Merge pull request #979 from ScilifelabDataCentre/develop

Updates W18

content/english/biobanks/_index.md

@@ -20,7 +20,7 @@ As of September 2021, the Sample Collection Database contains information about
 
 ### Submit information about sample collections
 
-Those wishing to submit information about their sample collections to the database should [contact Biobank Sverige](https://biobanksverige.se/provsamlingar-publicerade-i-covid-19-data-portal-sweden-underlattar-forskning-om-covid-19/) (the linked page also contains forms for adding new collections to the database). Questions, comments, or suggestions regarding the database itself can be sent to datacentre@scilifelab.se.
+Those wishing to submit information about their sample collections to the database should [contact Biobank Sverige](https://biobanksverige.se/provsamlingar-publicerade-i-covid-19-data-portal-sweden-underlattar-forskning-om-covid-19/) (the linked page also contains forms for adding new collections to the database). Questions, comments, or suggestions regarding the database itself can be sent to <datacentre@scilifelab.se>.
 
 ### Responsible organisations
 

content/english/biobanks/add_biobank.md

@@ -15,4 +15,4 @@ The personal data you provide in this form, your name, email address and phone n
 
 The information you provide will be processed for research purposes, i.e. using the lawful basis of public interest and following the Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 (General Data Protection Regulation) on the protection of natural persons about the processing of personal data and on the free movement of such data.
 
-The following parties will have access to processing your personal data: SciLifeLab Data Centre, Uppsala University and Biobank Sverige, Region Uppsala. Your personal data will be deleted when no longer needed, or when stipulated by the archival rules for the university as a government authority. If you want to update or remove your personal data please contact the controller SciLifeLab Data Centre at Uppsala University using datacentre@scilifelab.se.
+The following parties will have access to processing your personal data: SciLifeLab Data Centre, Uppsala University and Biobank Sverige, Region Uppsala. Your personal data will be deleted when no longer needed, or when stipulated by the archival rules for the university as a government authority. If you want to update or remove your personal data please contact the controller SciLifeLab Data Centre at Uppsala University using <datacentre@scilifelab.se>.

content/english/biobanks/add_collection.md

@@ -15,4 +15,4 @@ The personal data you provide in this form, your name, email address and phone n
 
 The information you provide will be processed for research purposes, i.e. using the lawful basis of public interest and following the Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 (General Data Protection Regulation) on the protection of natural persons about the processing of personal data and on the free movement of such data.  
 
-The following parties will have access to processing your personal data: SciLifeLab Data Centre, Uppsala University and Biobank Sverige, Region Uppsala. Your personal data will be deleted when no longer needed, or when stipulated by the archival rules for the university as a government authority. If you want to update or remove your personal data please contact the controller SciLifeLab Data Centre at Uppsala University using datacentre@scilifelab.se.
+The following parties will have access to processing your personal data: SciLifeLab Data Centre, Uppsala University and Biobank Sverige, Region Uppsala. Your personal data will be deleted when no longer needed, or when stipulated by the archival rules for the university as a government authority. If you want to update or remove your personal data please contact the controller SciLifeLab Data Centre at Uppsala University using <datacentre@scilifelab.se>.

content/english/dashboards/wastewater/covid_quant_GU.md

@@ -69,7 +69,7 @@ Influent wastewater samples were collected from Ryaverket wastewater treatment p
 ## Dataset
 
 **Download the data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://blobserver.dckube.scilifelab.se/blob/wastewater_data_gu_allviruses.xlsx). Results are available for SARS-CoV-2 from week 7 of 2020 (with a small gap over winter 2022-2023), and for enteric viruses from week 2 of 2023. Updated weekly.\
-**Contact:** helene.norder@gu.se
+**Contact:** <helene.norder@gu.se>
 
 **How to cite the dataset:**  Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501).
 

content/english/dashboards/wastewater/covid_quant_KTH.md

@@ -90,7 +90,7 @@ Please also note that although the same methods are used for all cities shown on
 ## Dataset
 
 **Download the data:** [N3-gene copy number per PMMoV gene copy number; Excel file](https://blobserver.dckube.scilifelab.se/blob/stockholm_wastewater_method_Sep_2021.xlsx). Results are available (partially) starting from week 16 of 2020 for Stockholm and starting from week 39 of 2021 for Malmö; updated weekly.\
-**Contact:** zeynepcg@kth.se
+**Contact:** <zeynepcg@kth.se>
 
 **How to cite dataset:**
 Cetecioglu, Z. G., Williams, C., Khatami, K., Atasoy, M., Nandy, P., Jafferali, M. H., Birgersson, M. (2021). SARS-CoV-2 Wastewater Data from Stockholm, Sweden. [https://doi.org/10.17044/scilifelab.14315483](https://doi.org/10.17044/scilifelab.14315483).

