Merge pull request #1041 from ScilifelabDataCentre/develop

make latest changes live

README.md

@@ -1,4 +1,4 @@
-# ![The Swedish Pathogens Portal](static/img/site_logo/eml_pathogens_logo.png)
+# ![The Swedish Pathogens Portal](static/img/site_logo/swe_pathogens_logo.png)
 
 ## The Swedish Pathogens Portal
 

config.yaml

@@ -5,7 +5,7 @@ params:
   title: "The Swedish Pathogens Portal"
   description: The Swedish Pathogens Portal
   images:
-    - /img/site_logo/eml_pathogens_logo.png
+    - /img/site_logo/swe_pathogens_logo.png
 
   # There is a hugo i18n package, but it seems like overkill for so few strings
   lang_strings:

content/english/highlights/COVseq_surveillance_VOCs.md

@@ -11,6 +11,7 @@ tags: [COVID-19, Variant of concern, Large scale, Genomic surveillance, WGS, COV
 aliases:
     - /news/covseq_surveillance_vocs
     - /sv/news/covseq_surveillance_vocs
+images: [/highlights/banners/COVseq_small.png]
 ---
 
 The COVID-19 pandemic has not only changed societies and challenged healthcare, but also accelerated life science research. Over the last year and a half, a number of vaccines against COVID-19 have been developed in record time, and today large-scale vaccination campaigns are carried out in many countries worldwide. The open sharing of SARS-CoV-2 genome sequences has been key in facilitating the unprecedented rate of research. Research groups have made SARS-CoV-2 sequences available in, for example, [European Nucleotide Archive](https://www.ebi.ac.uk/ena/browser/home) (ENA) and/or [GISAID](https://www.gisaid.org). The large quantities of genomic data openly available to the research community has, in turn, enabled the study of SARS-CoV-2 spread and viral evolution, as well as the identification of novel SARS-CoV-2 variants. Throughout the current COVID-19 pandemic, a number of SARS-CoV-2 variants have been detected. The [European Centre for Disease Prevention and Control](https://www.ecdc.europa.eu/en) (ECDC) designates some such variants as *variants of concern* (VOCs) and some others as *variants of interest* (VOIs). A variant designated as a VOC may, for example, have a higher transmissibility, cause a relatively increased severity of disease, and/or have greater immune escape capabilities (i.e. they are more able to infect those with previous immunity resulting from previous infection or vaccination). By contrast, VOIs may have specific genetic markers that are predicted to affect transmission, or be difficult to diagnose.

content/english/highlights/G3BP_antivirual_target.md

@@ -7,6 +7,7 @@ banner_large: /highlights/banners/G3BP_figure1.png
 banner_caption: "Source: Figure 1 Kruse et al. 2021"
 highlights_topics: [COVID-19, Infectious diseases]
 tags: [SARS-CoV-2, Phage display library,  Discovery, Proteomics data, Antiviral intervention]
+images: [/highlights/banners/G3BP_thumbnail.png]
 ---
 
 The current COVID-19 pandemic has challenged societies world-wide over the last two years. Although vaccines have been developed in record time, and therapeutic drugs have been developed and repurposed, the pandemic is still challenging healthcare. More treatment options (e.g. novel antivirals) are warranted in preparation for future pandemic outbreaks.

content/english/highlights/Interferon_signatures_Liver.md

@@ -10,6 +10,7 @@ tags: [COVID-19, SARS-CoV-2, Interferon, Type-1 interferon signalling]
 aliases:
     - /news/interferon_signatures_liver
     - /sv/news/interferon_signatures_liver
+images: [/highlights/banners/Interferon_liver_small.png]
 ---
 
 The research community has responded rapidly to the current COVID-19 pandemic, which has caused a global health crisis. The SARS CoV-2 virus has been shown to have similar clinical features to previously well-known coronaviruses such as SARS-CoV, and MERS-CoV. In addition, research has indicated that more severe forms of coronavirus diseases are associated with dysregulation of the human type-I interferon (IFN-I) response, but further studies into this topic are warranted. Previous studies (e.g. [McNab (2005)](https://doi.org/10.1038/nri3787)) have found that Type I IFNs have diverse effects on innate and adaptive immune cells during different infections (caused by viruses, bacteria, parasites or fungi). Type I IFNs have been found to be important for host defence against viruses, but more recent studies indicate that it can also cause pathogenesis in acute viral infections, e.g. influenza.

content/english/highlights/Metabolic_perturbation_therapeutic_target.md

@@ -10,6 +10,7 @@ tags: [SARS-CoV-2, Therapeutic target, Multiomics data, Metabolic pathways, Vira
 aliases:
     - /news/metabolic_perturbation_therapeutic_target
     - /sv/news/metabolic_perturbation_therapeutic_target
+images: [/highlights/banners/Krishnan_abstract_thumbnail.png]
 ---
 
