diff --git a/content/english/plp-program-background.md b/content/english/plp-program-background.md index 06c332be..81aa3db8 100644 --- a/content/english/plp-program-background.md +++ b/content/english/plp-program-background.md @@ -3,23 +3,27 @@ title: Pandemic Laboratory Preparedness (PLP) program toc: true --- -The Science for Life Laboratory (SciLifeLab) research community has been actively engaged in national and international COVID-19 research efforts sice early 2020. The ability to access established SciLifeLab infrastructure and expertise within that research community undoubtedly expedited studies on COVID-19/SARS-CoV-2 at the molecular, cellular, patient, population, and environmental levels. +The Science for Life Laboratory (SciLifeLab) research community has been actively engaged in national and international COVID-19 research efforts sice early 2020. Access to the wide-ranging expertise within that community, and to previously established SciLifeLab infrastructure, expedited COVID-19 research at the molecular, cellular, patient, population, and environmental levels. -As part of their efforts to tackle the pandemic, SciLifeLab was quick to establish programs to support research efforts. The first was the [The SciLifeLab/KAW National COVID-19 Research Program](https://www.scilifelab.se/pandemic-response/covid-19-research-program/), which was established in April 2020 and co-funded by the [Knut and Alice Wallenberg Foundation (KAW)](https://kaw.wallenberg.org/stiftelsens-satsningar-pa-atgarder-mot-coronaviruset). More recently, SciLifeLab was commissioned to establish a program focussed on pandemic preparedness. Here, we provide background and relevant links related to the resultant research program; the Pandemic Laboratory Preparedness (PLP) program. +SciLifeLab was quick to respond to the pandemic, and established multiple efforts to accelerate and support research throughout. The first program established to support research efforts was the [The SciLifeLab/KAW National COVID-19 Research Program](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/pandemic-response/national-program/), which was established in April 2020 and co-funded by the [Knut and Alice Wallenberg Foundation (KAW)](https://kaw.wallenberg.org/en). When the focus of the global research community started to shift towards pandemic preparedness, SciLifeLab was commissioned to establish a program to support pandemic preparedness in general. This resulted in SciLifeLab's Pandemic Laboratory Preparedness (PLP) program. This page details information about the PLP program itself, including progress to date and the capabilities (i.e. services, tools, and resources) funded. -## Progress to date +## Progress to date (previous calls) -In December 2020, the Swedish government [comissioned SciLifeLab to build capacity for future pandemics](https://www.regeringen.se/rattsliga-dokument/proposition/2020/12/forskning-frihet-framtid--kunskap-och-innovation-for-sverige/). The assignment broadly involved supporting **research related to infectious diseases** (e.g. in diagnostics, analysis of infection, immunity, and the development of resistance to therapies in pathogens), and **building competence** and **developing technologies** related to pandemic research (e.g. in sequencing, genetic analysis, immunology, and big data). The services, tools, and resources (termed 'capabilities') established through the PLP program are intended to assist and complement those established elsewhere in society (e.g. authorities, municipalities, and regions) to tackle future pandemics. As such, the PLP program works in close consultation with governmental agencies, e.g. [Swedish Public Health Agency (FoHM)](www.folkhalsomyndigheten.se). +In December 2020, the Swedish government [comissioned SciLifeLab to build capacity for future pandemics](https://www.regeringen.se/rattsliga-dokument/proposition/2020/12/forskning-frihet-framtid--kunskap-och-innovation-for-sverige/). The assignment broadly involved supporting **research related to infectious diseases** (e.g. in diagnostics, analysis of infection, immunity, and the development of resistance to therapies in pathogens), and **developing competence and technologies** related to pandemic research (e.g. in sequencing, genetic analysis, immunology, and big data). The capabilities established through the PLP program are intended to assist and complement those established elsewhere in society (e.g. government authorities, municipalities, and regions) to tackle future pandemics. As such, the PLP program works in close consultation with government agencies, e.g. [Swedish Public Health Agency (FoHM)](https://www.folkhalsomyndigheten.se). -In February 2021, the PLP program sent out a national open call for letters of intent to develop capabilities (i.e. tools/resources/services) that could be used to detect and monitor COVID-19, and/or to help combat future pandemics. +In February 2021, the PLP program sent out a national open call for letters of intent to develop capabilities that could be used to detect and monitor COVID-19, and/or to help combat future pandemics. -As of July 2021, the first eight capabilities were selected for support as part of the first stage of the program (PLP1) ([further information on the selection process is available on the main SciLifeLab.se website](https://www.scilifelab.se/pandemic-response/pandemic-laboratory-preparedness/)). The capabilities in PLP1 were focussed on: biosafety Level 3 (BSL3) capacity, biobanking and clinical sample handling, environmental detection of pathogens, immunomonitoring, serology, and sequencing. Refer to the [PLP1 section](/plp-program-background/#plp1-capabilities) below to find out more about these capabilities. +In July 2021, the first eight capabilities were selected for support as part of the first stage of the program (named PLP1) ([further information on the selection process is available on SciLifeLab's website](https://www.scilifelab.se/pandemic-response/pandemic-laboratory-preparedness/)). The capabilities in PLP1 were focused on: biosafety Level 3 (BSL3) capacity, biobanking and clinical sample handling, environmental detection of pathogens, immunomonitoring, serology, and sequencing. Refer to the [PLP1 section](/plp-program-background/#plp1-capabilities) below to find out more about these capabilities. A [funding call was established to extend funding for these projects (REPLP-1)](https://anubis.scilifelab.se/call/REPLP1) was established in September 2022, allowing funding to be extended until 2025. See the PLP1 capability pages below to see which received REPLP-1 funding. -A **laboratory preparedness expression of interest (EoI) call** was launched as the second call of the PLP program in spring 2022. The aim was to create a nationally significant infrastructure capability. Any proposals were expected to integrate real-world testing and proof-of-concepts. The resultant projects were expected to be able begin within a year. More background information on this second call (PLP2) is available on the [SciLifeLab website](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/pandemic-response/calls/call-for-new-pandemic-laboratory-preparedness-capabilities-plp-2/). Please see the [below section on PLP2](/plp-program-background/#plp2-capabilities) to find out more about the capabilities selected from this call. +In December 2021, the PLP program established a funding call for Technology Development Projects (TDPs). The intention with this call was to build closer connections between clinical microbiology laboratories in Sweden. All TDPs aimed to develop capabilities at major clinical microbiology laboratories in Sweden. For more information about the TDP call, please refer to the [SciLifeLab website](https://www.scilifelab.se/news/call-for-new-pandemic-laboratory-preparedness-capabilities-plp-cm-tdp/). See the [below TDP section](/plp-program-background/#plp-tdps) for more information about the TDPs resulting from this call. A [call to extend funding for the TDP projects (REPLPCM)](https://anubis.scilifelab.se/call/REPLPCM) was established in February 2023, allowing funding to be extended until 2025. Please see the TDP capability pages below to determine which received REPLPCM funding. -The PLP program also supports a number of Technology Development Projects (TDPs). The call for TDPs (which was in December 2021) was established in order to build closer associations between clinical microbiology laboratories in Sweden. The projects aimed to develop services and capabilities at major clinical microbiology laboratories in Sweden. For more information about this call please refer to the [SciLifeLab website](https://www.scilifelab.se/news/call-for-new-pandemic-laboratory-preparedness-capabilities-plp-cm-tdp/). Please see the [below TDP section](/plp-program-background/#plp-tdps) for more information about the TDPs resulting from this call. +A call for new capabilities (PLP2) was launched in spring 2022. The aim was to create nationally significant infrastructure capabilities. Any proposals were expected to integrate real-world testing and proof of concept work. The resultant capabilities were expected to be able begin within a year. More background information on the PLP2 call is available on the [SciLifeLab website](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/pandemic-response/calls/call-for-new-pandemic-laboratory-preparedness-capabilities-plp-2/). Please see the [below section on PLP2](/plp-program-background/#plp2-capabilities) to find out more about the capabilities resulting from this call. -In December 2021, a novel SARS-CoV-2 variant of