Explanipedia

Changes in the Streptococcus pneumoniae population responsible for invasive disease of young children after the implementation of conjugated vaccines in the National Immunization Program in Poland Open

Izabela Wróbel-Pawelczyk, Agnieszka Gołębiewska, Patrycja Ronkiewicz, Marlena Kiedrowska, K. Błaszczyk , et al. · 2025

In the first three years after the introduction of the PCV10 into the Polish NIP significant reduction in the prevalence of PCV10-VTs was observed. Molecular characterization of the studied population allowed us to link the observed change…

Case series of the first five human infections with monkeypox virus clade Ib and report on the public health response, United Kingdom, October to November 2024 Open

Muhammad Nadeem Alvi, Merav Kliner, William Welfare, N Claire Gordon, Sherine Thomas , et al. · 2025

We report two importations of monkeypox virus clade Ib infection to the United Kingdom in 2024. The first was a traveller returning from Tanzania, Rwanda and Uganda, the second from Uganda. Both presented with fever and typical skin lesion…

Descriptive Epidemiology of Travel and Non‐Travel Related SARS‐CoV‐2 Gamma (P.1/501Y.V3) Variant Cases in England, 2021 Open

Nurin Abdul Aziz, Katherine A. Twohig, Mary Sinnathamby, Asad Zaidi, Shirin Aliabadi , et al. · 2024

The Gamma (P.1/501Y.V3) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected through whole-genome sequencing (WGS) in Japan in early January 2021 among a group of travellers arriving from Brazil [1]. T…

A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK Open

Rachel Colquhoun, Áine O’Toole, Verity Hill, JT McCrone, Xiaoyu Yu , et al. · 2024

In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale genomic surveillance in the UK. By the end of 2020, 49% of all SARS-CoV-2 genome sequenc…

APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016 Open

Áine O’Toole, Richard A. Neher, Nnaemeka Ndodo, Vítor Borges, Ben Gannon , et al. · 2023

Historically, mpox has been characterized as an endemic zoonotic disease that transmits through contact with the reservoir rodent host in West and Central Africa. However, in May 2022, human cases of mpox were detected spreading internatio…

Descriptive epidemiology of SARS‐CoV‐2 Beta (B.1.351) variant cases in England, December 2020 to June 2022 Open

Mary Sinnathamby, Asad Zaidi, Katherine A. Twohig, Shirin Aliabadi, Nurin Abdul Aziz , et al. · 2023

The emergence of the SARS‐CoV‐2 Beta (B.1.351) variant in November 2020 raised concerns of increased transmissibility and severity. We describe the epidemiology of 949 confirmed SARS‐CoV‐2 Beta variant cases in England, identified between …

Vaccine effectiveness against hospitalisation estimated using a test-negative case-control study design, and comparative odds of hospital admission and severe outcomes with COVID-19 sub-lineages BQ.1, CH.1.1. and XBB.1.5 in England Open

Freja Kirsebom, Katie Harman, Rachel Lunt, Nick Andrews, Natalie Groves , et al. · 2023

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High attack rate in a large care home outbreak of SARS-CoV-2 BA.2.86, East of England, August 2023 Open

Lucy Reeve, Elise Tessier, Amy Trindall, Nurin Abdul Aziz, Nick Andrews , et al. · 2023

We investigated an outbreak of SARS-CoV-2 variant BA.2.86 in an East of England care home. We identified 45 infections (33 residents, 12 staff), among 38 residents and 66 staff. Twenty-nine of 43 PCR swabs were sequenced, all of which were…

Vaccine effectiveness against hospitalisation and comparative odds of hospital admission and severe outcomes with BQ.1, CH.1.1. and XBB.1.5 in England Open

Freja Kirsebom, Katie Harman, Rachel Lunt, Nick Andrews, Natalie Groves , et al. · 2023

Background Since the first emergence of Omicron BA.1 in England in November 2021, numerous sub-lineages have evolved. In September 2022, BA.5 dominated. The prevalence of BQ.1 increased from October, while the prevalence of CH.1.1 and XBB.…