 The COVID-19 pandemic has caused public health challenges. The research community has, in record time, increased knowledge and understanding about the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus. Recent studies have, for example, found that certain risk factors (e.g. obesity) affect the severity of the resultant COVID-19 disease. Recent observational studies indicated an association between disease severity, and altered energy and lipid metabolism. Metabolic profiling could therefore be one way to identify likely disease severity. One important aspect for future pandemic preparedness is the development of new antivirals. Today´s direct-acting antivirals work by weakening the replication of viruses, future antivirals could instead be based on host-based metabolic strategies to inhibit viruses.

content/english/highlights/Phenomics_method_drug_discovery.md

@@ -10,6 +10,7 @@ tags: [Phenomics, Pertubations, Antiviralm, Drug discovery]
 aliases:
     - /news/phenomics_method_drug_discovery
     - /sv/news/phenomics_method_drug_discovery
+images: [/highlights/banners/Rietdijk_abstract_small.png]
 ---
 
 The current pandemic has increased the demand for rapid development of COVID-19  treatments, therefore increasing the need to develop methods to screen for novel drugs and drugs that could be repurposed. SARS-CoV-2 belongs to the RNA family of viruses, a group of viruses known for their fast mutation rates and resilience to antiviral drugs. Therefore, investigations into how the viruses affect host cells are needed in order to discover novel drug targets.

content/english/highlights/adenovirus.md

@@ -10,6 +10,7 @@ tags: [COVID-19, Adenovirus, Vaccine, Vector]
 aliases:
     - /news/adenovirus/
     - /sv/news/adenovirus/
+images: [/highlights/banners/adenovirus.png]
 ---
 
 The COVID-19 pandemic has profoundly affected and changed society over the last year. Currently, in record time, a number of vaccines are under development. To date, two mRNA vaccines (Pfizer/BioNTech and Moderna) are in use in Sweden. Several other of the novel vaccines under development are based on genetically modified adenovirus vectors.

content/english/highlights/alpaca-nanobody.md

@@ -10,6 +10,7 @@ tags: [COVID-19 SARS-CoV-2, Nanobody, Ty1, Neutralization, Antiviral therapy]
 aliases:
     - /news/alpaca-nanobody
     - /sv/news/alpaca-nanobody
+images: [/highlights/banners/tyson.jpg]
 ---
 
 The COVID-19 research efforts are focused on finding potential targets for future treatments. Research has shown that the affinity of SARS-CoV-2 receptor-binding domain (RBD) for ACE2 is considerably higher than that of SARS-CoV-1 which may contribute to pathogenesis. The receptor-engaging part of the spike protein is an attractive target for coronavirus neutralization. A number of conventional neutralizing monoclonal antibodies that bind to RBD have been isolated from convalescent patients. Camelid-derived single domain antibody fragments, also called nanobodies, offer key advantages for specific therapies. Nanobodies are small, easy to clone and express, stable, and cost effective. Previous research has shown that nanobodies can be potent inhibitors of viral infections in vivo, for example respiratory infections.

content/english/highlights/antibiotic_resistance_development.md

@@ -8,6 +8,7 @@ banner_caption: Artistic illustration of perseverance courtesy Elf lab / Johan E
 highlights_topics: [Antibiotic resistance]
 tags: [Antibiotic resistance, Bacteria, Escherichia coli, Perseverance, Time-lapse microscopy]
 announcement: "This data highlight was also [published on the SciLifeLab Data Platform](https://data.scilifelab.se/highlights/antibiotic_resistance_development/), 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."
+images: [/highlights/banners/antibiotic_resistance_development_small.jpg]
 ---
 
 Antibiotics were introduced in the 1930s and have since revolutionised modern medicine and healthcare. However, over the last few decades, antimicrobial resistance has started to pose a serious threat to global healthcare, animal husbandry, and the agricultural industry. Antimicrobial resistance means that bacteria and other microbes develop the ability to survive and grow in the presence of antibiotic drugs. In 2019, [almost 1.3 million deaths were directly connected to antimicrobial resistance worldwide](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)02724-0/fulltext#%20), and about 3 million resistant infections in the US alone. In Sweden, the corresponding number is about 10,000. Antimicrobial resistance is often referred to as a silent, or long-term pandemic. Decreased resistance development is central to future pandemic preparedness efforts, as we may enter an era where preventable disease can no longer be easily treated.

content/english/highlights/antivirals.md

@@ -10,6 +10,7 @@ tags: [COVID-19, Host-targeted, Small molecule inhibitors, Antiviral screening ,
 aliases:
     - /news/antivirals
     - /sv/news/antivirals
+images: [/highlights/banners/antivirals.png]
 ---
 