concern (Omicron) emerged. At the time, the PLP program and wider SciLifeLab community rapidly put further resources into research on the novel variant. +In September 2023, the PLP-Test funding call was established to support up to 9 projects to test and improve existing PLP capabilities. The funding was available to those within PLP units and/or agencies related to pandemic preparedness, e.g. FoHM. More information about this call is available on the [SciLifeLab website](https://www.scilifelab.se/news/grants-for-testing-of-plp-capabilities-plp-test/). Please see the [below section on PLP-Test](/plp-program-background/#plp-test) to find out more about the capabilities resulting from this call. + +In February 2024, a further call for Clinical Technology Development Projects was established in collaboration with the Precision Medicine Capability at SciLifeLab. The call focuses on the creation of clinical technology development projects addressing clinical needs. For more information about this call, see the [Scilifelab website](https://www.scilifelab.se/capabilities/precision-medicine/call-for-clinical-technology-development-projects/). The call is open until 10th April 2024, and more information on the resulting projects will be added in due course. + +To view any current funding available from PLP, view our [funding page](/funding/). ## Pillars of the PLP program @@ -30,31 +34,35 @@ The PLP program is built on **four pillars**: - _National research program_ - _The Swedish Pathogens Portal_ -This portal (formerly the Swedish COVID-19 Data Portal) forms one of four pillars of PLP program. The scope of the portal includes pandemic preparedness topics, including antibiotic resistance and infectious disease. - ## The PLP network -The PLP program aims to build a national network of laboratory capabilities (the PLP network). Capabilities are funded in different calls (see above for basic information on previous calls). In this section, we list the capabilities funded in each call and provide links to further information on each capability. +The PLP program has built a national network of laboratory capabilities (the PLP network). These capabilities were funded in different calls (see above for basic information on [previous calls](/plp-program-background/#progress-to-date-previous-calls)), and are listed according to funding call below. Some capabilities received continuation funding in the REPLP-1 and REPLPCM calls. Whilst these calls are not listed below, receipt of continuation funding is indicated on the respective capability pages. All PLP capabilities are also shown on our [Pandemic Preparedness Capabilities page](/resources/). -All PLP capabilities are also linked on our [Pandemic Preparedness Resources page](/resources/). +As indicated above, The Swedish Pathogens Portal (formerly the Swedish COVID-19 Data Portal) is a [pillar of the PLP program](/plp-program-background/#pillars-of-the-plp-program). Whilst it is not listed below, it received funding from the PLP program during the PLP1 and REPLP1 calls. It works actively to support all capabilities. ### PLP1 capabilities -The following PLP capabilites are part of The Pandemic Laboratory Preparedness Program 1 (PLP1). +The following capabilites were established in the PLP1 call, some received continuation funding from REPLP-1. {{< plp_table category="plp1" >}} +### PLP TDPs + +The following capabilities were established during the Technology Development Project (TDP) call. Some projects also received continuation funding from REPLPCM. + +{{< plp_table category="tdp" >}} + ### PLP2 capabilities -The following PLP capabilites are part of The Pandemic Laboratory Preparedness Program 2 (PLP2). +The following capabilites were funded as part of the PLP2 call. {{< plp_table category="plp2" >}} -### PLP TDPs +### PLP-Test -The PLP network currently includes the following Technology Development Projects (TDPs). +The following capabilities resulted from the PLP-Test call. -{{< plp_table category="tdp" >}} +{{< plp_table category="test" >}} ## Further reading about the PLP program @@ -64,8 +72,8 @@ The PLP network currently includes the following Technology Development Projects ## Personnel and contact -**Scientific lead for the SciLifeLab Pandemic Laboratory Preparedness**: Professor Staffan Svärd. +**Scientific lead for the PLP program**: Professor Staffan Svärd. -**Coordinator for the Pandemic Laboratory Preparedness capability**: Alice Sollazzo. +**Coordinator for the PLP program**: Alice Sollazzo. -If you have any questions, please email Alice Sollazzo. +If you have any questions about the PLP program, please email Alice Sollazzo. diff --git a/content/english/resources/NG-serology.md b/content/english/resources/NG-serology.md new file mode 100644 index 00000000..247b2cd4 --- /dev/null +++ b/content/english/resources/NG-serology.md @@ -0,0 +1,15 @@ +--- +title: "Next-generation serology of emergent flavivirus infections" +category: "test" +resource_info: + name: "Next-generation serology of emergent flavivirus infections" + pi: Anders Bergqvist + host_organisation: Uppsala University Hospital/Akademiska Sjukhuset Clinical Microbiology, Dept. of Medical Sciences, Uppsala University + contact: "Anders Bergqvist
Uppsala University Hospital/Akademiska Sjukhuset Clinical Microbiology, Dept of Medical Sciences, Uppsala University
Email: [Anders.bergqvist@medsci.uu.se](mailto:Anders.bergqvist@medsci.uu.se) or [Anders.bergqvist@akademiska.se](mailto:Anders.bergqvist@akademiska.se)" +for_background_table: + pi: Anders Bergqvist + pi_affiliation: Uppsala University + lab: Uppsala University Hospital +--- + +The Flavivirus family comprises several mosquitos- or tick-borne infectious agents including tick-borne encephalitis (TBE), dengue virus (DENV), West Nile virus (WNV), Japanese encephalitis virus (JEV), yellow fever (YF) and Zika virus (ZIKV) and are estimated to annually infect 400 million individuals. The serological diagnostics of these viruses are hampered by several problems due to significant cross reactivity of available tools that often makes it difficult to make a correct assessment of the causative agent and the patient´s immune status. The reason for this unsatisfactory situation is likely that most commercial kits utilize suboptimal antigens based on incomplete polypeptides or single antigens produced in procaryotic or non-mammalian expression systems that lacks the natural systems for protein modifications/processing, which results in antigens that are skewed for linear epitopes and immature structures and lacks the important contribution of native antigen that are fully matured and ultimately are characterized by low analytic specificity and poor correlation with more clinically relevant neutralization tests. In our previous we have by using BK polyomaviruses (BKV) as model developed serologic diagnostic based on virus-like particles produced in a very efficient expression system that show high similarity with native antigen, high correlation with neutralization test, and allows proper discrimination of the very closely BKV types I and IV. In this project we will design serologic assays for important flaviviruses based on virus like particles expressed in the same system that are expected to discriminate at least equally well against the much less conserved members of this family and hopefully have a better correlation with protective immunity elicited during natural infection. If this turnout successfully for the existing flaviviruses, this platform can hopefully also be used for a new flavivirus that might emerge in the future. diff --git a/content/english/resources/_index.md b/content/english/resources/_index.md index 7ff3186e..6d661ecd 100644 --- a/content/english/resources/_index.md +++ b/content/english/resources/_index.md @@ -4,12 +4,12 @@ title: Pandemic Preparedness Capabilities ## Overview -The COVID-19 pandemic began in 2019, and had a tremendous, negative impact on society and healthcare systems globally. The speed of the response from all quarters was unprecedented, as was the level of cooperation within and around the scientific community. This helped to get the pandemic under control and prevent greater, more widespread damage. In order to minimise the impact of the next pandemic, we need to act to make sure that our response is as quick as possible. The best way to do this is to invest in pandemic preparedness now. Pandemic preparedness involves ensuring that the resources needed to fight a pandemic are ready for immediate use; preventing the need to invest significant time on development during the pandemic. +The COVID-19 pandemic had a tremendous, negative impact on society and healthcare systems globally. The speed of the response from all quarters was unprecedented, as was the level of cooperation within and around the scientific community. This helped to minimise the impact of the pandemic as much as possible. The scientific community is now focused on ensuring that the response is even faster for future pandemics, so that we can further mitigate the effects. The best way to achieve preparedness for future pandemic is to invest in it now. In part, future pandemic preparedness means ensuring that resources developed during the COVID-19 pandemic are kept up-to-date and ready for immediate use in the next pandemic. This will reduce the time and effort required to reuse these resources during the next pandemic. -This section of the Pathogens Portal is dedicted to capabilities related to pandemic preparedness (i.e. services or resources that can be used in current and future pandemics). At present, the capabilities listed are primarily related to the [Pandemic Laboratory Preparedness (PLP) program at SciLifeLab](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/) (refer to our [PLP program background page](/plp-program-background/) for additional information). However, any pandemic preparedness capabilities built by individuals associated with a Swedish university or research institute can be included. +This section of the Swedish Pathogens Portal is dedicted to capabilities related to pandemic preparedness (i.e. services or resources that can be used in current and future pandemics). At present, the capabilities listed are primarily related to the [Pandemic Laboratory Preparedness (PLP) program at SciLifeLab](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/) (refer to our [PLP program background page](/plp-program-background/) for additional information). However, any pandemic preparedness capabilities built by individuals associated with a Swedish university or research institute can be included. -The pages themselves are not static. They will be updated as soon as possible after more information becomes available. +The pages for each capability are regularly updated with new information as it becomes available.
