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1.
Genome Biol ; 22(1): 196, 2021 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-34210356

RESUMO

In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of CLIMB-COVID, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network.


Assuntos
Computação em Nuvem , Genômica/organização & administração , SARS-CoV-2/genética , COVID-19/epidemiologia , Monitoramento Epidemiológico , Genoma Viral , Humanos , Análise de Sequência de DNA , Reino Unido , Interface Usuário-Computador , Sequenciamento Completo do Genoma
5.
Viruses ; 13(5)2021 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-34070175

RESUMO

The ongoing coronavirus disease 2019 (COVID-19) pandemic has had devastating health and socio-economic impacts. Human activities, especially at the wildlife interphase, are at the core of forces driving the emergence of new viral agents. Global surveillance activities have identified bats as the natural hosts of diverse coronaviruses, with other domestic and wildlife animal species possibly acting as intermediate or spillover hosts. The African continent is confronted by several factors that challenge prevention and response to novel disease emergences, such as high species diversity, inadequate health systems, and drastic social and ecosystem changes. We reviewed published animal coronavirus surveillance studies conducted in Africa, specifically summarizing surveillance approaches, species numbers tested, and findings. Far more surveillance has been initiated among bat populations than other wildlife and domestic animals, with nearly 26,000 bat individuals tested. Though coronaviruses have been identified from approximately 7% of the total bats tested, surveillance among other animals identified coronaviruses in less than 1%. In addition to a large undescribed diversity, sequences related to four of the seven human coronaviruses have been reported from African bats. The review highlights research gaps and the disparity in surveillance efforts between different animal groups (particularly potential spillover hosts) and concludes with proposed strategies for improved future biosurveillance.


Assuntos
Infecções por Coronavirus/epidemiologia , Monitoramento Epidemiológico/veterinária , África/epidemiologia , Animais , Animais Selvagens/virologia , COVID-19/epidemiologia , Quirópteros/virologia , Coronaviridae/genética , Coronavirus/patogenicidade , Ecossistema , Variação Genética , Genoma Viral , Pandemias , Filogenia , SARS-CoV-2/patogenicidade , Glicoproteína da Espícula de Coronavírus/genética
6.
PLoS Biol ; 19(6): e3001307, 2021 06.
Artigo em Inglês | MEDLINE | ID: covidwho-1278163

RESUMO

More than 1.6 million Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) tests were administered daily in the United States at the peak of the epidemic, with a significant focus on individual treatment. Here, we show that objective-driven, strategic sampling designs and analyses can maximize information gain at the population level, which is necessary to increase situational awareness and predict, prepare for, and respond to a pandemic, while also continuing to inform individual treatment. By focusing on specific objectives such as individual treatment or disease prediction and control (e.g., via the collection of population-level statistics to inform lockdown measures or vaccine rollout) and drawing from the literature on capture-recapture methods to deal with nonrandom sampling and testing errors, we illustrate how public health objectives can be achieved even with limited test availability when testing programs are designed a priori to meet those objectives.


Assuntos
Monitoramento Epidemiológico , Pandemias , COVID-19/diagnóstico , COVID-19/epidemiologia , COVID-19/prevenção & controle , Teste para COVID-19 , Humanos , Pandemias/prevenção & controle , Saúde Pública , Alocação de Recursos , SARS-CoV-2/isolamento & purificação , Vigilância de Evento Sentinela , Estados Unidos/epidemiologia
7.
Viruses ; 13(5)2021 05 18.
Artigo em Inglês | MEDLINE | ID: covidwho-1234835

RESUMO

The ongoing coronavirus disease 2019 (COVID-19) pandemic has had devastating health and socio-economic impacts. Human activities, especially at the wildlife interphase, are at the core of forces driving the emergence of new viral agents. Global surveillance activities have identified bats as the natural hosts of diverse coronaviruses, with other domestic and wildlife animal species possibly acting as intermediate or spillover hosts. The African continent is confronted by several factors that challenge prevention and response to novel disease emergences, such as high species diversity, inadequate health systems, and drastic social and ecosystem changes. We reviewed published animal coronavirus surveillance studies conducted in Africa, specifically summarizing surveillance approaches, species numbers tested, and findings. Far more surveillance has been initiated among bat populations than other wildlife and domestic animals, with nearly 26,000 bat individuals tested. Though coronaviruses have been identified from approximately 7% of the total bats tested, surveillance among other animals identified coronaviruses in less than 1%. In addition to a large undescribed diversity, sequences related to four of the seven human coronaviruses have been reported from African bats. The review highlights research gaps and the disparity in surveillance efforts between different animal groups (particularly potential spillover hosts) and concludes with proposed strategies for improved future biosurveillance.