Household transmission of non-toxigenic diphtheria toxin gene-bearing Corynebacterium diphtheriae following a cluster of cutaneous cases in a specialist outpatient setting Open

Norman K. Fry, Ellen Pringle, William Newsholme, Margot Nicholls, Jim Stephenson , et al. · 2023

Introduction. Combination of PCR and Elek testing to identify toxigenic corynebacteria has revealed organisms described as non-toxigenic toxin-gene bearing (NTTB) Corynebacterium diphtheriae or C. ulcerans (i.e. PCR tox positive; Elek nega…

Generation of SARS-CoV-2 escape mutations by monoclonal antibody therapy Open

Manon Ragonnet‐Cronin, Rungtiwa Nutalai, Jiandong Huo, Aiste Dijokaite-Guraliuc, Raksha Das , et al. · 2023

Comparison of the risk of hospitalisation among BA.1 and BA.2 COVID‐19 cases treated with sotrovimab in the community in England Open

Katie Harman, Sophie Nash, Harriet Webster, Natalie Groves, Jo Hardstaff , et al. · 2023

There are concerns that sotrovimab has reduced efficacy at reducing hospitalisation risk against the BA.2 sub‐lineage of the Omicron SARS‐CoV‐2 variant. We performed a retrospective cohort (n = 8850) study of individuals treated with sotro…

Risk of severe outcomes among SARS-CoV-2 Omicron BA.4 and BA.5 cases compared to BA.2 cases in England Open

Nurin Abdul Aziz, Sophie Nash, Asad Zaidi, Tommy Nyberg, Natalie Groves , et al. · 2023

Clade IIb A.3 monkeypox virus: an imported lineage during a large global outbreak Open

Stephen Woolley, Rebecca Lester, Karen Devine, Clare E. Warrell, Natalie Groves , et al. · 2023

Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016 Open

Áine O’Toole, Richard A. Neher, Nnaemeka Ndodo, Vítor Borges, Ben Gannon , et al. · 2023

Mpox is often described as being endemic in West and Central Africa as a zoonotic disease that transmits through contact with the reservoir rodent host, likely a species of African squirrel. In May 2022, human cases of Mpox were detected s…

Comparative transmission of SARS-CoV-2 Omicron (B.1.1.529) and Delta (B.1.617.2) variants and the impact of vaccination: national cohort study, England Open

Hester Allen, Elise Tessier, Charlie Turner, Charlotte Anderson, Paula Blomquist , et al. · 2023

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (B.1.1.529) rapidly replaced Delta (B.1.617.2) to become dominant in England. Our study assessed differences in transmission between Omicron and Delta using t…

Representativeness of whole-genome sequencing approaches in England: the importance for understanding inequalities associated with SARS-CoV-2 infection Open

Katherine A. Twohig, Katie Harman, Asad Zaidi, Shirin Aliabadi, Sophie Nash , et al. · 2023

Whole-genome sequencing (WGS) information has played a crucial role in the SARS-CoV-2 (COVID-19) pandemic by providing evidence about variants to inform public health policy. The purpose of this study was to assess the representativeness o…

PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data Open

Carmen Sheppard, Sam Manna, Natalie Groves, David Litt, Zahin Amin‐Chowdhury , et al. · 2022

Determination of serotypes of Streptococcus pneumoniae is essential for monitoring current vaccine programmes. Since October 2017, pneumococcal serotypes in England have been derived from whole genome sequencing (WGS) data using our bioinf…

Effectiveness of the COVID-19 vaccines against hospitalisation with Omicron sub-lineages BA.4 and BA.5 in England Open

Freja Kirsebom, Nick Andrews, Julia Stowe, Natalie Groves, Meera Chand , et al. · 2022

Comparison of the risk of hospitalisation among BA.1 and BA.2 COVID-19 cases treated with Sotrovimab in the community in England Open

Katie Harman, Sophie Nash, Harriet Webster, Natalie Groves, Jo Hardstaff , et al. · 2022