- We welcome suggestions about relevant capabilities that could be included in this section. Those involved in the capabilities listed below are also invited to inform us of any updates. Please email us at pathogens@scilifelab.se or use our contact form to get in touch. + To add or update information about pandemic preparedness capabilities, email us at pathogens@scilifelab.se or use our contact form to get in touch.
diff --git a/content/english/resources/biobanking.md b/content/english/resources/biobanking.md new file mode 100644 index 00000000..b4b017f4 --- /dev/null +++ b/content/english/resources/biobanking.md @@ -0,0 +1,16 @@ +--- +title: "Testing and evaluating diagnostic preparedness and biobanking: A cross-platform collaboration for validating new diagnostic assays and reviewing PLP capacities" +category: "test" +resource_info: + name: "Testing and evaluating diagnostic preparedness and biobanking: A cross-platform collaboration for validating new diagnostic assays and reviewing PLP capacities" + pi: Jessica Alm + host_organisation: Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet + contact: "Jessica Alm
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet
Email: [jessica.alm@ki.se](mailto:jessica.alm@ki.se)" +for_background_table: + pi: Jessica Alm + pi_affiliation: Karolinska Institutet +--- + +In this PLP-Test project, we at National Pandemic Center (NPC) at KI will collaborate with PLP-, healthcare- and governmental partners to test our readiness and cross-collaboration capacity by validating new and broadened diagnostic analyses and to evaluate our achievements and experiences gained during previous PLP-project (G3P) and national tasks during the COVID-19 pandemic. These are important aspects for testing, maintaining and refining collaboration workflows and capabilities for continued laboratory preparedness. + +Started as a temporary COVID-19 diagnostic laboratory in March 2020 to support health care with PCR-testing, NPC has developed into a high throughput laboratory with activities within diagnostics, whole genome sequencing and biobanking at national scale. Importantly, all activities have involved several partners across healthcare, governmental partners, and academic partners, with established well-functioning collaborations and logistic chains with the Swedish regions, and productive cooperations with PLP-program partners. This project proposal focusses on validating a newly in-house developed multiplex qPCR for respiratory viral infections (Influenza A and B, RSV and SARS-CoV-2), and validating a DESI-MS-based direct diagnostic platform for COVID-19 and the respiratory viral infections in the multiplex qPCR. Validations involve other PLP-partners for testing assay performance and work- and data flow. We will further test and evaluate routines and accessibility of samples in the national COVID-19 sample collection stored at NPC (established as part of the PLP-project G3P). The proposal is designed to validate and develop new diagnostic platforms, while at the same time evaluate use and availability of the national sample collection, as well as sample logistics and collaboration within the PLP network. The overall aim is to evaluate the performance of our established PLP capabilities, while validating new diagnostic platforms. diff --git a/content/english/resources/enbiflu.md b/content/english/resources/enbiflu.md new file mode 100644 index 00000000..561fa681 --- /dev/null +++ b/content/english/resources/enbiflu.md @@ -0,0 +1,26 @@ +--- +title: "EnBiFlu, testing the efficiency of multifaceted environmental assessment of avian influenza threats and outbreaks" +category: "test" +resource_info: + name: "EnBiFlu, testing the efficiency of multifaceted environmental assessment of avian influenza threats and outbreaks" + pi: Anna J. Székely + host_organisation: "Swedish University of Agricultural Sciences, SLU." + data_etc: "[Dashboard: The amount of SARS-CoV-2 virus in wastewater across Sweden](https://www.pathogens.se/dashboards/wastewater/)" + publications_etc: + webpage: + contact: "Anna J. Székely
Researcher
Email: [anna.szekely@slu.se](mailto:anna.szekely@slu.se)" +for_background_table: + pi: Anna J. Székely + pi_affiliation: Swedish University of Agricultural Sciences +--- + +Avian influenza, commonly known as bird flu, poses a significant threat to both avian and human populations. The constant evolution of avian influenza viruses (IAVs) in natural reservoirs and their potential to jump the species barrier have made it essential to assess preparedness and response strategies. The EnBiFlu project focuses on evaluating the ability of the Swedish Environmental Epidemiology Center (SEEC) and its collaborators to address avian influenza threats and outbreaks. + +This project comprises four distinct working packages (WPs), each addressing specific aspects of avian influenza research and response: + +- WP1 aims to establish standardized methods for detecting avian IAVs in environmental samples including improvement of concentration and viral nucleic acid extraction methods and validation of qPCR and hpPCR-based assays for IAV detection. +- WP2 aims to assess the possibility to the detect avian IAVs in wild bird populations through sampling of lake water during the spring migration period. +- WP3 aims to measure transmission of respiratory viruses in high-density poultry farms, which are a critical concern. WP3 will assess the risk of windborne virus spread between poultry units using model respiratory viruses used as aerosolized vaccines. +- WP4 aims to evaluate the speed and efficiency of the SEEC PLP unit in detecting a potential human outbreak of avian IAV, or a novel IAV. This WP involves a real-time outbreak simulation, where wastewater monitoring protocols are put to the test in rapidly detecting, identifying and evaluating the novel IAV. + +As quick and efficient detection and identification are pivotal in responding to potential outbreaks and pandemics, the results of the collaborative work involved in EnvBiFlu will definitely enhance our preparedness and response to the realistic possibility of an avian influenza related threat. diff --git a/content/english/resources/gilp.md b/content/english/resources/gilp.md index f18a80e4..3e69a40d 100644 --- a/content/english/resources/gilp.md +++ b/content/english/resources/gilp.md @@ -30,3 +30,7 @@ We will use and develop these resources further to establish a pandemic prepared 5. Expand a high-throughput T cell assay pipeline for additional viruses. 6. Further develop our BSL3 competence for viral culture, neutralisation and antiviral assays. + +##### Continuation funding: + +This capability received funding from the REPLPCM call to continue their work. Please see our PLP background information page for more information about the REPLPCM call. With the funding, the capability is developing metagenomics methods for clinical samples, as this will become increasing important in diagnostics. The transfer to the Illumina platform will reduce the cost and improve performance by refining bioinformatics. The capability will also continue to develop existing methods used with processing wastewater, viral culture, and genomic signature analyses. Further, studies of ADAR-induced mutations and minor quasispecies will be expanded, by also using long-read platforms (PacBio) and investigating mutations induced by APOBEC. T cell assays will also be further developed and applied. diff --git a/content/english/resources/immunomonitoring.md b/content/english/resources/immunomonitoring.md index f297cef8..775e4253 100644 --- a/content/english/resources/immunomonitoring.md +++ b/content/english/resources/immunomonitoring.md @@ -7,7 +7,7 @@ resource_info: funded_project_title: "Systems-level immunomonitoring to unravel immune response to a novel pathogen" pi: Petter Brodin, Jochen Schwenk host_organisation: "Karolinska Institutet" - use: "Once this capability has been tested, validated and standardized it can be offered as a service capability and combined offering within the SciLifeLab, Clinical proteomics and immunology platform (see project aim 4)." + use: "Once this capability has been tested, validated and standardised it can be offered as a service capability and combined offering within the SciLifeLab, Clinical proteomics and immunology platform (see project aim 4)." contact: "Petter Brodin
Professor
Email: [petter.brodin@ki.se](mailto:petter.brodin@ki.se)