content/english/dashboards/wastewater/covid_quant_SLU.md

@@ -111,7 +111,7 @@ The group provide reports to summarise their latest findings. The latest report
 
 ## Dataset
 
-**Contact:** anna.szekely@slu.se and maja.malmberg@slu.se
+**Contact:** <anna.szekely@slu.se> and <maja.malmberg@slu.se>
 
 **Download the data:** [N1-gene copy number per PMMoV gene copy number, CSV file.](https://datagraphics.dckube.scilifelab.se/dataset/0ac8fa02871745048491de74e5689da9.csv). Data are available from week 38 of 2020; updated weekly.
 

content/english/dashboards/wastewater/historic_orebro_umea.md

@@ -7,7 +7,7 @@ aliases:
 
 This page displays data on the amount of SARS-CoV-2 in Umeå and Örebro wastewater between October 2020 and June 2021. After June 2021, a new method is used for analyses of wastewater, and [the most recent data can be found here](../).
 
-The data displayed here were collected as part of a research project led by associate professor Maja Malmberg (SLU, Swedish University of Agricultural Sciences; maja.malmberg@slu.se) in collaboration with the [SciLifeLab COVID-19 National Research Program](https://www.scilifelab.se/covid-19) and associate professor Mette Myrmel at the Norwegian University of Life Sciences. The amount of SARS-CoV-2 virus in the wastewater of Umeå is measured using samples taken from the wastewater treatment facilities in Umeå and Örebro. Please [consult this map for the exact catchment area of the wastewater collection channels in Umeå](/wastewater/map_umeaa.jpg). Please [consult this map for the exact catchment area of the wastewater collection channels in Örebro](/wastewater/map_orebro.pdf).
+The data displayed here were collected as part of a research project led by associate professor Maja Malmberg (SLU, Swedish University of Agricultural Sciences; <maja.malmberg@slu.se>) in collaboration with the [SciLifeLab COVID-19 National Research Program](https://www.scilifelab.se/covid-19) and associate professor Mette Myrmel at the Norwegian University of Life Sciences. The amount of SARS-CoV-2 virus in the wastewater of Umeå is measured using samples taken from the wastewater treatment facilities in Umeå and Örebro. Please [consult this map for the exact catchment area of the wastewater collection channels in Umeå](/wastewater/map_umeaa.jpg). Please [consult this map for the exact catchment area of the wastewater collection channels in Örebro](/wastewater/map_orebro.pdf).
 
 After preparation, the viruses were extracted using ultra filtration and analyzed using qPCR technique for SARS CoV-2 RNA. Primers were used to detect the SARS-COV-2 gene (previously used and verified by [Corman and colleagues (2020)](https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045)). qPCR samples were normalized against PMMV. Until January 2021, three samples per week were taken and their results were pooled to provide a weekly estimate. From February 2021, samples were instead collected weekly.
 

content/english/dashboards/wastewater/historic_stockholm.md

@@ -7,7 +7,7 @@ aliases:
 
 This page displays data on the amount of SARS-CoV-2 in Stockholm between April 2020 and August 2021 calculated as Gene copy number/week (raw wastewater) with bovine + PMMoV factor. From September 2021 onwards, the method was changed. Please [see this page for the most recent data](./).
 
-This project, led by associate professor Zeynep Cetecioglu Gurol and colleagues (KTH Royal Institute of Technology; zeynepcg@kth.se), is a collaboration between the [SciLifeLab COVID-19 National Research Program](https://www.scilifelab.se/covid-19) and the [SEED](https://www.kth.se/en/seed) and [Chemical Engineering](https://www.kth.se/ket/chemical-engineering-1.784196) departments at KTH, in close collaboration with Stockholm Vatten och Avfall and the Käppala Association. The sampling of wastewater, started in mid-April 2020, from Bromma, Henriksdal, and Käppala wastewater treatment plants (WWTP). These treatment plants receive wastewater from a population of approximately 360,000; 860,000 and 500,000, respectively. Please consult [this map for the exact catchment area of the wastewater collection channels in Käppala](/wastewater/map_Kappala.pdf) and [this map for the exact catchment area of the wastewater collection channels in Bromma and Henriksdal](/wastewater/map_Bromma_Henriksdal.pdf).
+This project, led by associate professor Zeynep Cetecioglu Gurol and colleagues (KTH Royal Institute of Technology; <zeynepcg@kth.se>), is a collaboration between the [SciLifeLab COVID-19 National Research Program](https://www.scilifelab.se/covid-19) and the [SEED](https://www.kth.se/en/seed) and [Chemical Engineering](https://www.kth.se/ket/chemical-engineering-1.784196) departments at KTH, in close collaboration with Stockholm Vatten och Avfall and the Käppala Association. The sampling of wastewater, started in mid-April 2020, from Bromma, Henriksdal, and Käppala wastewater treatment plants (WWTP). These treatment plants receive wastewater from a population of approximately 360,000; 860,000 and 500,000, respectively. Please consult [this map for the exact catchment area of the wastewater collection channels in Käppala](/wastewater/map_Kappala.pdf) and [this map for the exact catchment area of the wastewater collection channels in Bromma and Henriksdal](/wastewater/map_Bromma_Henriksdal.pdf).
 
