary: The study found that the infectivity of SARS-CoV-2 varies with case viral load, contact event type, and age. Those with high viral loads are the most infectious. The B.1.1.7 variant increases transmission by 50%. The best performing LFDs can detect most infectious cases.
CLINICAL INFECTIOUS DISEASES
(2022)
Letter
Infectious Diseases
Gina Cosentino et al.
JOURNAL OF INFECTION
(2022)
Letter
Medicine, General & Internal
Silje B. Jorgensen et al.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2022)
Article
Microbiology
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)
Article
Health Care Sciences & Services
Hester Allen et al.
Summary: This study indirectly assessed the differences in transmissibility between the SARS-CoV-2 Delta variant and the previously dominant Alpha variant. The results showed that the Delta variant had a higher rate of household transmission, potentially explaining its success in displacing the Alpha variant as the dominant strain in England. Understanding the transmissibility of this variant is important for informing international infection prevention and control policies.
LANCET REGIONAL HEALTH-EUROPE
(2022)
Article
Multidisciplinary Sciences
Jessica A. Plante et al.
Summary: The D614G substitution in the SARS-CoV-2 spike protein enhances viral replication and infectivity in human lung epithelial cells, primary airway tissues, and hamsters. This variant may increase transmission in the upper respiratory tract and doesn't seem to significantly reduce vaccine efficacy. Further research on therapeutic antibodies targeting the circulating G614 virus is recommended.
Article
Public, Environmental & Occupational Health
Koen B. Pouwels et al.
Summary: This study in England found significant changes in the number of individuals testing positive for SARS-CoV-2 and risk factors for positivity over time from April to November 2020. Important risk factors for testing positive varied between the first and second waves, with age being a key driver of increased positivity rates in the second wave. Continued monitoring for SARS-CoV-2 in the community will be important for managing the COVID-19 pandemic moving forwards.
LANCET PUBLIC HEALTH
(2021)
Article
Biochemistry & Molecular Biology
Koen B. Pouwels et al.
Summary: A large, community-based study in the United Kingdom indicates that the effectiveness of BNT162b2 and ChAdOx1 vaccines against SARS-CoV-2 infections with symptoms or high viral burden is reduced with the Delta variant compared to the Alpha variant. Although the effectiveness of two doses is at least as great as protection afforded by prior natural infection, there are significant differences in the dynamics of immunity after the second dose between BNT162b2 and ChAdOx1.
Article
Infectious Diseases
Paolo Calistri et al.
Summary: A targeted surveillance in the Abruzzo region of Italy detected 313 persons affected by lineage B.1.1.7, with statistically significant differences in viral load and persistence compared to other lineages. In individuals infected with B.1.1.7 lineage, lower values of C-T associated with the detection of the N protein encoding gene and longer persistence of SARS-CoV-2 RNA in nasopharyngeal swabs were observed.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Letter
Medicine, General & Internal
Stephen M. Kissler et al.
NEW ENGLAND JOURNAL OF MEDICINE
(2021)
Article
Immunology
Michael Kidd et al.
Summary: Analysis of recent test data shows that samples containing the SARS-CoV-2 variant B1.1.7 with mutation Delta 69/70 exhibit S gene target failure (SGTF) in ThermoFisher TaqPath RT-qPCR. Samples with SGTF profile are more likely to have higher viral loads, indicating higher infectivity and rapid spread of this variant.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
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.
Article
Multidisciplinary Sciences
Katrina A. Lythgoe et al.
Summary: The study found that SARS-CoV-2 infections in clinical samples in the UK are characterized by low levels of within-host diversity and a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with shared diversity not persisting.
Article
Genetics & Heredity
Dave J. Baker et al.
Summary: CoronaHiT is a flexible sequencing method for SARS-CoV-2 genomes, suitable for rapid expansion of global sequencing efforts. In experiments, CoronaHiT demonstrated good performance on both nanopore and Illumina platforms.
Article
Multidisciplinary Sciences
Frederik Plesner Lyngse et al.
Summary: The B.1.1.7 lineage (Alpha variant) became dominant in early 2021 with a higher transmissibility, infecting more households. The increased transmissibility of B.1.1.7 compared to other lineages is 1.5-1.7 times higher, with a multiplicative effect across age and viral load.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Aurelien Marc et al.
Summary: The relationship between SARS-CoV-2 viral load and infectiousness has been studied. Results show that a viral load greater than 10(10) copies per mL can lead to a transmission probability as high as 48%, with peak transmission probability at symptom onset and large individual variations. The model also predicts that variants of concern, which increase viral load, could lead to a relative increase in transmission probability in contacts.
Article
Infectious Diseases
Dan Frampton et al.
Summary: This study describes the emergence of the B.1.1.7 variant of concern, its virological characteristics, and clinical severity in patients. Increased viral load was found in B.1.1.7 infection, but no association with severe disease was identified in the hospitalized cohort.
LANCET INFECTIOUS DISEASES
(2021)
Review
Medicine, General & Internal
Qiuyue Ma et al.
Summary: This study evaluated the percentage of asymptomatic COVID-19 infections among individuals undergoing testing and those with confirmed COVID-19. The results showed the presence of asymptomatic infections in both populations.
Article
Multidisciplinary Sciences
Erik Volz et al.
Summary: Genetic and testing data from England indicate that the SARS-CoV-2 variant B.1.1.7 has a transmission advantage over other lineages, showing a rapid expansion during autumn 2020. Analysis of S gene target failures (SGTF) in community-based diagnostic PCR testing suggests that B.1.1.7 is more transmissible than non-variant of concern lineages and has a significant transmission advantage, with a reproduction number 50% to 100% higher. Additionally, cases of B.1.1.7 appear to include a larger share of under 20-year-olds compared to non-variant cases.
Review
Microbiology
Nancy H. L. Leung
Summary: Respiratory virus infections cause a significant global health problem, with different viruses varying in transmission modes and transmissibility. Understanding the relative contributions of different transmission modes is crucial for guiding the effectiveness of non-pharmaceutical interventions.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
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.
Article
Biology
A Sarah Walker et al.
Article
Virology
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.
Letter
Rehabilitation
Min Cheol Chang et al.
AMERICAN JOURNAL OF PHYSICAL MEDICINE & REHABILITATION
(2020)
Article
Microbiology
David Bonsall et al.
JOURNAL OF CLINICAL MICROBIOLOGY
(2020)
Article
Virology
Chris Wymant et al.