Jochen Schwenk
Professor
Email: [jochen.schwenk@scilifelab.se](mailto:jochen.schwenk@scilifelab.se)" for_background_table: pi: Petter Brodin diff --git a/content/english/resources/infections_travelers.md b/content/english/resources/infections_travelers.md new file mode 100644 index 00000000..3f32f656 --- /dev/null +++ b/content/english/resources/infections_travelers.md @@ -0,0 +1,21 @@ +--- +title: "Infections in travelers" +category: "test" +resource_info: + name: "Infections in travelers" + pi: Tobias Allander + host_organisation: Clinical Microbiology at Karolinska University Hospital + contact: "Tobias Allander
Dept. of Clinical Microbiology, Karolinska University Hospital and Dept. of Microbiology, Tumor, and Cell Biology, Karolinska Institutet
Email: [tobias.allander@regionstockholm.se](mailto:tobias.allander@regionstockholm.se)" +for_background_table: + pi: Tobias Allander + pi_affiliation: Karolinska University + lab: Karolinska University Hospital +--- + +Correct diagnosis of infectious diseases is the foundation of infection control and surveillance. There are excellent diagnostic tools for common infections, but rare or unexpected infectious agents are more difficult to identify, and risk being missed. A more widespread use of unbiased diagnostic methods, such as metagenomic sequencing, would therefore improve surveillance and early identification of pandemic threats, including known and unknown pathogens. + +With the support of PLP grants, we have developed a diagnostic metagenomic sequencing pipeline, which is now available for clinical diagnostic use. The main intended areas of use are severe, unexplained infections (CNS, respiratory or generalized), particularly cases when unusual pathogens are more likely, such as in immunosuppressed patients and travelers from tropical regions. A study evaluating the diagnostic yield in immunosuppressed patients with pneumonia is ongoing. The present study proposal aims for evaluation of metagenomic sequencing in patients suffering from febrile infections following travel in tropical countries. + +The “Tropical fever study” at Karolinska University Hospital has included 521 patients seeking care for fever after travel in the tropics during 2017-2020. Approximately half of the cases lack etiological diagnosis. We will analyze an estimated 100 selected stored serum samples by metagenomic sequencing, with the aims to evaluate the diagnostic value of metagenomic sequencing of serum samples in this patient group, to identify additional causative microorganisms, and to describe the microbial genomes present in the serum of patients with fever of unknown etiology. We will also investigate paired acute and convalescent serum samples by a subtractive bioinformatic approach, to identify sequences associated with the disease episode independently from taxonomic classification. + +Improved diagnosis of rare infections in travelers is important for early identification of pandemic threats. diff --git a/content/english/resources/integrative_outbreak-sim.md b/content/english/resources/integrative_outbreak-sim.md new file mode 100644 index 00000000..e0fc9f46 --- /dev/null +++ b/content/english/resources/integrative_outbreak-sim.md @@ -0,0 +1,21 @@ +--- +title: "Integrative Outbreak Simulation: A One Health Approach for Enhanced Pandemic Preparedness" +category: "test" +resource_info: + name: "Integrative Outbreak Simulation: A One Health Approach for Enhanced Pandemic Preparedness" + pi: Rene Kaden + host_organisation: Uppsala University Hospital/Akademiska Sjukhuset Clinical Microbiology, Dept. of Medical Sciences, Uppsala University + contact: "Rene Kaden
Uppsala University Hospital/Akademiska Sjukhuset Clinical Microbiology, Dept of Medical Sciences, Uppsala University
Email: [rene.kaden@medsci.uu.se](mailto:rene.kaden@medsci.uu.se) or [rene.kaden@akademiska.se](mailto:rene.kaden@akademiska.se)" +for_background_table: + pi: Rene Kaden + pi_affiliation: Uppsala University + lab: Uppsala University Hospital +--- + +This collaborative project, involving six PLP partners and the National Veterinary Institute (SVA), is designed to simulate an outbreak scenario by dispatching clinical samples that are spiked with unusual microorganisms to the contributing clinical microbiology laboratories. These samples are delivered in a manner that facilitates enrichment and mimick authentic patient and wastewater samples. The scenarios may encompass complex, potentially zoonotic outbreaks, thus embracing the One Health concept by engaging partners from both human and animal health. + +All project phases will be meticulously documented, and progress updates on the outbreak scenario will be shared via the Swedish Pathogens Portal. This approach ensures real-time project monitoring and public accessibility to information. + +The primary objectives include assessing response times and the laboratory's capacity to detect and identify the pathogen, developing diagnostic methods, treatment recommendations, but also scaling up sequencing, bioinformatics, and investigate storage capacities at the National Pandemic Center (NPC). The project leverages the synergistic effects of collaborations between laboratories. Participating laboratories will receive samples in a time series, emulating a natural pathogen distribution. + +The project serves to evaluate pandemic preparedness effectiveness and identify areas for potential enhancement. Through these concerted efforts, this initiative aims to strengthen our collective capacity to respond swiftly and effectively to emerging infectious threats. diff --git a/content/english/resources/metagenomic_seq_pathogens.md b/content/english/resources/metagenomic_seq_pathogens.md index 2f17e5d8..35cab514 100644 --- a/content/english/resources/metagenomic_seq_pathogens.md +++ b/content/english/resources/metagenomic_seq_pathogens.md @@ -22,3 +22,7 @@ In parallel, we have started testing three different RNA extraction techniques t A literature review has been performed regarding library preparation, and as a result, we have ordered library preparation kits for metagenomic RNA-seq on Illumina and Nanopore. These will be tested and evaluated on human samples with varying concentrations of known viruses (influenza, RS and SARS-CoV-2). Different bioinformatic approaches will be developed, evaluated and optimized. Once the laboratory and bioinformatic methods are validated on samples of known content, they will be further tested on samples from patients with unknown infections. With this technology development, the laboratory will have an increased preparedness to quickly analyze novel pathogens and to follow and quickly respond to future pandemic situations. + +##### Continuation funding: + +This capability received funding from the REPLPCM call to continue their work. Please see our PLP background information page for more information about the REPLPCM call. With this funding, the capability aimed to further develop the methodology into a clinical routine method for analysis of samples of unknown etiology. This will include the addition of CNS pathogens in cerebrospinal fluid samples. The capability also aimed to establish quicker sequencing using long-read technology to decrease the turn-around-time in cases where time is essential for patient outcome. Further development was also planned for bioinformatic pipelines and databases, in part to allow more samples to be analysed by medical doctors, bioinformaticians, and biologists to build experience with interpreting complex results. diff --git a/content/english/resources/monitoring_nursing_homes.md b/content/english/resources/monitoring_nursing_homes.md new file mode 100644 index 00000000..bef70275 --- /dev/null +++ b/content/english/resources/monitoring_nursing_homes.md @@ -0,0 +1,14 @@ +--- +title: "Utilizing large scale bio monitoring of nursing home residents for rapid detection of emerging respiratory infections and immunity" +category: "test" +resource_info: + name: "Utilizing large scale bio monitoring of nursing home residents for rapid detection of emerging respiratory infections and immunity" + pi: Mattias Forsell + host_organisation: Umeå University + contact: "Mattias Forsell
Associate Professor
