Virus World

Genetic analysis of 50,000-year-old Neanderthal skeletons has uncovered the remnants of three viruses related to modern human pathogens, and the researchers think they could be recreated. Genetic sequences from three common viruses that plague humanity today have been isolated from the remains of Neanderthals who lived more than 50,000 years ago. Marcelo Briones at the Federal University of São Paulo, Brazil, says it may be possible to synthesise these viruses and infect modern human cells with them in the lab...

Preprint of the study in bioRxiv:

https://doi.org/10.1101/2023.03.16.532919 

Illumina has secured an emergency use authorisation (EUA) from the US Food and Drug Administration (FDA) for its sequencing-based Covid-19 diagnostic test. Illumina COVIDSeq test is a high-throughput, sequencing-based and in vitro diagnostic (IVD) workflow test that facilitates the detection of SARS-CoV-2. The sequencing-based diagnostic test, which uses upper respiratory specimens such as nasopharyngeal or oropharyngeal swab, offers sample receipt to result in 24 hours using the NovaSeq 6000 sequencing system. The differentiated diagnostic design is comprised of 98 amplicons, which target the full SARS-CoV-2 genome, enabling to create precise detection and high sensitivity.

Illumina is currently offering COVIDSeq test to a limited number of early access sites, and plans to increase the supply by summer. The workflow holds the capacity to accommodate up to 3,072 samples per NovaSeq run through leveraging the S4 flow cell. It is comprised of steps for viral RNA extraction, RNA-to-CDNA conversion, PCR, library preparation, sequencing and report generation. 

FDA Letter of Approval:

https://www.fda.gov/media/79226/download

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples.

Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Nature  preprint (July 2022):

https://www.nature.com/articles/s41586-022-05049-6_reference.pdf