 After concentration, filtering, and preparation, the samples are analyzed using qPCR technique for SARS CoV-2 RNA. Primers of the nucleocapsid (N) gene were used to detect the SARS-COV-2 gene (previously used and verified by [Medema and colleagues (2020)](https://doi.org/10.1016/j.scitotenv.2020.142939)). In some cases, the raw wastewater has been frozen at –20 degrees, and  concentrated wastewater or purified RNA have been stored at -80 C before the next analysis step was carried out. The concentration method used by prof. Zeynep Cetecioglu Gurol and her colleagues is based on their published study ([Jafferali and colleagues, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)) comparing four different concentration methods. The study concluded that the double ultrafiltration method adapted by KTH has a significantly higher efficiency compared to single filtration and adsorption methods. For detailed information about the concentration method, see the publication.
 

content/english/highlights/igh_antibody_genes.md

@@ -0,0 +1,47 @@
+---
+title: Variability in IGH antibody genes influences the response to SARS-CoV-2
+date: 2023-05-05
+summary: Pushparaj and colleagues use genotyping and haplotype analysis to show high genetic diversity in IGH genes among humans, which may influence our response to infections. Data, and IgDiscover software shared.
+banner: /highlights/banners/igh_antibody_genes_small.jpg
+banner_large: /highlights/banners/igh_antibody_genes.jpg
+banner_caption: Graphical abstract (Image courtesy Pushparaj et al. 2023)
+highlights_topics: [COVID-19, Infectious Diseases]
+announcement: "This data highlight was also [published on the SciLifeLab Data Platform](https://data.scilifelab.se/highlights/igh_antibody_genes/), as the work described in this highlight constitutes data-driven life science. The Platform is a hub for data-driven life science in Sweden, containing multiple relevant resources, tools, and services. It includes information on multiple subjects, including infectious diseases, please check out the [Data Platform](https://data.scilifelab.se/) for more."
+---
+
+The COVID-19 pandemic has highlighted the importance of research focused on our ability to control infections and to explore why certain individuals respond differently than others to disease and vaccination. Recent COVID-19 research has contributed valuable information about how immune-related genes influence the ability to control SARS-CoV-2 infection. While some genes are connected with increased risk of serious infection, e.g. inborn deficiencies in type I interferon, other genes may confer protective effects against the development of severe COVID-19 disease, e.g. archaic-derived isoform of oligoadenylate synthetase (OAS), which is an interferon-induced effector molecule. These studies focused on explaining how variations in our innate immune system influence our control of SARS-CoV-2. So far, much less is known about how genetic variations underpinning our adaptive immune responses influence how we react to viral infections and our ability to form immunological memory to viruses such as SARS-CoV-2.
+
+New studies show that immunoglobulin heavy chain (IGH) genes, specifically IGHV1-69, is used by many S-specific SARS-CoV-2 neutralizing antibodies. The IGHV1-69 gene is known for being both highly polymorphic and subject to copy number variation, features that shape different person’s naïve B cell repertoires. As such, it is likely that this variation has implications for the human response to infection, and vaccination.
+
+In a recently published article in _Immunity_, researchers from Karolinska Institutet (_First author:_ Pradeepa Pushparaj, _Corresponding author:_ Gunilla B Karlsson Hedestam) studied the role of IGH germline gene variation in antibody response against SARS-CoV-2. They isolated SARS-CoV-2 spike-specific monoclonal antibodies from a previously collected cohort of convalescent healthcare workers (N=14, seropositive for S-IgG) and selected a set of potently neutralizing IGHV1-69-using antibodies. They used the IG genotyping tool IgDiscover (learn more about the software here) and inferred haplotype analysis to study the variation in IGHV allele composition between the study participants. While one participant was homozygous for IGHV1-69∗01, nine had two or three different alleles of this gene and two were found to have four different IGHV1-69 alleles. Six different alleles, e.g. IGHV1-69∗20, were found among the participants.
+