Email: [mattias.forsell@umu.se](mailto:mattias.forsell@umu.se)" +for_background_table: + pi: Mattias Forsell + pi_affiliation: Umeå University +--- + +The PLP2 program "Preparedness by early detection of infections in the elderly" has led to the establishment of a platform where immune responses to vaccination and infections at Swedish nursing homes can be coupled and combined with national registry data of vaccinations, infections, comorbidities and medication. We have provided proof-of-concept that the platform can be utilized to produce information of high national and international interest for the development of prophylactic strategies against COVID-19 infections (Vikström et al, Lancet Regional Health-Europe, 2023 and Blom et al, Lancet Infectious Diseases 2023). Here, we will expand on these studies to demonstrate the versatility of the platform for pandemic preparedness against other respiratory infections of clinical relevance, and for the detection of impending outbreaks in the nursing home population. Hence, we aim to (1) transition from measuring immunity COVID-19 vaccines to addition respiratory infectious agents or vaccines of clinical interest (i.e. RSV, Influenza, Metapneumovirus, etc), (2) to monitoring infectious agents that are circulating in the air of nursing homes and (3) to effectivize sampling and processing strategies of capillary blood samples. The end goals of this proposal is to provide further proof-of-concept of the dynamic potential of the platform for its general use (i.e. looking at any infectious agent/vaccine of interest, not only COVID-19), to demonstrate the potential of the platform to act as an “early warning system” for spread of known and emerging infectious agents within an environment where susceptible individuals live, and to enhance processing and analysis of capillary samples. diff --git a/content/english/resources/mould_yeast.md b/content/english/resources/mould_yeast.md new file mode 100644 index 00000000..4413d51b --- /dev/null +++ b/content/english/resources/mould_yeast.md @@ -0,0 +1,19 @@ +--- +title: "Identification of molds and yeasts using Nanopore sequencing and MALDI-TOF." +category: "test" +banner: +resource_info: + name: "Identification of molds and yeasts using Nanopore sequencing and MALDI-TOF." + pi: Johan Lindh + host_organisation: Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet + contact: "Johan Lindh
Department of Medical Sciences, Clinical Microbiology, Uppsala University
Email: [johan.lindh@icm.uu.se](mailto:johan.lindh@icm.uu.se)" +for_background_table: + pi: Johan Lindh + pi_affiliation: Uppsala University +--- + +The department of Clinical microbiology and hygiene (KMB) at Uppsala university hospital adopted to the pandemic situation very fast, we were up and running with in-house established methods for RT-PCR analyses of SARS-CoV2 already in February, 2020. We have since then developed several different methods including sequencing protocols using Nanopore technology and mutantRTPCR. + +We have today a large capacity in the area of SARS-CoV-2 analyses, both whole genome sequencing and in RTPCR and are also ready to detect new viruses. We have developed qualified methods and the use of 96 hole plates in all steps of above. Since all methods and instruments are validated and quality assured they are also used in other routine diagnosis. Our future perspectives in this area are to develop 18S sequencing methods in order to identifye molds and yeasts together with protocols to detect the same using MALDI-TOF. + +Another method which can detect different microbes at a high output is the MALDI-TOF system. Today we have the system running at a capacity of 96 samples per hour and per instrument. A big advantage with this system, if compared with RTPCR, is that the detection is at the level of expressed proteins instead of genetic material. This is especially true if resistance to drugs will be measured. diff --git a/content/english/resources/ng_clinical_virology.md b/content/english/resources/ng_clinical_virology.md index b0128a09..abc0a26b 100644 --- a/content/english/resources/ng_clinical_virology.md +++ b/content/english/resources/ng_clinical_virology.md @@ -13,6 +13,10 @@ for_background_table: lab: Karolinska University Hospital --- +
+ This project received continuation funding from the REPLPCM call, see our PLP background information page for more information. +
+ Next generation sequencing offers numerous possibilities for improved diagnostics and management of infectious diseases. A comprehensive goal for Clinical Microbiology at Karolinska is to apply viral metagenomics and human immune transcriptomics in healthcare, and develop the following capabilities: - Diagnostic metagenomic sequencing. @@ -24,3 +28,7 @@ Next generation sequencing offers numerous possibilities for improved diagnostic Activities so far have focused on establishing diagnostic metagenomic sequencing with a focus on viral infections. Wet lab protocols have been developed for Illumina and Nanopore sequencing and a first bioinformatics pipeline is in place. Further development is ongoing within the Genomic Medicine Sweden (GMS) collaboration. We have analyzed 25 samples (respiratory tract samples, serum, cerebrospinal fluid) with known viral findings and compared metagenomics by both Illumina (25M reads) and Nanopore sequencing with real-time PCR results. Results indicate that the sensitivity of metagenomic sequencing by Illumina is better than our target value corresponding to Ct 30. Nanopore sequencing as expected has somewhat lower sensitivity but has proven useful because of its short turn-around time. We are appointed a reference center by ECDC for metagenomic sequencing of non-A-E hepatitis cases. We have also made progress in the characterization of unclassified genomes, where we are currently focusing on two previously unknown picornavirus species. Future activities will be to complete the validation of diagnostic metagenomic sequencing, release the assay to health care and set up a clinical study protocol for the received samples, so that the data can be used for research. We will also initiate immune transcriptome studies. + +##### Continuation funding: + +This capability received funding from the REPLPCM call to continue their work. Please see our PLP background information page for more information about the REPLPCM call. With this funding, the capability will further develop the wet lab and bioinformatics protocols for metagenomic sequencing, Nanopore-based metagenomic sequencing, and transcriptome profiling as a diagnostic tool. It will also evaluate the diagnostic value of mNGS and the collection of data through clinical study protocols, initiate virus surveillance, and develop new virus classification tools. diff --git a/content/english/resources/ngs_surveillance.md b/content/english/resources/ngs_surveillance.md index f66c35cd..f4c53267 100644 --- a/content/english/resources/ngs_surveillance.md +++ b/content/english/resources/ngs_surveillance.md @@ -1,7 +1,7 @@ --- title: "Development of a targeted metagenomic NGS platform for diagnostics and epidemiological surveillance of viral pandemic threats" category: "tdp" -banner: "/resources_thumbs/next-gen-clin-microbio.jpg" +banner: "/resources_thumbs/ngs-diagnositics.jpg" resource_info: name: "Development of a targeted metagenomic NGS platform for diagnostics and epidemiological surveillance of viral pandemic threats" pi: Lisa Pettersson @@ -33,4 +33,8 @@ The proposed system includes implementation of validated methods for: We have hired a laboratory technician that is under training to perform the laboratory work needed. We are developing a web application that can translate and present the NGS data as clinically relevant information. The application must be sufficiently user-friendly from a clinical point of view to allow the platform to be used in clinical routine. The platform will, however, also be used for projects from the academic research community. -This fall we plan to analyse clinical samples with common viruses (for example Influenza A and calicivirus) and samples spiked with inactivated viral species constituting possible pandemic threats to investigate the performance of the panel. +We plan to analyse clinical samples with common viruses (for example Influenza A and calicivirus) and samples spiked with inactivated viral species constituting possible pandemic threats to investigate the performance of the panel. + +##### Continuation funding: + +This capability received funding from the REPLPCM call to continue their work. Please see our PLP background information page for more information about the REPLPCM call. With this funding, the capability will focus on the implementation of the metagenomic NGS platform and develop a workflow for clinical use, both for diagnostics and surveillance. Effort will also be put into reaching out to clinicians to inform of the new possibilities that the NGS platform has to offer as a novel diagnostic tool for viral diseases – including unknown viruses. diff --git a/content/english/resources/rapid-seq-entero.md b/content/english/resources/rapid-seq-entero.md new file mode 100644 index 00000000..9e1525ed --- /dev/null +++ b/content/english/resources/rapid-seq-entero.md @@ -0,0 +1,23 @@ +--- +title: "Rapid establishment of comprehensive laboratory pandemic preparedness for enteroviruses - RAPID-SEQ-Entero" +category: "test" +resource_info: + name: "Rapid establishment of comprehensive laboratory pandemic preparedness for enteroviruses - RAPID-SEQ-Entero" + funded_project_title: "Rapid establishment of comprehensive laboratory pandemic preparedness for enteroviruses - RAPID-SEQ-Entero" + pi: Jan Albert + host_organisation: "Karolinska Institutet" + contact: "Jan Albert
