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Article ; Online: Multiplex Serology for Sensitive and Specific Flavivirus IgG Detection: Addition of Envelope Protein Domain III to NS1 Increases Sensitivity for Tick-Borne Encephalitis Virus IgG Detection.

Valle, Coralie / Shrestha, Sandhya / Godeke, Gert-Jan / Hoogerwerf, Marieke N / Reimerink, Johan / Eggink, Dirk / Reusken, Chantal

Viruses

2024 Volume 16, Issue 2

Abstract: Tick-borne encephalitis is a vaccine-preventable disease of concern for public health in large parts of Europe, with EU notification rates increasing since 2018. It is caused by the orthoflavivirus tick-borne encephalitis virus (TBEV) and a diagnosis of ... ...

Abstract	Tick-borne encephalitis is a vaccine-preventable disease of concern for public health in large parts of Europe, with EU notification rates increasing since 2018. It is caused by the orthoflavivirus tick-borne encephalitis virus (TBEV) and a diagnosis of infection is mainly based on serology due to its short viremic phase, often before symptom onset. The interpretation of TBEV serology is hampered by a history of orthoflavivirus vaccination and by previous infections with related orthoflaviviruses. Here, we sought to improve TBEV sero-diagnostics using an antigen combination of in-house expressed NS1 and EDIII in a multiplex, low-specimen-volume set-up for the detection of immune responses to TBEV and other clinically important orthoflaviviruses (i.e., West Nile virus, dengue virus, Japanese encephalitis virus, Usutu virus and Zika virus). We show that the combined use of NS1 and EDIII results in both a specific and sensitive test for the detection of TBEV IgG for patient diagnostics, vaccination responses and in seroprevalence studies. This novel approach potentially allows for a low volume-based, simultaneous analysis of IgG responses to a range of orthoflaviviruses with overlapping geographic circulations and clinical manifestations.
MeSH term(s)	Humans ; Encephalitis Viruses, Tick-Borne ; Protein Domains ; Seroepidemiologic Studies ; Antibodies, Viral ; Flavivirus Infections/diagnosis ; Encephalitis, Tick-Borne ; Encephalitis, Viral ; Immunoglobulin G ; Zika Virus ; Zika Virus Infection
Chemical Substances	Antibodies, Viral ; Immunoglobulin G
Language	English
Publishing date	2024-02-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v16020286
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Asymmetrical Biantennary Glycans Prepared by a Stop-and-Go Strategy Reveal Receptor Binding Evolution of Human Influenza A Viruses.

Ma, Shengzhou / Liu, Lin / Eggink, Dirk / Herfst, Sander / Fouchier, Ron A M / de Vries, Robert P / Boons, Geert-Jan

JACS Au

2024 Volume 4, Issue 2, Page(s) 607–618

Abstract: Glycan binding properties of respiratory viruses have been difficult to probe due to a lack of biologically relevant glycans for binding studies. Here, a stop-and-go chemoenzymatic methodology is presented that gave access to a panel of 32 asymmetrical ... ...

Abstract	Glycan binding properties of respiratory viruses have been difficult to probe due to a lack of biologically relevant glycans for binding studies. Here, a stop-and-go chemoenzymatic methodology is presented that gave access to a panel of 32 asymmetrical biantennary
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Journal Article
ISSN	2691-3704
ISSN (online)	2691-3704
DOI	10.1021/jacsau.3c00695
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Article: Evolution of transient RNA structure-RNA polymerase interactions in respiratory RNA virus genomes.

Rigby, Charlotte / Sabsay, Kimberly / Bisht, Karishma / Eggink, Dirk / Jalal, Hamid / Te Velthuis, Aartjan J W

bioRxiv : the preprint server for biology

2023

Abstract: RNA viruses are important human pathogens that cause seasonal epidemics and occasional pandemics. Examples are influenza A viruses (IAV) and coronaviruses (CoV). When emerging IAV and CoV spill over to humans, they adapt to evade immune responses and ... ...

