Introduction and community transmission of SARS-CoV-2 lineage A.2.5 in Florida with novel spike INDELS

AbstractSARS-CoV-2 (SC2) variants of concern (VOC) continue to emerge and spread globally, threatening the use of monoclonal antibody therapies and vaccine effectiveness. Several mutations in the SC2 spike glycoprotein have been associated with reduction in antibody neutralization. Genomic surveillance of SC2 variants has been imperative to inform the public health response regarding the use of clinical therapies in specific jurisdictions based on the proportion of particular variants (e.g., Gamma (P.1)) in a region. Florida Department of Health Bureau of Public Health Laboratories (BPHL) performs tiled-amplicon whole genome sequencing for baseline and targeted surveillance of SC2 isolates in Florida from clinical specimens collected from county health departments and hospitals throughout the state. Here, we describe the introduction of SC2 lineage A.2.5 in Florida, which contains S:L452R (a substitution of therapeutic concern) and two novel Spike INDELS, the deletion of 141-143 and ins215AGY, with unknown implications on immune response. The A.2.5 lineage was first detected in Florida among an outbreak at a healthcare facility in January 2021, and subsequent A.2.5 isolates were detected across all geographical regions throughout the state. A time-scaled maximum clade credibility phylogeny determined there were at least eight separate introductions of A.2.5 in the state. The time of introduction of a monophyletic Florida clade was established to be December 2020. The Spike INDELS were determined to reside in the N-terminal domain, a region associated with antibody neutralization. As community transmission of SARS-CoV-2 in Florida continues, genomic surveillance of circulating variants in Florida and the detection of emerging variants are critical for informing public health response to COVID-19.

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Public health response to two imported, epidemiologically related cases of Lassa fever in the Netherlands (ex Sierra Leone), November 2019

Eurosurveillance ◽

10.2807/1560-7917.es.2020.25.15.2000265 ◽

2020 ◽

Vol 25 (15) ◽

Author(s):

Femke Overbosch ◽

Mark de Boer ◽

Karin Ellen Veldkamp ◽

Pauline Ellerbroek ◽

Chantal P Bleeker-Rovers ◽

...

Keyword(s):

Public Health ◽

The Netherlands ◽

Sierra Leone ◽

Healthcare Facility ◽

Lassa Fever ◽

Low Risk ◽

Lassa Virus ◽

Public Health Response ◽

Health Response

On 20 November 2019, Lassa fever was diagnosed in a physician repatriated from Sierra Leone to the Netherlands. A second physician with suspected Lassa fever, repatriated a few days later from the same healthcare facility, was confirmed infected with Lassa virus on 21 November. Comprehensive contact monitoring involving high- and low-risk contacts proved to be feasible and follow-up of the contacts did not reveal any case of secondary transmission in the Netherlands.

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Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses

10.1101/2020.01.06.896548 ◽

2020 ◽

Cited By ~ 4

Author(s):

Nancy A. Chow ◽

José F. Muñoz ◽

Lalitha Gade ◽

Elizabeth Berkow ◽

Xiao Li ◽

...

Keyword(s):

Public Health ◽

Population Structure ◽

Healthcare Facility ◽

Antifungal Resistance ◽

Nosocomial Transmission ◽

Phylogenetic Study ◽

Candida Auris ◽

Public Health Response ◽

Fluconazole Resistance ◽

Health Response

AbstractCandida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (Clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in over 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; Clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single healthcare facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 339 years; outbreak-causing clusters from Clades I, III, and IV originated 34-35 years ago. We observed high rates of antifungal resistance in Clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in Clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. auris.ImportanceIn less than a decade, C. auris has emerged in healthcare settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology.

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Early COVID-19 Interventions Failed to Replicate 1918 St. Louis vs. Philadelphia Outcomes in the United States

10.1101/2020.07.02.20145367 ◽

2020 ◽

Author(s):

Aliea M. Jalali ◽

Brent M. Peterson ◽

Thushara Galbadage

Keyword(s):

Public Health ◽

United States ◽

State Level ◽

The United States ◽

The State ◽

Health Interventions ◽

Public Health Interventions ◽

Public Health Response ◽

Health Response ◽

The Us

The Coronavirus disease 2019 (COVID-19) pandemic has elicited an abrupt pause in the United States in multiple sectors of commerce and social activity. As the US faces this health crisis, the magnitude, and rigor of their initial public health response was unprecedented. As a response, the entire nation shutdown at the state-level for the duration of approximately one to three months. These public health interventions, however, were not arbitrarily decided, but rather, implemented as a result of evidence-based practices. These practices were a result of lessons learned during the 1918 influenza pandemic and the city-level non-pharmaceutical interventions (NPIs) taken across the US. During the 1918 pandemic, two model cities, St. Louis, MO, and Philadelphia, PA, carried out two different approaches to address the spreading disease, which resulted in two distinctly different outcomes. Our group has evaluated the state-level public health response adopted by states across the US, with a focus on New York, California, Florida, and Texas, and compared the effectiveness of reducing the spread of COVID-19. Our assessments show that while the states mentioned above benefited from the implementations of early preventative measures, they inadequately replicated the desired outcomes observed in St. Louis during the 1918 crisis. Our study indicates that there are other factors, including health disparities that may influence the effectiveness of public health interventions applied. Identifying more specific health determinants may help implement targeted interventions aimed at preventing the spread of COVID-19 and improving health equity.

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Government response to COVID-19 in the Czech Republic: February–July 2020

Zdrowie Publiczne i Zarządzanie ◽

10.4467/20842627oz.20.007.12661 ◽

2020 ◽

Vol 18 (1) ◽

pp. 75-79

Author(s):

Olga Löblová

Keyword(s):

Public Health ◽

Czech Republic ◽

Isolate System ◽

The Novel ◽

Public Health Response ◽

The Czech Republic ◽

Government Response ◽

Health Response ◽

Community Transmission ◽

Novel Coronavirus

The Czech Republic initially managed the outbreak of the novel coronavirus remarkably, with relatively few cases and low death rate. Its public health response was characterized by swift implementation of public health measures driven by an implicit precautionary principle, but also chaotic communication of measures and a lack of transparency in justifying individual policies. June and July 2020 have seen a rise in COVID-19 cases linked to two regional clusters but later associated with community transmission, which exposed weaknesses in the country’s test-trace-isolate system.

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