Christopher H. Tomkins-Tinch
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View article: Genomic epidemiology uncovers the origin of the mpox epidemic in Sierra Leone
Genomic epidemiology uncovers the origin of the mpox epidemic in Sierra Leone Open
In January 2025, Sierra Leone reported its first mpox case in eight years, followed by a rapid nationwide surge that made it the epicenter of the continental mpox virus (MPXV) Clade IIb A.2.2 outbreak, with more than 5,000 confirmed cases …
View article: Genomics reveals zoonotic and sustained human mpox spread in West Africa
Genomics reveals zoonotic and sustained human mpox spread in West Africa Open
Five years before the 2022 multi-country mpox outbreak, Nigeria and Cameroon reported their first cases in more than three decades 1,2 . Whereas the outbreak in Nigeria is recognized as an ongoing human epidemic, the drivers of the resurge…
View article: Polyphonia: detecting inter-sample contamination in viral genomic sequencing data
Polyphonia: detecting inter-sample contamination in viral genomic sequencing data Open
Summary In viral genomic research and surveillance, inter-sample contamination can affect variant detection, analysis of within-host evolution, outbreak reconstruction, and detection of superinfections and recombination events. While sampl…
View article: Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans
Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans Open
Five years before the 2022–2023 global mpox outbreak Nigeria reported its first cases in nearly 40 years, with the ongoing epidemic since driven by sustained human-to-human transmission. However, limited genomic data has left questions abo…
View article: Molecular epidemiology of recurrent zoonotic transmission of mpox virus in West Africa
Molecular epidemiology of recurrent zoonotic transmission of mpox virus in West Africa Open
Nigeria and Cameroon reported their first mpox cases in over three decades in 2017 and 2018 respectively. The outbreak in Nigeria is recognised as an ongoing human epidemic. However, owing to sparse surveillance and genomic data, it is not…
View article: Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems
Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems Open
The COVID-19 pandemic has profoundly impacted health systems globally and robust surveillance has been critical for pandemic control, however not all countries can currently sustain community pathogen surveillance programs. Wastewater surv…
View article: Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria
Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria Open
View article: Utilizing river and wastewater as a SARS-CoV-2 surveillance tool to predict trends and identify variants of concern in settings with limited formal sewage systems.
Utilizing river and wastewater as a SARS-CoV-2 surveillance tool to predict trends and identify variants of concern in settings with limited formal sewage systems. Open
The COVID-19 pandemic continues to impact health systems globally and robust surveillance is critical for pandemic control, however not all countries can sustain community surveillance programs. Wastewater surveillance has proven valuable …
View article: Distinguishing Severe Acute Respiratory Syndrome Coronavirus 2 Persistence and Reinfection: A Retrospective Cohort Study
Distinguishing Severe Acute Respiratory Syndrome Coronavirus 2 Persistence and Reinfection: A Retrospective Cohort Study Open
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection is poorly understood, partly because few studies have systematically applied genomic analysis to distinguish reinfection from persistent RNA detection rela…
View article: Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework
Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework Open
View article: Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework
Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework Open
Universities are particularly vulnerable to infectious disease outbreaks and are also ideal environments to study transmission dynamics and evaluate mitigation and surveillance measures when outbreaks occur. Here, we introduce a SARS-CoV-2…
View article: Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA Open
View article: Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak
Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak Open
An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021-the first large outbreak mostly in vaccinated individuals in the US-prompted a comprehensive public health response, motivating changes to national …
View article: Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts
Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts Open
Multiple summer events, including large indoor gatherings, in Provincetown, Massachusetts (MA), in July 2021 contributed to an outbreak of over one thousand COVID-19 cases among residents and visitors. Most cases were fully vaccinated, man…
View article: Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA Open
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was…
View article: The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response
The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response Open
While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that the gene plays a critical role in Lassa virus binding and entry. This led us to pursue field work …
View article: Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant Open
View article: Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs
Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs Open
View article: Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018
Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018 Open
Dengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is k…
View article: SARS-CoV-2 Reinfection in a Liver Transplant Recipient
SARS-CoV-2 Reinfection in a Liver Transplant Recipient Open
Letters20 April 2021SARS-CoV-2 Reinfection in a Liver Transplant RecipientFREEChristopher H. Tomkins-Tinch, BS, Jennifer S. Daly, MD, Adrianne Gladden-Young, MS, Nicole M. Theodoropoulos, MD, MS, Michael P. Madaio, DO, Neng Yu, MD, Vijay K…
View article: Sustainable data analysis with Snakemake
Sustainable data analysis with Snakemake Open
Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognized that da…
View article: Sustainable data analysis with Snakemake
Sustainable data analysis with Snakemake Open
Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognized that da…
View article: Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events
Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events Open
Phylogenetics of superspreading One important characteristic of coronavirus epidemiology is the occurrence of superspreading events. These are marked by a disproportionate number of cases originating from often-times asymptomatic individua…
View article: Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018
Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018 Open
Dengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is k…
View article: Sustainable data analysis with Snakemake
Sustainable data analysis with Snakemake Open
<p>Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognize…
View article: SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs
SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs Open
T cell-mediated immunity may play a critical role in controlling and establishing protective immunity against SARS-CoV-2 infection; yet the repertoire of viral epitopes responsible for T cell response activation remains mostly unknown. Ide…
View article: Sustainable data analysis with Snakemake
Sustainable data analysis with Snakemake Open
<p>Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognize…
View article: Sustainable data analysis with Snakemake
Sustainable data analysis with Snakemake Open
Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognized that da…
View article: Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant Open
View article: Powassan Virus Neuropathology and Genomic Diversity in Patients With Fatal Encephalitis
Powassan Virus Neuropathology and Genomic Diversity in Patients With Fatal Encephalitis Open
Background Powassan virus (POWV) is an emerging cause of severe encephalitis; very little is known about human pathogenicity due to challenges in diagnosis and viral RNA recovery. We present 3 patients with fatal encephalitis due to POWV l…