Professor
Email: [jan.albert@ki.se](mailto:jan.albert@ki.se)" +for_background_table: + pi: Jan Albert + pi_affiliation: Karolinska Institutet +--- + +"In this proposal we aim to extend our ongoing RAPID-SEQ project on pandemic laboratory preparedness for SARS-CoV-2 and metagenomics to include research and surveillance on enteroviruses, which have the capacity to cause large worldwide outbreaks. Historically, poliomyelitis is the most well-known and feared enterovirus disease, but many other disease outbreaks have been caused enteroviruses. This includes recent reports on neonatal cases with fulminant and fatal hepatitis due to echovirus 11, polio-like acute flaccid myelitis due to enterovirus D68 (EV-D68), myocarditis due to coxsackie B3 and B4 and neonatal sepsis and meningoencephalitis. Despite the serious consequences and threats from enterovirus infections, Sweden lacks a comprehensive program for surveillance of enteroviruses, apart from the WHO mandated surveillance for poliovirus. + +This proposal aims to build capacity and preparedness for comprehensive laboratory surveillance of enteroviruses by: + +1. Implementing NGS-based methods for partial and whole genome sequencing (WGS) of enteroviruses and rhinoviruses. +2. Performing enterovirus genotyping on respiratory specimens. +3. Analyzing (i) genotypes from patients sampled at an intensive care unit vs other unit, (ii) circulating genotypes over time, and (iii) genotypes across age groups. + +Our laboratory is excellently suited to take on the above tasks as being the largest clinical microbiology laboratory in Sweden with continuous access to large numbers of patient samples and results from routine diagnostics. In addition, we are the national reference laboratory for non-polio enteroviruses and a partner in the European non-polio enterovirus network (ENPEN). Within ENPEN we have contributed to several studies on EV-D68. In this proposal we will extend this work to other species and types of enteroviruses and rhinoviruses. We will build on the capacity in our current PLP project (RAPID-SEQ) by adapting the workflow for SARS-CoV-2 to another pathogen." diff --git a/content/english/resources/rapid_type_variants.md b/content/english/resources/rapid_type_variants.md index ad3f2a4e..193f9573 100644 --- a/content/english/resources/rapid_type_variants.md +++ b/content/english/resources/rapid_type_variants.md @@ -14,3 +14,7 @@ for_background_table: --- Throughout the recent SARS-CoV-2 pandemic, it has been evident that a swift response relies on the capacity to quickly establish methodologies for clinical diagnostics and epidemiologic surveillance. The first generation of commercial kits were sold as "Research Use Only", had low capacity, and were often characterised by poor performance. Robust methodologies were, despite tremendous effort from the manufacturers and the frequent use of "Emergency Use" labelling by regulatory agencies, not available until the first wave was almost over. When the virus variants of concern (VOCs) emerged, it was clear that ambitious sequencing programs, although remarkably impressive and invaluable for the generation of big data, were nevertheless insufficient in terms of capacity and sensitivity, and were inherently too slow for clinical usage. Instead, first line surveillance had to be accomplished by simpler methods that focused on critical sites for defining polymorphism, rather than whole genome sequencing. From spring 2021 to summer 2022, we have typed almost all positive samples and monitored the emergence of different VOCs, including B.1.1.7/Alpha, B.617.2/Delta, as well as the Omicron variants BA.1, BA.2 and BA.5. Whilst the resolution is lower, the sensitivity is higher and its focus on relevant mutations mostly provides sufficient information to correctly identify the VOCs. For both contact tracing and clinical decisions regarding type-specific therapy, rapid typing was far superior compared to whole genome sequencing. In this project, we will develop a generalised platform based on focused sequencing techniques combined with serological testing that can be used for the rapid detection and characterisation of emerging variants of any etiologic agent. + +##### Continuation funding: + +This capability received funding from the REPLPCM call to continue their work. Please see our PLP background information page for more information about the REPLPCM call. diff --git a/content/english/resources/sample_handling.md b/content/english/resources/sample_handling.md new file mode 100644 index 00000000..f62b0ab5 --- /dev/null +++ b/content/english/resources/sample_handling.md @@ -0,0 +1,22 @@ +--- +title: "Enhancing Pandemic Laboratory Preparedness through Rapid Biopsy Sample Handling" +category: "test" +resource_info: + name: "Enhancing Pandemic Laboratory Preparedness through Rapid Biopsy Sample Handling" + pi: Annika Karlsson + host_organisation: "Department of Laboratory Medicine, Karolinska Institutet" + contact: "Annika Karlsson
Researcher
Email: [annika.karlsson@ki.se](mailto:annika.karlsson@ki.se)" +for_background_table: + pi: Annika Karlsson + pi_affiliation: Karolinska Institutet +--- + +"In this proposal we aim to extend our ongoing RAPID-SEQ project on pandemic laboratory preparedness for SARS-CoV-2 and metagenomics to include research and surveillance on enteroviruses, which have the capacity to cause large worldwide outbreaks. Historically, poliomyelitis is the most well-known and feared enterovirus disease, but many other disease outbreaks have been caused enteroviruses. This includes recent reports on neonatal cases with fulminant and fatal hepatitis due to echovirus 11, polio-like acute flaccid myelitis due to enterovirus D68 (EV-D68), myocarditis due to coxsackie B3 and B4 and neonatal sepsis and meningoencephalitis. Despite the serious consequences and threats from enterovirus infections, Sweden lacks a comprehensive program for surveillance of enteroviruses, apart from the WHO mandated surveillance for poliovirus. + +This proposal aims to build capacity and preparedness for comprehensive laboratory surveillance of enteroviruses by: + +1. Implementing NGS-based methods for partial and whole genome sequencing (WGS) of enteroviruses and rhinoviruses. +2. Performing enterovirus genotyping on respiratory specimens. +3. Analyzing (i) genotypes from patients sampled at an intensive care unit vs other unit, (ii) circulating genotypes over time, and (iii) genotypes across age groups. + +Our laboratory is excellently suited to take on the above tasks as being the largest clinical microbiology laboratory in Sweden with continuous access to large numbers of patient samples and results from routine diagnostics. In addition, we are the national reference laboratory for non-polio enteroviruses and a partner in the European non-polio enterovirus network (ENPEN). Within ENPEN we have contributed to several studies on EV-D68. In this proposal we will extend this work to other species and types of enteroviruses and rhinoviruses. We will build on the capacity in our current PLP project (RAPID-SEQ) by adapting the workflow for SARS-CoV-2 to another pathogen." diff --git a/content/english/resources/seec.md b/content/english/resources/seec.md index c3083d2c..fbb37518 100644 --- a/content/english/resources/seec.md +++ b/content/english/resources/seec.md @@ -8,8 +8,8 @@ resource_info: pi: Anna J. Székely host_organisation: "" use: "SEEC provides weekly data on Wastewater-based Epidemiology: SEEC actively monitors wastewater levels of the virus responsible for Covid-19 disease, SARS-CoV-2, in various municipalities of Sweden, covering more than 25% of the population. This data is continuously updated and freely accessible on the Covid-19 Data Portal of Sweden.

