New rules for genomics-informed COVID-19 responses-Lessons learned from the first waves of the Omicron variant in Australia

Article Multidisciplinary Sciences

AusTrakka: Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic

Tuyet Hoang et al.

Summary: The COVID-19 pandemic has driven the development of Australia's pathogen genomics platform AusTrakka, enabling rapid data sharing and real-time genomic surveillance.

NATURE COMMUNICATIONS (2022)

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Editorial Material Biochemical Research Methods

Unlocking capacities of genomics for the COVID-19 response and future pandemics

Sergey Knyazev et al.

Summary: During the COVID-19 pandemic, genomics and bioinformatics have become crucial tools in public health. They have been used to acquire genomic data that support global health responses, aid in the development of testing methods, and enable the timely tracking of novel SARS-CoV-2 variants. However, the rapid generation and analysis of genomic data present unique technical, scientific, and organizational challenges.

NATURE METHODS (2022)

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Editorial Material Parasitology

Progress and challenges in virus genomic epidemiology

Verity Hill et al.

Summary: Genomic epidemiology, linking pathogen genomes with metadata to understand disease transmission, has become crucial in outbreak response. With decreasing sequencing costs and increased computational power, opportunities to analyze large viral genomic datasets have expanded, though challenges remain in integrating diverse data sources, handling big datasets, and establishing robust sampling frameworks.

TRENDS IN PARASITOLOGY (2021)

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Article Biochemistry & Molecular Biology

Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

Nicole L. Washington et al.

Summary: The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has been spreading in the United States with multiple introductions as early as late November 2020. The variant shows a logistic growth rate with roughly weekly doubling and increased transmission, requiring immediate action to minimize COVID-19 morbidity and mortality.

CELL (2021)

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Editorial Material Biochemistry & Molecular Biology

Tracking the emergence of new SARS-CoV-2 variants in South Africa

Anise N. Happi et al.

Summary: A large genomic surveillance effort in South Africa identified 16 new lineages of SARS-CoV-2 through the analysis of 1,365 high-quality whole genomes, which had not been previously identified in other countries.

NATURE MEDICINE (2021)

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Article Ecology

Infectious disease phylodynamics with occurrence data

Leo A. Featherstone et al.

Summary: The article discusses incorporating un-sequenced case occurrence data alongside sequenced data in Phylodynamic analysis, demonstrating through simulations that this approach can eliminate bias in estimates of the basic reproductive number due to misspecification of the sampling process. Additionally, it emphasizes that occurrence data are a valuable source of information for future Phylodynamic analyses.

METHODS IN ECOLOGY AND EVOLUTION (2021)

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Article Multidisciplinary Sciences

SARS-CoV-2 infection and transmission in the North American deer mouse

Bryan D. Griffin et al.

Summary: The study demonstrates that North American deer mice are susceptible to SARS-CoV-2 infection and can replicate and transmit the virus without showing significant symptoms.

NATURE COMMUNICATIONS (2021)

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Article Public, Environmental & Occupational Health

Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study

Courtney R. Lane et al.

Summary: This study conducted genomic sequencing of COVID-19 cases in Victoria, Australia, identifying the source of the second wave outbreak and showing the effectiveness of genomic epidemiology in eliminating COVID-19 for a second time. The results indicated that a single incursion from hotel quarantine led to a large outbreak, but strict interventions and decisive public health responses were successful in controlling the spread. Real-time genomic surveillance played a crucial role in shaping public health strategies during the outbreak.

LANCET PUBLIC HEALTH (2021)

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Article Virology

Coordinating SARS-CoV-2 genomic surveillance in the United States

Martha Nelson et al.

VIRUS EVOLUTION (2021)

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Article Multidisciplinary Sciences

Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Bas B. Oude Munnink et al.

Summary: Animal experiments have shown that various animals can be infected by SARS-CoV-2, with evidence of animal-to-human transmission within mink farms. Investigation into mink farm outbreaks revealed that the virus was initially introduced by humans and has since evolved, causing transmission between mink farms. Despite enhanced biosecurity measures and culling, transmission occurred between farms in three large clusters with unknown modes of transmission, resulting in a high percentage of infections among mink farm residents and employees.

SCIENCE (2021)

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Article Biochemistry & Molecular Biology