Abstract	RNA viruses are important human pathogens that cause seasonal epidemics and occasional pandemics. Examples are influenza A viruses (IAV) and coronaviruses (CoV). When emerging IAV and CoV spill over to humans, they adapt to evade immune responses and optimize their replication and spread in human cells. In IAV, adaptation occurs in all viral proteins, including the viral ribonucleoprotein (RNP) complex. RNPs consists of a copy of the viral RNA polymerase, a double-helical coil of nucleoprotein, and one of the eight segments of the IAV RNA genome. The RNA segments and their transcripts are partially structured to coordinate the packaging of the viral genome and modulate viral mRNA translation. In addition, RNA structures can affect the efficiency of viral RNA synthesis and the activation of host innate immune response. Here, we investigated if RNA structures that modulate IAV replication processivity, so called template loops (t-loops), vary during the adaptation of pandemic and emerging IAV to humans. Using cell culture-based replication assays and
Language	English
Publishing date	2023-08-02
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.25.542331
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Article ; Online: Assessment of hybrid population immunity to SARS-CoV-2 following breakthrough infections of distinct SARS-CoV-2 variants by the detection of antibodies to nucleoprotein.

den Hartog, Gerco / Andeweg, Stijn P / Hoeve, Christina E / Smits, Gaby / Voordouw, Bettie / Eggink, Dirk / Knol, Mirjam J / van Binnendijk, Robert S

Scientific reports

2023 Volume 13, Issue 1, Page(s) 18394

Abstract: Immunity induced by vaccination and infection, referred to as hybrid immunity, provides better protection against SARS-CoV-2 infections compared to immunity induced by vaccinations alone. To assess the development of hybrid immunity we investigated the ... ...

Abstract	Immunity induced by vaccination and infection, referred to as hybrid immunity, provides better protection against SARS-CoV-2 infections compared to immunity induced by vaccinations alone. To assess the development of hybrid immunity we investigated the induction of Nucleoprotein-specific antibodies in PCR-confirmed infections by Delta or Omicron in vaccinated individuals (n = 520). Eighty-two percent of the participants with a breakthrough infection reached N-seropositivity. N-seropositivity was accompanied by Spike S1 antibody boosting, and independent of vaccination status or virus variant. Following the infection relatively more antibodies to the infecting virus variant were detected. In conclusion, these data show that hybrid immunity through breakthrough infections is hallmarked by Nucleoprotein antibodies and broadening of the Spike antibody repertoire. Exposure to future SARS-CoV-2 variants may therefore continue to maintain and broaden vaccine-induced population immunity.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19 ; Breakthrough Infections ; Antibodies ; Nucleoproteins/genetics ; Vaccination ; Antibodies, Viral ; Antibodies, Neutralizing
Chemical Substances	Antibodies ; Nucleoproteins ; Antibodies, Viral ; Antibodies, Neutralizing
Language	English
Publishing date	2023-10-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-45718-8
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Article: Evolution of transient RNA structure-RNA polymerase interactions in respiratory RNA virus genomes.

Rigby, Charlotte V / Sabsay, Kimberly R / Bisht, Karishma / Eggink, Dirk / Jalal, Hamid / Te Velthuis, Aartjan J W

Virus evolution

2023 Volume 9, Issue 2, Page(s) vead056

Abstract	RNA viruses are important human pathogens that cause seasonal epidemics and occasional pandemics. Examples are influenza A viruses (IAV) and coronaviruses (CoV). When emerging IAV and CoV spill over to humans, they adapt to evade immune responses and optimize their replication and spread in human cells. In IAV, adaptation occurs in all viral proteins, including the viral ribonucleoprotein (RNP) complex. RNPs consist of a copy of the viral RNA polymerase, a double-helical coil of nucleoprotein, and one of the eight segments of the IAV RNA genome. The RNA segments and their transcripts are partially structured to coordinate the packaging of the viral genome and modulate viral mRNA translation. In addition, RNA structures can affect the efficiency of viral RNA synthesis and the activation of host innate immune response. Here, we investigated if RNA structures that modulate IAV replication processivity, so-called template loops (t-loops), vary during the adaptation of pandemic and emerging IAV to humans. Using cell culture-based replication assays and
Language	English
Publishing date	2023-08-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/vead056
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Article: Asymmetrical Bi-antennary Glycans Prepared by a Stop-and-Go Strategy Reveal Receptor Binding Evolution of Human Influenza A Viruses.

Ma, Shengzhou / Liu, Lin / Eggink, Dirk / Herfst, Sander / Fouchier, Ron A M / de Vries, Robert P / Boons, Geert-Jan

bioRxiv : the preprint server for biology

2023

Abstract: Glycan binding properties of respiratory viruses have been difficult to probe due to a lack of biological relevant glycans for binding studies. Here, a stop-and-go chemoenzymatic methodology is presented that gave access to a panel of 32 asymmetrical bi- ... ...

Abstract	Glycan binding properties of respiratory viruses have been difficult to probe due to a lack of biological relevant glycans for binding studies. Here, a stop-and-go chemoenzymatic methodology is presented that gave access to a panel of 32 asymmetrical bi-antennary
Language	English
Publishing date	2023-11-09
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.08.566285
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Article ; Online: High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment.