SEEC offers analysis of diverse environmental samples (e.g., water including wastewater, surface samples, air samples), for presence of pathogens, using both targeted approaches such as qPCR or amplicon sequencing as well as unbiased metagenomics approaches.

Built Environment Epidemiology: SEEC is involved in the worldwide analysis and profiling of built environment surfaces and air, with intermittent sampling of air in clinics, schools, subways, and indoor malls. Through an extensive network, datasets, sampling methods and analysis pipelines are readily available for comparative studies of environmental signals.

SEEC also offers support in experimental design, sampling, logistics, storage and other monitoring relevant processes." - access: "Data (relative virus quantity) is weekly uploaded by Zeynep Cetecioglu Gurol (KTH) and Anna Székely (SLU). Uploaded data [can be openly accessed by the general public](https://www.covid19dataportal.se/dashboards/wastewater/). Capacities of the resource are available to researchers upon request." - data_etc: "[Dashboard: The amount of SARS-CoV-2 virus in wastewater across Sweden](https://www.covid19dataportal.se/dashboards/wastewater/)" + access: "Data (relative virus quantity) is weekly uploaded by Zeynep Cetecioglu Gurol (KTH) and Anna Székely (SLU). Uploaded data [can be openly accessed by the general public](https://www.pathogens.se/dashboards/wastewater/). Capacities of the resource are available to researchers upon request." + data_etc: "[Dashboard: The amount of SARS-CoV-2 virus in wastewater across Sweden](https://www.pathogens.se/dashboards/wastewater/)" publications_etc: webpage: contact: "Anna J. Székely
Researcher
Email: [anna.szekely@slu.se](mailto:anna.szekely@slu.se)" diff --git a/content/english/resources/seq_based_diagnostics.md b/content/english/resources/seq_based_diagnostics.md index c4c228a5..c04af05d 100644 --- a/content/english/resources/seq_based_diagnostics.md +++ b/content/english/resources/seq_based_diagnostics.md @@ -13,6 +13,15 @@ for_background_table: lab: Lund University and Region Skåne --- -This proposal builds on the collaboration between the Dept. of Clinical Microbiology at Region Skåne, the Dept. of Translational Medicine, Section of Clinical Virology at Lund University, and Clinical Ge- nomics Lund at SciLifeLab, to develop and disseminate new state-of-the-art viral diagnostics meth- ods for improved Swedish healthcare. This collaboration already successfully established and im- plemented whole-genome sequencing (WGS) of SARS-CoV-2 during the pandemic (since February 2021). +This proposal builds on the collaboration between the Dept. of Clinical Microbiology at Region Skåne, the Dept. of Translational Medicine, Section of Clinical Virology at Lund University, and Clinical Genomics Lund at SciLifeLab, to develop and disseminate new state-of-the-art viral diagnostics methods for improved Swedish healthcare. This collaboration already successfully established and implemented whole-genome sequencing (WGS) of SARS-CoV-2 during the pandemic (since February 2021). -WGS of pathogens is becoming increasingly important for clinical science and practice. Moreover, as witnessed by the current pandemic, WGS has proven to be indispensable for tracking the dynam- ics of SARS-CoV-2 and will be similarly crucial for emerging outbreaks. However, the adoption of WGS in clinical diagnostic laboratories is currently limited and very few WGS protocols for other viruses have been validated for clinical use. In virology, WGS is crucial to inform the development of novel treatments and vaccines, and increases the resolution of molecular epidemiology (for example, in nosocomial transmission) and viral genetic variation as exemplified by the current pandemic. We envision that routine establishment of WGS-based diagnostics of viruses in a clinical setting will become increasingly important for patient care and the wider society, which also will contribute to Pandemic Laboratory preparedness. This proposal specifically aims to accelerate the development of laboratory and bioinformatic WGS protocols in a clinical diagnostic setting for a large number of viruses, to train personnel and increase know-how of WGS in the clinical laboratory, and facilitate data sharing. +WGS of pathogens is becoming increasingly important for clinical science and practice. Moreover, as witnessed by the current pandemic, WGS has proven to be indispensable for tracking the dynamics of SARS-CoV-2 and will be similarly crucial for emerging outbreaks. However, the adoption of WGS in clinical diagnostic laboratories is currently limited and very few WGS protocols for other viruses have been validated for clinical use. In virology, WGS is crucial to inform the development of novel treatments and vaccines, and increases the resolution of molecular epidemiology (for example, in nosocomial transmission) and viral genetic variation as exemplified by the current pandemic. We envision that routine establishment of WGS-based diagnostics of viruses in a clinical setting will become increasingly important for patient care and the wider society, which also will contribute to Pandemic Laboratory preparedness. This proposal specifically aims to accelerate the development of laboratory and bioinformatic WGS protocols in a clinical diagnostic setting for a large number of viruses, to train personnel and increase know-how of WGS in the clinical laboratory, and facilitate data sharing. + +##### Continuation funding: + +This capability received funding from the REPLPCM call to continue their work. Please see our PLP background information page for more information about the REPLPCM call. With this funding, the capability will establish a protocol for the detection of unknown pathogens (i.e. direct shotgun sequencing of the metagenomic libraries). The overall aim is to adapt versatile approaches towards clinical implementation. Specifically, the capability is using the funding to: + +- Optimise a shutgun metagenomic protocol for use in unknown pathogen detection in a clinical setting. +- Adapt methods to reduce background genetic information that is inherently present in clinical specimens. +- Adapt real-time bioinformatic detection using the MinION Oxford Nanopore using a real-time detection protocol. +- Establish the methodology in the clinical laboratory using a workshop series. diff --git a/content/english/resources/test_bsl3.md b/content/english/resources/test_bsl3.md new file mode 100644 index 00000000..e5a599c8 --- /dev/null +++ b/content/english/resources/test_bsl3.md @@ -0,0 +1,24 @@ +--- +title: "Testing BSL3 Biomedicum capabilities and more" +category: "test" +resource_info: + name: "Testing BSL3 Biomedicum capabilities and more" + pi: Antonio Rothfuchs + host_organisation: Karolinska Institute + contact: "Marianna Tampere
Coordinator Swedish BSL3 Network
Email: [marianna.tampere@ki.se](mailto:marianna.tampere@ki.se)

