Adding final changes for editorials

content/english/editorials/_index.md

@@ -1,7 +1,5 @@
 ---
 title: Editorials
-cascade:
-  banner: /img/site_logo/SciLifeLab_logo.svg
 ---
 
 The Editorials are short opinion-style pieces centred around topics related to pandemic preparedness. They can be written by members of the [Portal team](/about/), the [editorial committee](/about/editorial_committee/), or researchers affiliated with a Swedish research organisation. The goal of the editorials is to show the ‘current thinking’ in a given area.

content/english/editorials/influenza.md

@@ -1,25 +1,17 @@
 ---
 title: "Influenza A(H5) virus: A potential pandemic threat"
-date: 2023-10-24
+date: 2023-10-31
 summary: A perspective on the potential for influenza viruses to be the next pandemic threat and how to be better prepared for the next pandemic.
-tags: [Influenza, Pandemic]
+banner: /editorials/topic_influenza.jpg
+#banner_large: /topic_thumbs/topic_influenza.jpg
+banner_caption: A colourised transmission electron microscopic (TEM) image of Avian Influenza A H5N1 viruses (gold) (Credit- CDC).
+tags: [Influenza, Pandemic, pandemic preparedness, avian influenza, zoonoses]
 editorials_topics: [Influenza]
 editorials_authors: [Mahmoud M. Naguib]
 ---
 
-Wild aquatic birds are the natural reservoir for influenza A virus of subtypes H1–H16 and N1–N9 <sup>[4]</sup>, named avian influenza virus. Virus transmission from wildlife reservoirs to domestic animals is a critical step in a chain of events that leads to exposure and infection of humans. This has been exemplified by the recent COVID-19 pandemic, in addition to the influenza A viruses (IAVs) that have caused four pandemics during the last 100 years <sup>[1-3]</sup>. In nature, maintained IAV lineages are adapted to particular host species, thus successful interspecies transmission may be very challenging for the virus <sup>[5]</sup>. The first attention to influenza A(H5) was in the 1990s when the first highly pathogenic avian influenza (HPAI) virus of subtype H5 was recorded in birds and then found in humans in Guangdong province in China. Since then, the H5 virus continued to evolve into 10 clades (0–9) and several subclades based on phylogenetic inference of the hemagglutinin (HA) gene segment <sup>[6]</sup>. During 2020 through 2023, several countries around the globe have suffered from the worst epizootic of HPAI virus ever, causing severe economic losses to the poultry industry, thousands of outbreaks among wild and domestic birds, as well as human cases caused by subtypes of H5N8, H5N6, and H5N1 <sup>[10, 11]</sup>. In addition, the recent HPAI virus of subtype H5 has been reported in a high number of mammalian species and has shown markers for mammalian adaptation <sup>[8]</sup>. Although the total number of H5Nx infections in humans still remains low, as compared to seasonal outbreaks of truly human-adapted influenza viruses, the threat to Public Health remains high due to the extreme case fatality rate of HPAI in humans of up to 60% <sup>[12]</sup>.
+Wild aquatic birds are the natural reservoir for influenza A virus of subtypes H1–H16 and N1–N9 ([Krammer _et al._, 2018](https://www.nature.com/articles/s41572-018-0002-y)), named avian influenza virus. Virus transmission from wildlife reservoirs to domestic animals is a critical step in a chain of events that leads to exposure and infection of humans. This has been exemplified by the recent COVID-19 pandemic, in addition to the influenza A viruses (IAVs) that have caused four pandemics during the last 100 years ([de Wit _et al._, 2016](https://pubmed.ncbi.nlm.nih.gov/27344959/); [Guarner, 2020](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109697/); [Hilgenfeld and Peiris, 2013](https://pubmed.ncbi.nlm.nih.gov/24012996/)). In nature, maintained IAV lineages are adapted to particular host species, thus successful interspecies transmission may be very challenging for the virus ([Subbarao, 2019](https://pubmed.ncbi.nlm.nih.gov/31027299/)). The first attention to influenza A(H5) was in the 1990s when the first highly pathogenic avian influenza (HPAI) virus of subtype H5 was recorded in birds and then found in humans in Guangdong province in China. Since then, the H5 virus continued to evolve into 10 clades (0–9) and several subclades based on phylogenetic inference of the hemagglutinin (HA) gene segment ([Sonnberg _et al._, 2013](https://pubmed.ncbi.nlm.nih.gov/23735535/)). During 2020 through 2023, several countries around the globe have suffered from the worst epizootic of HPAI virus ever, causing severe economic losses to the poultry industry, thousands of outbreaks among wild and domestic birds ([European Centre for Disease Prevention and Control (ECDC), 2023](https://www.ecdc.europa.eu/en/publications-data/avian-influenza-overview-june-september-2023#:~:text=Between%2024%20June%20and%201%20September%202023%2C%20highly%20pathogenic%20avian,few%20HPAI%20virus%20detections%20inland.)), as well as human cases caused by subtypes of H5N8, H5N6, and H5N1 ([European Centre for Disease Prevention and Control (ECDC), 2021](https://www.ecdc.europa.eu/en/publications-data/threat-assessment-first-human-cases-avian-influenza-h5n8); [World Health Organisation (WHO), 2022](https://iris.who.int/bitstream/handle/10665/351652/AI-20220204.pdf?sequence=14&isAllowed=y)). In addition, the recent HPAI virus of subtype H5 has been reported in a high number of mammalian species and has shown markers for mammalian adaptation ([Adlhoch _et al._, 2023](https://www.ecdc.europa.eu/sites/default/files/documents/avian-influenza-overview-march-2023.pdf)). Although the total number of H5Nx infections in humans still remains low, as compared to seasonal outbreaks of truly human-adapted influenza viruses, the threat to Public Health remains high due to the extreme case fatality rate of HPAI in humans of up to 60% ([World Health Organisation (WHO), 2021](<https://www.who.int/publications/m/item/cumulative-number-of-confirmed-human-cases-for-avian-influenza-a(h5n1)-reported-to-who-2003-2021-15-april-2021>)).
 
