From genomic epidemiology to host reaction

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From the early stages of SARS-CoV-2 emergence, researchers have used real-time nanopore sequencing to generate and generate important genetic data to understand the virus and signal public health responses to COVID-19. I’ve shared it. In London Calling 2021 online, scientists from around the world shared their findings and experiences.^*

Nick Loman explains how he and his team at the University of Birmingham in the United Kingdom used nanopore sequencing to quickly track the SARS-CoV-2 epidemic in early 2020. I explained if you used it. His colleague Josh Quick changed the method previously used for the Ebola, Zika, and Yellow fever virus sequences. The open source protocol released by the ARTIC network uses a PCR tiling approach to amplify the SARS-CoV-2 genome from small samples. This is then sequenced to ensure good coverage throughout the genome. The ARTIC analysis pipeline then generates a consensus sequence of viruses and calls variants in real time as the sequence progresses. A complete end-to-end workflow became available in January 2020.

In March, the COVID-19 Genomics UK Consortium (COG-UK) was established. This is a decentralized network that links academia with public health agencies and sequence labs. Nick’s team running high-throughput SARS-CoV-2 sequencing on GridION and PromethION devices is just one of many teams across the UK doing rapid sequencing and analysis of samples. As of May 2021,> 460,000 SARS-CoV-2 genomes have been contributed and data shared.

This genomic epidemiological data can be used to infer or rule out potential transmission routes and to identify and investigate clusters. By linking sequence data with travel data, COG-UK was able to reveal more than 1,300 independent introductions of SARS-CoV-2 from mainland Europe to the United Kingdom in early March. Genomic epidemiological data also enable the identification and tracking of variant strains of concern in the viral genome. This can change the nature of the disease it causes and help develop future treatments and vaccines. Nick explains how sequencing data revealed that the December 2020 surge in cases in Kent, UK, was associated with more than 50% of new strains in the region’s sample. Did. This strain was later found to share mutations with strains associated with the proliferation of cases in South Africa and similar mutations with other strains that began to predominate in Brazil. Finally, Nick emphasized the recent surge in cases in India. This is also believed to be associated with a new variant of the virus.

Based at Sichuan University in China, Lu Chen used a MinION device to sequence SARS-CoV-2 samples from cities in Sichuan and Wuhan, China, from January to March 2020.Genome, one-deleted by analysis of sequence data Nsp— Present in> 20% of samples. Phylogenetic analysis revealed city-specific clusters, but further analysis also showed broader propagation between multiple cities. After identifying 35 recurrent mutations in the Sichuan SARS-CoV-2 sample, Lu found 117 associations between these and clinical phenotypes. They also found that deletion of Nsp1 was associated with a less severe clinical phenotype and correlated with viral load and a significant decrease in cytokine IFN-β levels.

George Githinji, a member of the KEMRI-Wellcome Trust Research Program, explained how he and his colleagues quickly scaled up the existing infrastructure of the SARS-CoV-2 sequence in Kenya through partnerships with GeMVi, ARTIC Network and others. explained. Utilizing the ARTIC method and nanopore sequencing, we have set up a rapid end-to-end pipeline for analyzing SARS-CoV-2 samples. Less than three weeks after the first COVID-19 case was reported in Kenya, the team sequenced the first SARS-CoV-2 sample and generated genomic epidemiological data early in the pandemic. This data provided insights into the introduction of SARS-CoV-2 in Kenya and revealed transnational, locally and travel-related transmission routes.

George emphasized the important need to expand sequencing capabilities across Africa, working with other KEMRI institutions within Kenya and in other low- and middle-income countries through partnerships with the Africa CDC and the WHO Africa Regional Office. We talked about how we achieved.

In Düsseldorf, Germany, his team of Alexander Dilthey and Heinrich Heine University Düsseldorf has set out to integrate genomic surveillance with public health and city-wide contact tracing data. When using only traditional tracing methods, the source of infection remained unknown at 40%. COVID 19 cases. Alexander primarily applied an ARTIC-based approach to show how to perform nanopore sequencing of SARS-CoV-2 samples and shared results online in real time, including putative infection clusters. Comparing post-hoc contact tracing and case information with these estimated clusters showed individual transmission chains “in all cases”, allowing for further investigation. The data reveals that some transmission chains are much more complex than previously recognized, emphasizing the important role of sequence data in the notification of containment and intervention strategies. Using this data, he said, “it is possible to track the SARS-CoV-2 infection chain across the population, even during periods of ongoing community infection and very high incidence.” I concluded.

The use of sequencing in the COVID-19 study also extends to investigating how the human immune system responds to the SARS-CoV-2 virus. Rebekah Penrice-Randal, a member of the Hiscox Lab at the University of Liverpool, UK, used the cDNA sequences of GridION and MinION Mk1C to compare the host transcriptome of a clinical study sample infected with COVID-19 or influenza with a healthy control. .. They identified hundreds of genes that are differentially expressed between sample groups, including fatal and non-fatal cases of COVID-19, and their future potential as biomarkers of the disease and its severity. Suggested.

Meanwhile, Irina Chelysheva of the Oxford Vaccine Group at Oxford University in the United Kingdom used a high-throughput cDNA sequence of the human transcriptome in PromethION to compare the host response to COVID-19 with the response of typhoid fever. It is difficult to distinguish between the symptoms of the two illnesses, which can lead to misdiagnosis. The team found differential expression between samples taken at the time of diagnosis and healthy controls, and beyond this, found that certain genes were upregulated only in COVID-19 or typhoid fever. Did. Their studies show the future potential to rapidly identify COVID-19 and distinguish it from other diseases through the transcriptome signature of the infection found in the host.

Nick Loman emphasized that the more allowed the virus to spread, the more likely it is to evolve a combination of mutations that can increase infectivity and alter antigenicity. He said that SARS-CoV-2 could increase infectivity or avoid immunity if the virus could circulate in areas where the virus did not have sufficient public health measures to control it or access vaccination. He emphasized that it is likely to evolve. Looking to the future, he emphasized the importance of further leveraging and optimizing SARS-CoV-2 sequences around the world. together. “

* LondonCalling2021 online conference hosted by Oxford Nanopore Technologies. May 19-21, 2021.