 The ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had severe social and economic consequences in many countries. The world has also seen recent serious outbreaks of other RNA viruses like Ebola virus (EBOV) and Crimean-Congo haemorrhagic fever virus (CCHFV) in the last decades. New antiviral strategies are therefore urgently needed. Targeting host cell pathways supporting viral replication is one approach to develop antiviral compounds. This could be especially important with new, unexplored viruses with limited information of virus biology.

content/english/highlights/bacterial_replication.md

@@ -8,6 +8,7 @@ banner_caption: Image courtesy Johan Elf lab
 highlights_topics: [Infectious Diseases]
 tags: [Infectious diseasese, Replication, Escherichia coli]
 announcement: "This data highlight was also [published on the SciLifeLab Data Platform](https://data.scilifelab.se/highlights/bacterial_replication/), 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."
+images: [/highlights/banners/ELF_banner.png]
 ---
 
 It is commonly known that all cells must coordinate DNA replication with cell growth; each chromosome should, on average, replicate once per generation. Bacteria, e.g. _Escherichia coli_, have optimised their division speed in order to survive in a very competitive environment. Fast division makes replication coordination extra challenging, especially in cases when the bacterial generation times are shorter than the time it takes to replicate the chromosome. This means that bacteria must have two complete copies of their chromosome ready before cell division, but still keep the ratio between the number of chromosome copies and cell divisions constant.

content/english/highlights/bevacizumab_treatment.md

@@ -10,6 +10,7 @@ tags: [COVID-19, Drug repurposing, Bevacizumab, Severe COVID]
 aliases:
     - /news/bevacizumab_treatment
     - /sv/news/bevacizumab_treatment
+images: [/highlights/banners/bevacizumab_small.png]
 ---
 The COVID-19 pandemic has caused a serious health emergency and a global challenge for demand of novel drug development. Drug repurposing has emerged as one way to meet the demand for new COVID-19 treatments.
 

content/english/highlights/bispecific_monomeric_nanobody.md

@@ -7,6 +7,7 @@ banner_large: /highlights/banners/bispecific_monomeric_nanobody_large.png
 banner_caption: Fig 2-f Modelling of simultaneous spike-Fu2-ACE2 binding shows that Fu2 blocks the binding of ACE2, from Hanke, L., Das, H., Sheward, D.J. et al (2022)
 highlights_topics: [COVID-19, Infectious diseases]
 tags: [COVID-19, SARS-CoV-2, Variant of concern, Nanobody, Neutralization, Antiviral]
+images: [/highlights/banners/bispecific_monomeric_nanobody.png]
 ---
 
 The COVID-19 pandemic, which is going into its third year, has had major societal and economic consequences worldwide. Despite lockdowns and non-pharmaceutical interventions (NPIs), such as restrictions on gatherings, social distancing requirements, and face mask mandates, the pandemic is still ongoing. The vaccine roll-out is progressing, and several treatment options and drugs are now registered for use. However, the continuous emergence of new [*Variants of Concern* (VoC)](/voc/) has delayed the re-opening of society. It is unfortunately likely to continue to do so, as research has confirmed that new variants are less effectively neutralised by antibodies elicited by the first-generation vaccines (*cf* [Cele et al. 2021](https://www.nature.com/articles/s41586-021-03471-w)). The development of novel treatments and vaccines that protects against SARS-CoV-2 variants, particularly VoCs, is therefore urgently needed.

content/english/highlights/cellular_response.md

@@ -10,6 +10,7 @@ tags: [COVID-19, Proteomics, Signaling pathway, Stype-I interferon regulation]
 aliases:
     - /news/cellular_response
     - /sv/news/cellular_response
+images: [/highlights/banners/cellular_response.png]
 ---
 
 The COVID-19 pandemic has caused an unprecedented global public health challenge, as well as challenged societies and economies over the last years. The COVID-19 disease is caused by the SARS-CoV-2 virus, found to be a highly pathogenic coronavirus. Although SARS-CoV-2 is primarily known to affect the lung, cardiovascular, gastrointestinal, liver, neurological, hematological, and skin manifestations have also been documented in the disease pathology. Research suggests that all these anatomical sites could be vulnerable to the virus.

content/english/highlights/covidtest_spatiotemp_uppsala.md

@@ -7,6 +7,7 @@ banner_large: /highlights/banners/COV_spatiopredict_fig7.png
 banner_caption: "Source: Figure 7 of van Zoest et al. (2022)"
 highlights_topics: [COVID-19, Infectious diseases]
 tags: [COVID-19, Spatio-temportal prediction, Pandemic preparedness]
+images: [/highlights/banners/COV_spatiopredict_fig7.png]
 ---
 