-Is the influenza A (H5) virus likely to be the cause of the next human pandemic? The currently circulating strain of highly pathogenic avian influenza (HPAI) virus of subtype H5 has shown the ability to cross species barriers; spreading from wild birds to domestic poultry and then eventually to many other mammalian species (for example cats, seals, and minks). There have been sporadic human deaths but, so far, no report of human-to-human virus transmission.  Because of the segmented nature of the influenza virus genome, reassortment (gene exchange) between AIV strains could occur when two different sub- or genotypes co-infect the same cell <sup>[13]</sup>. Reassortment between influenza viruses of animal (avian) and human origin, respectively, preceded the emergence of at least the last three influenza pandemics (H2N2-1957, H3N2-1968, and H1N1-2009) <sup>[14-16]</sup>. During the last few years, an increased level of activity of different novel reassortants of HPAI virus of subtype H5Nx of clade 2.3.4.4 has been reported in many countries <sup>[19-21]</sup>. By late 2021, a novel reassortant virus of the HPAI H5N1 of clade 2.3.4.4b has emerged as a result of a reassortment event between the H5N8 of clade 2.3.4.4b and an unknown virus that donated the N1 gene segment. The HPAI H5N1 viruses currently circulating already underwent multiple reassortments with unknown AIVs to form at least 16 different genotypes. Current evidence suggests that the new H5N1 virus of clade 2.3.4.4 should be considered of low risk to humans. However, co-infection with this HPAI virus and other influenza strains in animals or humans could result in the emergence of novel virus strain(s); having gained the capacity for efficient spread between humans while retaining the highly pathogenic phenotype - the key to becoming a pandemic virus. Therefore, a key question is how to be prepared for the next pandemic.
+Is the influenza A (H5) virus likely to be the cause of the next human pandemic? The currently circulating strain of highly pathogenic avian influenza (HPAI) virus of subtype H5 has shown the ability to cross species barriers; spreading from wild birds to domestic poultry and then eventually to many other mammalian species (for example cats, seals, and minks). There have been sporadic human deaths but, so far, no report of human-to-human virus transmission. Because of the segmented nature of the influenza virus genome, reassortment (gene exchange) between AIV strains could occur when two different sub- or genotypes co-infect the same cell ([Greenbaum _et al._, 2012](https://www.pnas.org/doi/10.1073/pnas.1113300109)). Reassortment between influenza viruses of animal (avian) and human origin, respectively, preceded the emergence of at least the last three influenza pandemics (H2N2-1957, H3N2-1968, and H1N1-2009) ([Horimoto and Kawaoka, 2001](https://pubmed.ncbi.nlm.nih.gov/11148006/); [Katz _et al._, 2009](https://www.sciencedirect.com/science/article/pii/S0032579119391655); [Yen and Webster, 2009](https://pubmed.ncbi.nlm.nih.gov/19768398/)). During the last few years, an increased level of activity of different novel reassortants of HPAI virus of subtype H5Nx of clade 2.3.4.4 has been reported in many countries ([European Centre for Disease Prevention and Control (ECDC), 2023](https://www.ecdc.europa.eu/en/publications-data/avian-influenza-overview-june-september-2023#:~:text=Between%2024%20June%20and%201%20September%202023%2C%20highly%20pathogenic%20avian,few%20HPAI%20virus%20detections%20inland.); [Xie _et al._, 2023](<https://www.nature.com/articles/s41586-023-06631-2#:~:text=Highly%20pathogenic%20avian%20influenza%20(HPAI,mitigation%20strategies%20still%20remain%20unclear.)>)). By late 2021, a novel reassortant virus of the HPAI H5N1 of clade 2.3.4.4b has emerged as a result of a reassortment event between the H5N8 of clade 2.3.4.4b and an unknown virus that donated the N1 gene segment. The HPAI H5N1 viruses currently circulating already underwent multiple reassortments with unknown AIVs to form at least 16 different genotypes. Current evidence suggests that the new H5N1 virus of clade 2.3.4.4 should be considered of low risk to humans. However, co-infection with this HPAI virus and other influenza strains in animals or humans could result in the emergence of novel virus strain(s); having gained the capacity for efficient spread between humans while retaining the highly pathogenic phenotype - the key to becoming a pandemic virus. Therefore, a key question is how to be prepared for the next pandemic.
 