Antonio Gigliotti Rothfuchs
BSL3 Director
Email: [antonio.rothfuchs@ki.se](mailto:antonio.rothfuchs@ki.se)" +for_background_table: + pi: Antonio Rothfuchs + pi_affiliation: Karolinska Institute +--- + +**The Biosafety Level 3 (BSL3) research infrastructure at Biomedicum** has been seamlessly integrated into the PLP capability of SciLifeLab (see [details on the previous project grant](/bsl3/)). The facility offers specialized platforms in BSL3 for high-throughput (HTP) drug screening and pathogen aerobiology. The facility also leads the Swedish BSL3 Network (SB3N), a first-of-kind network for academic BSL3 laboratories in Sweden to interact with each other. The project has 3 aims divided into 3 work packages (WPs), and uses the pandemic pathogen **Monkeypox virus (MPXV)** as a demonstrator. + +**The Aims of the project are to:** + +**1. Test the access pipelines for MPXV isolates from the latest outbreak (WP1)** + +**2. Test the workflows of the specialized platforms build in BSL3 Biomedicum (WP2)** + +**3. Perform a comprehensive consequence analysis of identified bottlenecks (WP3)** + +There is an overwhelming consensus among the academic members of SB3N that Swedish SARS-CoV-2 strains were difficult to obtain during the COVID-19 pandemic. In WP1 we will investigate this by requesting access to Swedish MPXV isolates from the 2022 outbreak. Isolates will be requested from FoHM and from laboratories in the healthcare regions that have PLP projects. We will map hurdles in delivery of isolates. In WP2 we will test the ability of BSL3 Biomedicum to adapt MPXV to its high-end platforms for HTP antiviral screening and pathogen investigation in aerosols. These activities support both PLP and biodefense applications. In WP3 we will perform a consequence analysis to evaluate workflows in access to isolates and in the adaptation of our specialized platforms to MPXV. We will be supported by FoHM in this process to systematically analyze pros, cons, and challenges. Finally, risk mitigation measures will be proposed and communicated to counter hurdles in access to strains, and to counter choke points in our established high-end platforms. This will prepare us when we shift gears again to wartime/early pandemic activities. diff --git a/content/english/resources/track_path.md b/content/english/resources/track_path.md index 7d30aff4..fb3b1a8d 100644 --- a/content/english/resources/track_path.md +++ b/content/english/resources/track_path.md @@ -21,4 +21,13 @@ The project consists of three parts: We have selected >40 isogenic mutants of _Escherichia coli_, _Klebsiella pneumoniae_, _Pseudomonas aeruginosa_, and _Acinetobacter baumannii_ with resistance to at least one of the two novel antimicrobials cefiderocol and aztreonam-avibactam. The strains are ready to be analyzed regarding transcriptomics, as well as for some chromosomal mechanisms of resistance that are not presently mapped in publicly available pipelines. The goal is to be able to study outer membrane porins, penicillin-binding proteins, multidrug efflux pumps, as well as iron transporters of importance for cefiderocol uptake. The work with the pipelines is already advanced. -We have also explored methods for characterizing antifungal resistance in _Candida_ spp, in collaboration with the European reference laboratory at Statens Serum Institut, Copenhagen, Denmark. Finally, we have started collecting lower respiratory samples for assessment of host transcriptomics. This is done in close collaboration with the Niklas Björkström laboratory. The goal is to provide ex vivo information of the ongoing host response and how it differs compared to wildtype variants whilst the latter will yield more reductionistic insights into host responses. +We have also explored methods for characterizing antifungal resistance in _Candida_ spp, in collaboration with the European reference laboratory at Statens Serum Institut, Copenhagen, Denmark. Finally, we have started collecting lower respiratory samples for assessment of host transcriptomics. This is done in close collaboration with the Niklas Björkström laboratory. The goal is to provide _ex vivo_ information of the ongoing host response and how it differs compared to wildtype variants whilst the latter will yield more reductionistic insights into host responses. + +##### Continuation funding: + +This capability received funding from the REPLPCM call to continue their work. Please see our PLP background information page for more information about the REPLPCM call. This funding was intended to enable the capability to: + +- Provide guidance on optimal usage of novel antibiotics (e.g. cefiderocol). +- Identify outbreaks in a timely manner by implementing pipelines to identify clusters of SLVs and monitor virulence genes. +- Predict and track antifungal resistance. +- Use a large-scale transcriptomics approach to study host transcriptomics in bloodstream and respiratory tract infections to identify host-pathogen biological imprint. diff --git a/layouts/resources/list.html b/layouts/resources/list.html index 18608051..b5d06381 100644 --- a/layouts/resources/list.html +++ b/layouts/resources/list.html @@ -7,18 +7,20 @@ {{ $pages := .RegularPages }} -{{ $project_types := slice "plp1" "plp2" "tdp" }} +{{ $project_types := slice "plp1" "plp2" "tdp" "test" "replp"}} {{ range $project_type := $project_types }} {{ $resources_available := where $pages "Params.category" $project_type }} {{ with $resources_available }}
{{ if eq $project_type "plp1" }} -

Pandemic Laboratory Preparedness Capabilities Stage 1, 2021 (PLP1):

- {{ else if eq $project_type "plp2" }} -

Pandemic Laboratory Preparedness Capabilities Stage 2, 2022 (PLP2):

+

Pandemic Laboratory Preparedness Capabilities round 1 (PLP1):

{{ else if eq $project_type "tdp" }}

Technology Development Projects (PLP TDPs):

+ {{ else if eq $project_type "plp2" }} +

Pandemic Laboratory Preparedness Capabilities round 2 2022 (PLP2):

+ {{ else if eq $project_type "test" }} +

Testing PLP Capabilities (PLP-Test):

{{ end }}
{{ range . }} diff --git a/static/resources_thumbs/ngs-diagnositics.jpg b/static/resources_thumbs/ngs-diagnositics.jpg new file mode 100644 index 00000000..90cfd590 Binary files /dev/null and b/static/resources_thumbs/ngs-diagnositics.jpg differ