 <script>

content/english/highlights/crimean_congo_interactions.md

@@ -7,6 +7,7 @@ banner_large: /highlights/banners/crimean_congo_interactions_large.jpg
 banner_caption: Fig 3c. from Neogi et al. (2022). Heatmap of significant correlation (adj. p < 0.05) between key metabolic and signaling pathways. Column and row annotation denotes corresponding pathways.
 highlights_topics: [Infectious diseases]
 tags: [Crimean-Congo haemorrhagic fever, CCHFV, Pathogenesis, Host-viral interaction, Drug]
+images: [/highlights/banners/crimean_congo_interactions.jpg]
 ---
 
 The COVID-19 pandemic is now moving into a more endemic phase in Sweden, as well as many other parts of the world. Regardless, SARS-CoV-2 still poses a serious global health threat, particularly when considering the potential effects of novel variants. Continuous pandemic preparedness efforts are therefore warranted. Global preparedness is also beneficial to safeguard against the threat of pandemics caused by other emerging pathogens.

content/english/highlights/drug_repurposing.md

@@ -7,6 +7,7 @@ banner_large: /highlights/banners/drug_repurposing.jpeg
 banner_caption: "Source: Figure 4 of Rivero-García et al. 2021"
 highlights_topics: [COVID-19, Infectious diseases]
 tags: [COVID-19 Drug repurposing, Fostamatinib, Network and module-based perspective]
+images: [/highlights/banners/drug_repurposing_small.jpeg]
 ---
 
 The COVID-19 pandemic has over almost two years challenged global healthcare. Vaccines towards COVID-19 have been developed in record-time but therapeutics to treat the novel disease are still warranted. World-wide efforts to identify new and effective therapeutics candidates for COVID-19 have been going on since the beginning of the pandemic, for example the [Coronavirus Treatment Acceleration Program](https://www.fda.gov/drugs/coronavirus-covid-19-drugs/coronavirus-treatment-acceleration-program-ctap) started by the FDA in the US. The traditional *“one drug—one gene—one disease”* in Drug discovery has been successful in many cases in past but may have economical downsides as well as risk leaving patients suffering from rare conditions with limited therapeutic options. *Polypharmacology* which refers to a drugs' ability to target more than one protein and *drug repurposing ("repositioning")* defined as using an already approved drug for a new therapeutic indication are approaches to mitigate these problems.

content/english/highlights/estimating_impact_mobility_patterns.md

@@ -11,6 +11,7 @@ tags: [COVID-19, SARS-CoV-2 mobility data, Bayesian modelling]
 aliases:
     - /news/estimating_impact_mobility_patterns
     - /sv/news/estimating_impact_mobility_patterns
+images: [/highlights/banners/bryant_elofsson.png]
 ---
 During the Covid-19 pandemic governments across Europe have issued non-pharmaceutical interventions (NPIs), for example social distancing and school closing, to slow down the pandemic. European countries have recommended different NPIs and the effect on mobility patterns vary between countries.
 

content/english/highlights/fragments_nsp10.md

@@ -7,6 +7,7 @@ banner_large: /highlights/banners/fragments_nsp10_large.png
 banner_caption: "Figure 3A from Kozielski et al 2022"
 highlights_topics: [COVID-19, Infectious diseases]
 tags: [COVID-19, SARS-CoV-2 replication, NSP10, Drug therapy, Nano differential scanning fluorometry, X-ray crystallography, Drug therapy]
+images: [/highlights/banners/fragments_nsp10.png]
 ---
 
 The COVID-19 vaccine program is the cornerstone of global pandemic management. Whilst vaccines were rolled out in record-time and have proven very effective, many important research questions remain. For example, there is still some uncertainty regarding the duration of vaccine protection, the optimal intervals for the administration of booster doses, the potential for vaccine escape by novel [*Variants of Concern* (VoCs)](/voc/), among others. These questions, together with the fact that not everyone is able to be vaccinated, mean that the development of new drugs for treating SARS-CoV-2 infections is warranted. These drugs would act as a “second line defense” in the event of vaccine escape, and for individuals that do not respond well to vaccines, and are key for treating those that did not receive the vaccine for any reason.

content/english/highlights/igh_antibody_genes.md

@@ -8,6 +8,7 @@ banner_caption: Graphical abstract (Image courtesy Pushparaj et al. 2023)
 highlights_topics: [COVID-19, Infectious Diseases]
 tags: [SARS-CoV-2, Genotyping, Haplotype analysis, Cryo-EM, IGHV1-69, Variability, Individual response, Infection]
 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."
+images: [/highlights/banners/igh_antibody_genes_small.jpg]
 ---
 
 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.