 How to be better prepared for the next pandemic? Sustained genetic monitoring for the detection of novel influenza strains, coupled with early reporting and sharing sequencing and surveillance data between different authorities, collectively constitute pivotal strategies for better pandemic preparedness. Ultimately, the One Health approach is imperative to enhance the prospects of early identification of zoonotic pathogens with pandemic potential and thus preventing their spillover into the human population.
-
-#### References
-
-1. Guarner J. 2020. Three Emerging Coronaviruses in Two Decades. Am J Clin Pathol 153:420-421.
-2. de Wit E, van Doremalen N, Falzarano D, Munster VJ. 2016. SARS and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol 14:523-34.
-3. Hilgenfeld R, Peiris M. 2013. From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses. Antiviral Res 100:286-95.
-4. Olsen B, Munster VJ, Wallensten A, Waldenstrom J, Osterhaus AD, Fouchier RA. 2006. Global patterns of influenza a virus in wild birds. Science 312:384-8.
-5. Kuiken T, Holmes EC, McCauley J, Rimmelzwaan GF, Williams CS, Grenfell BT. 2006. Host species barriers to influenza virus infections. Science 312:394-7.
-6. Sonnberg S, Webby RJ, Webster RG. 2013. Natural history of highly pathogenic avian influenza H5N1. Virus research 178:63-77.
-7. Authority EFS, Prevention ECfD, Control, Influenza EURLfA, Adlhoch C, Fusaro A, Gonzales JL, Kuiken T, Marangon S, Mirinaviciute G, Niqueux É, Stahl K, Staubach C, Terregino C, Broglia A, Baldinelli F. 2023. Avian influenza overview December 2022 – March 2023. EFSA Journal 21:e07917.
-8. Adlhoch C, Fusaro A, Gonzales JL, Kuiken T, Marangon S, Mirinaviciute G, Niqueux É, Stahl K, Staubach C, Terregino C, Broglia A, Baldinelli F. 2023. Avian influenza overview December 2022 - March 2023. Efsa j 21:e07917.