Objectives Sotrovimab is one of several therapeutic agents that have been licensed to treat people at risk of severe outcomes following COVID-19 infection. However, there are concerns that it has reduced efficacy to treat people with the B…

Hospitalisation and mortality risk of SARS-COV-2 variant omicron sub-lineage BA.2 compared to BA.1 in England Open

Harriet Webster, Tommy Nyberg, Mary Sinnathamby, Nurin Abdul Aziz, Neil M. Ferguson , et al. · 2022

The Omicron variant of SARS-CoV-2 became the globally dominant variant in early 2022. A sub-lineage of the Omicron variant (BA.2) was identified in England in January 2022. Here, we investigated hospitalisation and mortality risks of COVID…

Genome-first detection of emerging resistance to novel therapeutic agents for SARS-CoV-2 Open

Manon Ragonnet‐Cronin, Rungtiwa Nutalai, Jiandong Huo, Aiste Dijokaite-Guraliuc, Raksha Das , et al. · 2022

Summary Some COVID-19 patients are unable to clear their infection or are at risk of severe disease, requiring treatment with neutralising monoclonal antibodies (nmAb) and/or antivirals. The rapid roll-out of novel therapeutics means there…

The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK Open

Verity Hill, Louis du Plessis, Thomas P. Peacock, Dinesh Aggarwal, Rachel Colquhoun , et al. · 2022

The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered in December 2020, it spread rapidly and caused large w…

SARS-CoV-2 Delta–Omicron Recombinant Viruses, United States Open

Kristine A. Lacek, Benjamin L. Rambo‐Martin, Dhwani Batra, Xiaoyu Zheng, Norman Hassell , et al. · 2022

To detect new and changing SARS-CoV-2 variants, we investigated candidate Delta-Omicron recombinant genomes from Centers for Disease Control and Prevention national genomic surveillance. Laboratory and bioinformatic investigations identifi…

Descriptive Epidemiology of SARS-CoV-2 Gamma (P.1/501Y.V3) variant cases in England, August 2021 Open

Nurin Abdul Aziz, Katherine A. Twohig, Mary Sinnathamby, Asad Zaidi, Shirin Aliabadi , et al. · 2022

Purpose The Gamma variant of SARS-CoV-2, first detected in travellers from Brazil, was found to have high transmissibility and virulence; following this finding, this paper aims to describe the epidemiology of Gamma cases in England from i…

COVID-19 vaccine effectiveness against the omicron (BA.2) variant in England Open

Freja Kirsebom, Nick Andrews, Julia Stowe, Samuel Toffa, Ruchira Sachdeva , et al. · 2022

COVID-19 Vaccine Effectiveness against the Omicron BA.2 variant in England Open

Freja Kirsebom, Nick Andrews, Julia Stowe, Samuel Toffa, Ruchira Sachdeva , et al. · 2022

The BA.1 sub-lineage of the Omicron (B.1.1.529) variant, first detected in the UK in mid-November 2021, rapidly became the dominant strain partly due to reduced vaccine effectiveness. An increase in a second Omicron sub-lineage BA.2 was ob…

The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK Open

Verity Hill, Louis du Plessis, Thomas P. Peacock, Dinesh Aggarwal, Rachel Colquhoun , et al. · 2022

The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organisation (WHO) as Alpha. Originating in early Autumn but discovered in December 2020, it spread rapidly and caused l…

Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission Open

Dinesh Aggarwal, Andrew J. Page, Ulf Schaefer, George M. Savva, Richard Myers , et al. · 2022

Comparative transmission of SARS-CoV-2 Omicron (B.1.1.529) and Delta (B.1.617.2) variants and the impact of vaccination: national cohort study, England Open

Hester Allen, Elise Tessier, Charlie Turner, Charlotte Anderson, Paula Blomquist , et al. · 2022

Summary Background The SARS-CoV-2 Omicron variant (B.1.1.529) has rapidly replaced the Delta variant (B.1.617.2) to become dominant in England. This epidemiological study assessed differences in transmissibility between the Omicron and Del…

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