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Robert provided an overview of real-world sample collection. Relative efficiency of Midnight vs ARTICv3 workflows for SARS-CoV-2 sequencing Meanwhile, as the team plan to continue to perform SARS-CoV-2 sequencing, they are transitioning from the ARTIC to the Midnight protocol to improve throughput and decrease cost. They also plan to expand their work beyond SARS-CoV-2: investigating prolonged infection in the context of influenza. Julie explained that her team have a contract with the CDC to sequence and investigate SARS-CoV-2 in individuals with immune failure, such as infection despite vaccination, reinfection, and persistent infection a major focus will be sequencing the virus from immunocompromised individuals, such as transplant recipients, those living with HIV/AIDS, and cancer patients receiving immunosuppressive therapies. Julie questioned if the change might have been initiated somehow by the antibody therapy. The patient had started neutralising antibody therapy at around day 200, and subsequent sequencing of research samples from the individual revealed a globally unique variant E484T. This revealed a mutation in the receptor binding motif of the spike gene (E484A) that had been observed previously in other immunocompromised patients. Unfortunately, there was no sample available from the timepoint of diagnosis for them to use, but they obtained a research sample from around day 100 which Julie’s team sequenced. The Ct level of the PCR assay never rose about 30. The individual had common variable immunodeficiency and MALT lymphoma they were initially diagnosed with COVID-19 using standard PCR testing, and then repeated PCR testing was performed over the course of around 300 days. Alongside other sequence data, they also detected multiple subsequent introductions of SARS-CoV-2 in both Dane and Milwaukee Counties, with more introductions but less extensive community spread in Dane County.Īnother interesting example was that of persistent SARS-CoV-2 infection in an immunocompromised patient, in which the team monitored SARS-CoV-2 levels over time. Julie’s team sequenced a research sample from this individual, and revealed that they had no descendent viruses, i.e., its transmission was contained. Madison (Dane County) had the 12th diagnosed SARS-CoV-2 case in the US in early February 2020. Julie explained how her team have been able to look at ‘ some very interesting cases’ throughout the pandemic she next presented two of these.
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Julie noted that, throughout the pandemic, there were generally only two full-time employees at a time focusing on these efforts, as they were just one of the many projects in their lab.
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The third largest contributor of sequences was her team. Milwaukee County, the most populous county, had ~140,000 of these confirmed cases the second most populous county, Dane County, where Julie’s team are located, had ~57,000 confirmed cases, of which ~7.2% were sequenced. This includes Wisconsin ― where their own sequencing efforts are located state-wide, there have been >800,000 confirmed cases here, of which ~3.7% have been sequenced. Within the United States, all states have submitted several SARS-CoV-2 sequences to public databases, such as GISAID and NCBI. These efforts are ‘ thanks largely to the ARTIC and ONT teams, for rapidly developing a protocol, deployable on such an easily accessible sequencing device’. Julie pointed out, however, that ‘ while vaccination efforts are reducing the numbers of severe cases’, SARS-CoV-2 is still actively circulating everywhere, with variants of concern arising.Ĭompared to previous pandemics, ‘ this virus is remarkably well studied’: as of November 11th, over 5 million SARS-CoV-2 genome sequences had been submitted to the GISAID database, from around the world. A total of >7 billion vaccine doses had been administered. At that point, there were 251,266,207 confirmed cases worldwide and 5,070,244 deaths (as reported by the World Health Organisation). Julie introduced the global picture of the COVID-19 epidemic as it stood on November 11th, 2021, almost two years after the first detected case. Julie and Robert (University of Wisconsin-Madison, USA) discussed their team’s SARS-CoV-2 sequencing efforts in the state of Wisconsin, and their recent switch to the Midnight protocol. Global sequencing efforts in the COVID-19 pandemic