content/english/editorials/pandemic_data_sharing.md

@@ -1,8 +1,19 @@
 ---
 title: "The pandemic has paved the way for data sharing"
-date: 2023-10-24
+date: 2023-10-31
 summary: Details the importance of sharing data, tools, and techniques in the COVID-19 pandemic and for future pandemic preparedness. Highlights how this applies to this year’s Nobel Prize in Medicine.
-tags: [Pandemic, Data sharing]
+banner: /editorials/topic_covid.jpg
+#banner_large: updates/banners/topic_covid.jpg
+banner_caption: Ultrastructural morphology exhibited by coronaviruses (Credit - CDC).
+tags: [
+    Pandemic,
+    Data sharing,
+    Nobel prize,
+    # Coronaviruses,
+    # SARS-CoV-2,
+    # Covid,
+    pandemic preparedness,
+  ]
 editorials_topics: [COVID-19]
 editorials_authors: [Katarina Öjefors Stark]
 ---
@@ -11,6 +22,10 @@ The COVID-19 pandemic has had a major impact on society. It has caused changes i
 
 The Swedish research community quickly became involved in research and research collaborations during the pandemic. This was made possible by the rapid response from the researchers themselves, as well as funders, government, and health agencies. There has therefore been significant output (e.g. publications, preprints, datasets) from the Swedish research community throughout the pandemic. This has constituted a major contribution to global knowledge about COVID-19, e.g. in how to control outbreaks, why responses to the virus and vaccinations differ between individuals, and the pathogenesis of SARS-CoV-2 strains.
 
-The [Nobel Prize in Medicine](https://www.nobelprize.org/prizes/medicine/2023/press-release/) 2023 was awarded to two Nobel Laureates (Drs Karikó and Weissmann, both working in the USA). Their [2005 article](https://doi.org/10.1016/j.immuni.2005.06.008) in Immunity deepened our understanding of how mRNA interacts with the human immune system. This information was critical in the development of mRNA vaccines against SARS-CoV-2 during the COVID-19 pandemic. In future, the same mRNA technique could be used against other potential pandemic threats, like influenza.
+The [Nobel Prize in Medicine](https://www.nobelprize.org/prizes/medicine/2023/press-release/) 2023 was awarded to two Nobel Laureates (Drs Karikó and Weissmann, both working in the USA). Their article in Immunity ([Karikó _et al._, 2005](https://www.sciencedirect.com/science/article/pii/S1074761305002116?via%3Dihub)) deepened our understanding of how mRNA interacts with the human immune system. This information was critical in the development of mRNA vaccines against SARS-CoV-2 during the COVID-19 pandemic. In future, the same mRNA technique could be used against other potential pandemic threats, like influenza.
 
