First Report of SARS-CoV-2 Lineage B.1.1.7 (Alpha Variant) in Ecuador, January 2021

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Abstract

On January 5 2021, Ecuadorian COVID-19 genomic surveillance program detected a suspicious case of the B.1.1.7 lineage (alpha variant) of SARS-CoV-2 in Los Rios province, later confirmed by genome sequencing. The patient travelled from the UK by the end of December 2020. By contact tracing, several new cases were detected confirming B.1.1.7 transmission and spreading in Ecuador.

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Re-epithelialization and immune cell behaviour in an ex vivo human skin model

Ana Rakita, Nenad Nikolić, Michael Mildner … (2020)

A large body of literature is available on wound healing in humans. Nonetheless, a standardized ex vivo wound model without disruption of the dermal compartment has not been put forward with compelling justification. Here, we present a novel wound model based on application of negative pressure and its effects for epidermal regeneration and immune cell behaviour. Importantly, the basement membrane remained intact after blister roof removal and keratinocytes were absent in the wounded area. Upon six days of culture, the wound was covered with one to three-cell thick K14+Ki67+ keratinocyte layers, indicating that proliferation and migration were involved in wound closure. After eight to twelve days, a multi-layered epidermis was formed expressing epidermal differentiation markers (K10, filaggrin, DSG-1, CDSN). Investigations about immune cell-specific manners revealed more T cells in the blister roof epidermis compared to normal epidermis. We identified several cell populations in blister roof epidermis and suction blister fluid that are absent in normal epidermis which correlated with their decrease in the dermis, indicating a dermal efflux upon negative pressure. Together, our model recapitulates the main features of epithelial wound regeneration, and can be applied for testing wound healing therapies and investigating underlying mechanisms.

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The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application

Stephen A. Lauer, Kyra Grantz, Qifang Bi … (2020)

Background: A novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified in China in December 2019. There is limited support for many of its key epidemiologic features, including the incubation period for clinical disease (coronavirus disease 2019 [COVID-19]), which has important implications for surveillance and control activities. Objective: To estimate the length of the incubation period of COVID-19 and describe its public health implications. Design: Pooled analysis of confirmed COVID-19 cases reported between 4 January 2020 and 24 February 2020. Setting: News reports and press releases from 50 provinces, regions, and countries outside Wuhan, Hubei province, China. Participants: Persons with confirmed SARS-CoV-2 infection outside Hubei province, China. Measurements: Patient demographic characteristics and dates and times of possible exposure, symptom onset, fever onset, and hospitalization. Results: There were 181 confirmed cases with identifiable exposure and symptom onset windows to estimate the incubation period of COVID-19. The median incubation period was estimated to be 5.1 days (95% CI, 4.5 to 5.8 days), and 97.5% of those who develop symptoms will do so within 11.5 days (CI, 8.2 to 15.6 days) of infection. These estimates imply that, under conservative assumptions, 101 out of every 10 000 cases (99th percentile, 482) will develop symptoms after 14 days of active monitoring or quarantine. Limitation: Publicly reported cases may overrepresent severe cases, the incubation period for which may differ from that of mild cases. Conclusion: This work provides additional evidence for a median incubation period for COVID-19 of approximately 5 days, similar to SARS. Our results support current proposals for the length of quarantine or active monitoring of persons potentially exposed to SARS-CoV-2, although longer monitoring periods might be justified in extreme cases. Primary Funding Source: U.S. Centers for Disease Control and Prevention, National Institute of Allergy and Infectious Diseases, National Institute of General Medical Sciences, and Alexander von Humboldt Foundation.

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RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Alexey M. Kozlov, Diego Darriba, Tomáš Flouri … (2019)

Abstract Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets. Results We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric. Availability and implementation The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng . RAxML-NG web service (maintained by Vital-IT) is available at https://raxml-ng.vital-it.ch/ . Supplementary information Supplementary data are available at Bioinformatics online.

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Journal

Journal ID (nlm-ta): Infect Drug Resist

Journal ID (iso-abbrev): Infect Drug Resist

Journal ID (publisher-id): idr

Title: Infection and Drug Resistance

Publisher: Dove

ISSN (Electronic): 1178-6973

Publication date (Electronic): 06 December 2021

Publication date Collection: 2021

Volume: 14

Pages: 5183-5188

Affiliations

[1 ]Dirección de Investigación, Desarrollo e Innovación, Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez” , Guayaquil, Ecuador

[2 ]Centro de Referencia Nacional de Influenza y otros Virus Respiratorios, Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez” , Guayaquil, Ecuador

[3 ]Universidad Agraria del Ecuador , Guayaquil, Ecuador

[4 ]Centro de Referencia Nacional de Virus Exantemáticos, Gastroentéricos y Transmitidos por Vectores, Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez” , Guayaquil, Ecuador

[5 ]Universidad de Guayaquil , Guayaquil, Ecuador

[6 ]Ministerio de Salud Pública, Zonal 5 , Guayaquil, Ecuador

[7 ]Instituto Nacional del Niño San Borja , Lima, Perú

[8 ]One Health Research Group, Universidad de Las Américas , Quito, Ecuador

[9 ]Laboratorio Cruz Vida, Cruz Roja Ecuatoriana , Quito, Ecuador

Author notes

Correspondence: Miguel Angel Garcia-Bereguiain; Leandro Patino Email magbereguiain@gmail.com; lpatino@inspi.gob.ec

[*]

These authors contributed equally to this work

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Miguel Angel Garcia-Bereguiain http://orcid.org/0000-0003-0025-3609

Article

Publisher ID: 319439

DOI: 10.2147/IDR.S319439

PMC ID: 8664343

PubMed ID: 34908852

SO-VID: 070dff26-a5d0-47b0-a592-57f62de587f0

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This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution – Non Commercial (unported, v3.0) License ( http://creativecommons.org/licenses/by-nc/3.0/). By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms ( https://www.dovepress.com/terms.php).

History

Date received : 12 May 2021

Date accepted : 16 October 2021

Page count

Figures: 3, Tables: 2, References: 13, Pages: 6

Funding

Funded by: Instituto Nacional de Investigación en Salud Pública, Universidad de Las Américas;

This study was supported by Instituto Nacional de Investigación en Salud Pública and Universidad de Las Américas.

First Report of SARS-CoV-2 Lineage B.1.1.7 (Alpha Variant) in Ecuador, January 2021

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Novel Coronavirus Disease COVID-19

Most cited references 11

Re-epithelialization and immune cell behaviour in an ex vivo human skin model

The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

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