+The team focused on an individual who had three IGHV1-69 alleles from whom they cloned the IGHV1-69∗20-using CAB-I47 antibody, and two highly similar antibodies that were isolated from an independent donor. They then engineered the three IGHV1-69∗20-using mAbs to assess if germline-encoded polymorphisms that characterize the IGHV1-69*20 allele were required for the neutralization activity of the antibodies. They found this to be the case. By using cryo-EM to analyze structural data, they found that the CAB-I47 Fab, in complex with the SARS-CoV-2 spike, docked into the receptor-binding domain (RBD) of the virus, with two germline-encoded polymorphisms in IGHV1-69, R50 and F55, being required for the high affinity RBD interaction. They also confirmed this finding experimentally.
+
+>Gunilla B. Karlsson Hedestam, the corresponding author says "Antibody genetics is a notoriously complex field. Thanks to new experimental methods and our computational tool, IgDiscover, we can now resolve the fine details of antibody genes. These studies reveal a surprising level of genetic variability among humans, which influence how we respond to infections".
+
+In summary, this study showed that human IGH antibody genes are highly variable and germline-encoded residues specific to given IGHV1-69 alleles can shape the neutralizing antibody response to SARS-CoV-2. These results demonstrate that genetic differences can influence our antibody response to SARS-CoV-2 and thus also shape long-lived memory B cell responses induced by infection or vaccination.
+
+#### Data
+
+Adhering to Open Science and FAIR the researchers have shared sequence data in GenBanka and data in several repositories such as ProteomeXchange, PDB, EMD and SciLifeLab Data Repository.
+
+* HC (VDJ) and LC (VJ) sequences of neutralizing mAbs available in GenBank ([OP497961 - OP497964](https://www.ncbi.nlm.nih.gov/nuccore/?term=OP497961%3AOP497964%5Bpacc%5D) and [ON086918 - ON086947](https://www.ncbi.nlm.nih.gov/nuccore/?term=ON086918%3AON086947%5Bpacc%5D)).
+* The repertoire sequence data is available in [Figshare](http://doi.org/10.17044/scilifelab.19317512) hosted by SciLifeLab.
+* Cryo-EM structures of CAB-I47 Fabs in complex with the spike trimer are deposited Protein Data Bank ([8A99](https://www.rcsb.org/structure/unreleased/8A99), [8A94](https://www.rcsb.org/structure/8A94), and [8A96](https://www.rcsb.org/structure/8A96)) and Electron Microscopy Data Bank ([EMD-15273](https://www.ebi.ac.uk/emdb/EMD-15273), [EMD-15269](https://www.ebi.ac.uk/emdb/EMD-15269), and [EMD-15271](https://www.ebi.ac.uk/emdb/EMD-15271)).
+* Mass spectrometry raw files and HDX analysis, deposited on ProteomeXchange Consortium via PRIDE. Can be accessed by [PXD031945](https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD031945).
+* The IgDiscover software can be found [here](http://docs.igdiscover.se/en/stable/) _(The plot allele module and the rep-seq analysis tools can be found under IgDiscover v0.12.4.dev22+g0bc3365)_.
+* Supplemental Tables are available [here](https://doi.org/10.17632/mg7p5msrfs.1).
+
+#### Article
+
+DOI: [10.1016/j.immuni.2022.12.005](https://doi.org/10.1016/j.immuni.2022.12.005)
+
+Pushparaj, P., Nicoletto, A., Sheward, D. J., Das, H., Castro Dopico, X., Perez Vidakovics, L., Hanke, L., Chernyshev, M., Narang, S., Kim, S., Fischbach, J., Ekström, S., McInerney, G., Hällberg, B. M., Murrell, B., Corcoran, M., & Karlsson Hedestam, G. B. (2023). Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies. In Immunity (Vol. 56, Issue 1, pp. 193-206.e7).
+
+#### Funding
+
+This project was funded the Swedish Research Council, grants from the SciLifeLab National COVID-19 Research Program financed by the Knut and Alice Wallenberg Foundation and the SciLifeLab Pandemic Laboratory Preparedness (PLP) program 2022–2023. Additional funding was provided from the Knut and Alice Wallenberg Foundation and the European Union’s Horizon 2020 research and innovation programme.
+
+#### Infrastructure
+
+Part of this work was supported by the Swedish National Infrastructure for Biological Mass Spectrometry (BioMS) and the SciLifeLab (Sweden) Integrated Structural Biology platform. All cryo-EM data were collected at the Karolinska Institutet’s 3D-EM facility, and surface plasmon resonance analysis was performed at the Protein Science Facility at Karolinska Institutet.

content/english/pathogens/mpox.md

@@ -20,7 +20,7 @@ Information regarding mortality rate is limited, but there is significant variat
 
 In this section, we present announcements about ongoing research efforts primarily by (but not limited to) researchers and institutions based in Sweden. The intention is to 'highlight' these efforts as soon as possible, so that we can maximise their usefulness to researchers.
 
-Please feel free to submit an announcement using the form below or by sending an e-mail to datacentre@scilifelab.se.
+Please feel free to submit an announcement using the form below or by sending an e-mail to <datacentre@scilifelab.se>.
 
 Lists of data, tools, publications, and other potentially useful information are provided further down on the page and likely to be more complete.