Sluimer, John / van den Akker, Willem M R / Goderski, Gabriel / Swart, Arno / van der Veer, Bas / Cremer, Jeroen / Chung, Ngoc Hoa / Molenkamp, Richard / Voermans, Jolanda / Guldemeester, Judith / Eggink, Dirk / Presser, Lance D / Meijer, Adam

Scientific reports

2024 Volume 14, Issue 1, Page(s) 1378

Abstract: A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This ... ...

Abstract	A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; COVID-19/epidemiology ; Laboratories ; Clinical Laboratory Techniques/methods ; COVID-19 Testing ; Benchmarking ; Pathology, Molecular ; Sensitivity and Specificity
Language	English
Publishing date	2024-01-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-50912-9
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Article ; Online: Effectiveness of Omicron XBB.1.5 vaccine against infection with SARS-CoV-2 Omicron XBB and JN.1 variants, prospective cohort study, the Netherlands, October 2023 to January 2024.

Huiberts, Anne J / Hoeve, Christina E / de Gier, Brechje / Cremer, Jeroen / van der Veer, Bas / de Melker, Hester E / van de Wijgert, Janneke Hhm / van den Hof, Susan / Eggink, Dirk / Knol, Mirjam J

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2024 Volume 29, Issue 10

Abstract: We estimated vaccine effectiveness (VE) of SARS-CoV-2 Omicron XBB.1.5 vaccination against self-reported infection between 9 October 2023 and 9 January 2024 in 23,895 XBB.1.5 vaccine-eligible adults who had previously received at least one booster. VE was ...

Abstract	We estimated vaccine effectiveness (VE) of SARS-CoV-2 Omicron XBB.1.5 vaccination against self-reported infection between 9 October 2023 and 9 January 2024 in 23,895 XBB.1.5 vaccine-eligible adults who had previously received at least one booster. VE was 41% (95% CI: 23-55) in 18-59-year-olds and 50% (95% CI: 44-56) in 60-85-year-olds. Sequencing data suggest lower protection against the BA.2.86 (including JN.1) variant from recent prior infection (OR = 2.8; 95% CI:1.2-6.5) and, not statistically significant, from XBB.1.5 vaccination (OR = 1.5; 95% CI:0.8-2.6).
MeSH term(s)	Adult ; Humans ; Netherlands/epidemiology ; SARS-CoV-2/genetics ; Prospective Studies ; COVID-19/prevention & control ; Vaccines
Chemical Substances	Vaccines
Language	English
Publishing date	2024-02-22
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2024.29.10.2400109
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Article ; Online: Increased incidence of

Bolluyt, Dita C / Euser, Sjoerd M / Souverein, Dennis / van Rossum, Annemarie Mc / Kalpoe, Jayant / van Westreenen, Mireille / Goeijenbier, Marco / Snijders, Dominic / Eggink, Dirk / Jongenotter, Femke / van Lelyveld, Steven Fl / van Houten, Marlies A

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2024 Volume 29, Issue 4

Abstract: Mycoplasma ... ...

Abstract	Mycoplasma pneumoniae
MeSH term(s)	Child ; Humans ; Adult ; Pneumonia, Mycoplasma/epidemiology ; Pneumonia, Mycoplasma/diagnosis ; Netherlands/epidemiology ; Incidence ; Mycoplasma pneumoniae ; Hospitals
Language	English
Publishing date	2024-01-11
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2024.29.4.2300724
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Article: Possible host-adaptation of SARS-CoV-2 due to improved ACE2 receptor binding in mink.

Welkers, Matthijs R A / Han, Alvin X / Reusken, Chantal B E M / Eggink, Dirk

Virus evolution

2021 Volume 7, Issue 1, Page(s) veaa094

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections on mink farms are increasingly observed in several countries, leading to the massive culling of animals on affected farms. Recent studies showed multiple (anthropo)zoonotic ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections on mink farms are increasingly observed in several countries, leading to the massive culling of animals on affected farms. Recent studies showed multiple (anthropo)zoonotic transmission events between humans and mink on these farms. Mink-derived SARS-CoV-2 sequences from The Netherlands and Denmark contain multiple substitutions in the S protein receptor binding domain (RBD). Molecular modeling showed that these substitutions increase the mean binding energy, suggestive of potential adaptation of the SARS-CoV-2 S protein to the mink angiotensin-converting enzyme 2 (ACE2) receptor. These substitutions could possibly also impact human ACE2 binding affinity as well as humoral immune responses directed to the RBD region of the SARS-CoV-2 S protein in humans. We wish to highlight these observations to raise awareness and urge for the continued surveillance of mink (and other animal)-related infections.
Language	English
Publishing date	2021-01-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/veaa094
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