 It was, in part, the unprecedented levels of sharing and collaboration that enabled this research to be turned into the production of SARS-CoV-2 so quickly during the pandemic. This means that it forms a crucial part of pandemic preparedness efforts, alongside things such as the development of novel vaccines. It is crucial that we continue to raise the importance of sharing techniques, tools, and data in order to ensure that we are able to mount an even quicker response to the next pandemic. Many efforts are now focused on this, including the [Pandemic Laboratory Preparedness Program](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/), of which the Swedish Pathogens Portal is a central part.
+
+#### References
+
+Karikó, K., Buckstein, M., Ni, H., Weissman, D. (2005). Suppression of RNA Recognition by Toll-like Receptors: The Impact of Nucleoside Modification and the Evolutionary Origin of RNA. _Immunity_, 23:165-175.

content/english/highlights/_index.md

@@ -5,16 +5,16 @@ cascade:
   banner_caption: "3D rendering of a SARS-CoV-2 virion."
   toc: false
 menu:
-    homepage_highlights:
-        name: Data highlights
-        identifier: highlights
-        post: Recent research that openly shares data and promote data reuse. <a href="/highlights/">See all highlights <i class="bi bi-arrow-right-circle-fill"></i></a>
+  homepage_highlights:
+    name: Data highlights
+    identifier: highlights
+    post: Recent research that openly shares data and promote data reuse. <a href="/highlights/">See all highlights <i class="bi bi-arrow-right-circle-fill"></i></a>
 aliases:
-      - /news
-      - /sv/news
-      - /highlights_topics/
-      - /highlights_vocs/
+  - /news
+  - /sv/news
+  - /highlights_topics/
+  - /highlights_vocs/
 recaptcha: true
 ---
 
-The *Data Highlights* section showcases recently published datasets relevant to pandemic preparedness research by researchers affiliated with a Swedish research institute. Specifically, in our case we write about COVID-19 and SARS-CoV-2, infectious diseases in general, and antibiotic resistance. The goal is to highlight openly shared data that can potentially be used by many other researchers to make further discoveries.
+The _Data Highlights_ section showcases recently published datasets relevant to pandemic preparedness research by researchers affiliated with a Swedish research institute. Specifically, in our case we write about e.g. COVID-19 and SARS-CoV-2, infectious diseases in general, and antibiotic resistance. The goal is to highlight openly shared data that can potentially be used by many other researchers to make further discoveries.

content/english/updates/Influenza_topic.md

@@ -0,0 +1,11 @@
+---
+title: Influenza added as a topic
+date: 2023-10-31
+summary: The content of the portal is broadly organised into 'topics' related to pathogens and pandemic preparedness. Influenza is our latest topic.
+banner: /updates/banners/topic_influenza.jpg
+banner_caption: Avian influenza virus image (Photo credit- CDC).
+---
+
+It is possible to filter the content of this portal according to [topics](/topics/) related to infectious disease and pandemic preparedness. For each [topic](/topics/), we provide some basic background information and then show any content related to that topic (including, e.g. highlights and dashboards). We have been adding new topics over time, and expanding the content within them. [Influenza](/topics/influenza/) is the latest topic to be added.
+
+The influenza topic currently includes a dashboard and an editorial. The dashboard is the [wastewater epidemiology dashboard](/dashboards/wastewater/), which has recently been expanded to include data about two influenza viruses. This dashboard includes data and information related to the levels of viral genomes in wastewater (often termed sewage) from multiple research groups across Sweden. The levels of viruses in wastewater have been shown to be predictive of future outbreaks. For example, [Wang et al. (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/) showed that the level of SARS-CoV-2 viral genomes in wastewater increased 1-2 weeks before there was an increase in the number of hospitalised COVID-19 patients. This means that it can be used to inform the decisions of officials when preparing for an outbreak. At present, the dashboard includes data on [SARS-CoV-2](/dashboards/wastewater/covid_quantification/), [enteric viruses](/dashboards/wastewater/enteric_quantification/), and [influenza](/dashboards/wastewater/influenza_quantification/), and covers areas inhabited by 34% of the Swedish population. The [editorial](/editorials/) on influenza was written by [Mahmoud Naguib](https://www.katalog.uu.se/profile/?id=N17-1318), a researcher working on influenza at Uppsala University. This [new editorial](/editorials/influenza) discusses the potential for influenza viruses to be the next pandemic threat and how we might prepare to tackle that threat.