Assuntos
Infecções por Coronavirus/epidemiologia , Monitoramento Epidemiológico/veterinária , África/epidemiologia , Animais , Animais Selvagens/virologia , COVID-19/epidemiologia , Quirópteros/virologia , Coronaviridae/genética , Coronavirus/patogenicidade , Ecossistema , Variação Genética , Genoma Viral , Pandemias , Filogenia , SARS-CoV-2/patogenicidade , Glicoproteína da Espícula de Coronavírus/genética
10.
MMWR Morb Mortal Wkly Rep ; 70(23): 846-850, 2021 Jun 11.
Artigo em Inglês | MEDLINE | ID: covidwho-1264713

RESUMO

SARS-CoV-2, the virus that causes COVID-19, is constantly mutating, leading to new variants (1). Variants have the potential to affect transmission, disease severity, diagnostics, therapeutics, and natural and vaccine-induced immunity. In November 2020, CDC established national surveillance for SARS-CoV-2 variants using genomic sequencing. As of May 6, 2021, sequences from 177,044 SARS-CoV-2-positive specimens collected during December 20, 2020-May 6, 2021, from 55 U.S. jurisdictions had been generated by or reported to CDC. These included 3,275 sequences for the 2-week period ending January 2, 2021, compared with 25,000 sequences for the 2-week period ending April 24, 2021 (0.1% and 3.1% of reported positive SARS-CoV-2 tests, respectively). Because sequences might be generated by multiple laboratories and sequence availability varies both geographically and over time, CDC developed statistical weighting and variance estimation methods to generate population-based estimates of the proportions of identified variants among SARS-CoV-2 infections circulating nationwide and in each of the 10 U.S. Department of Health and Human Services (HHS) geographic regions.* During the 2-week period ending April 24, 2021, the B.1.1.7 and P.1 variants represented an estimated 66.0% and 5.0% of U.S. SARS-CoV-2 infections, respectively, demonstrating the rise to predominance of the B.1.1.7 variant of concern† (VOC) and emergence of the P.1 VOC in the United States. Using SARS-CoV-2 genomic surveillance methods to analyze surveillance data produces timely population-based estimates of the proportions of variants circulating nationally and regionally. Surveillance findings demonstrate the potential for new variants to emerge and become predominant, and the importance of robust genomic surveillance. Along with efforts to characterize the clinical and public health impact of SARS-CoV-2 variants, surveillance can help guide interventions to control the COVID-19 pandemic in the United States.


Assuntos
COVID-19/virologia , SARS-CoV-2/genética , COVID-19/epidemiologia , Monitoramento Epidemiológico , Humanos , SARS-CoV-2/isolamento & purificação , Estados Unidos/epidemiologia
11.
PLoS One ; 16(6): e0252990, 2021.
Artigo em Inglês | MEDLINE | ID: covidwho-1264225

RESUMO

The outbreak of the COVID-19 disease was first reported in Wuhan, China, in December 2019. Cases in the United States began appearing in late January. On March 11, the World Health Organization (WHO) declared a pandemic. By mid-March COVID-19 cases were spreading across the US with several hotspots appearing by April. Health officials point to the importance of surveillance of COVID-19 to better inform decision makers at various levels and efficiently manage distribution of human and technical resources to areas of need. The prospective space-time scan statistic has been used to help identify emerging COVID-19 disease clusters, but results from this approach can encounter strategic limitations imposed by constraints of the scanning window. This paper presents a different approach to COVID-19 surveillance based on a spatiotemporal event sequence (STES) similarity. In this STES based approach, adapted for this pandemic context we compute the similarity of evolving daily COVID-19 incidence rates by county and then cluster these sequences to identify counties with similarly trending COVID-19 case loads. We analyze four study periods and compare the sequence similarity-based clusters to prospective space-time scan statistic-based clusters. The sequence similarity-based clusters provide an alternate surveillance perspective by identifying locations that may not be spatially proximate but share a similar disease progression pattern. Results of the two approaches taken together can aid in tracking the progression of the pandemic to aid local or regional public health responses and policy actions taken to control or moderate the disease spread.


Assuntos
COVID-19/epidemiologia , Monitoramento Epidemiológico , Análise por Conglomerados , Surtos de Doenças , Humanos , Incidência , Saúde Pública , SARS-CoV-2/isolamento & purificação , Análise Espaço-Temporal , Fatores de Tempo , Estados Unidos/epidemiologia
12.
PLoS Biol ; 19(6): e3001307, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34138840

RESUMO

More than 1.6 million Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) tests were administered daily in the United States at the peak of the epidemic, with a significant focus on individual treatment. Here, we show that objective-driven, strategic sampling designs and analyses can maximize information gain at the population level, which is necessary to increase situational awareness and predict, prepare for, and respond to a pandemic, while also continuing to inform individual treatment. By focusing on specific objectives such as individual treatment or disease prediction and control (e.g., via the collection of population-level statistics to inform lockdown measures or vaccine rollout) and drawing from the literature on capture-recapture methods to deal with nonrandom sampling and testing errors, we illustrate how public health objectives can be achieved even with limited test availability when testing programs are designed a priori to meet those objectives.


Assuntos
Monitoramento Epidemiológico , Pandemias , COVID-19/diagnóstico , COVID-19/epidemiologia , COVID-19/prevenção & controle , Teste para COVID-19 , Humanos , Pandemias/prevenção & controle , Saúde Pública , Alocação de Recursos , SARS-CoV-2/isolamento & purificação , Vigilância de Evento Sentinela , Estados Unidos/epidemiologia
14.
Mayo Clin Proc ; 96(6): 1592-1608, 2021 06.
Artigo em Inglês | MEDLINE | ID: covidwho-1198962

RESUMO

The coronavirus disease 2019 (COVID-19) pandemic continues its global spread. Coordinated effort on a vast scale is required to halt its progression and to save lives. Electronic health record (EHR) data are a valuable resource to mitigate the COVID-19 pandemic. We review how the EHR could be used for disease surveillance and contact tracing. When linked to "omics" data, the EHR could facilitate identification of genetic susceptibility variants, leading to insights into risk factors, disease complications, and drug repurposing. Real-time monitoring of patients could enable early detection of potential complications, informing appropriate interventions and therapy. We reviewed relevant articles from PubMed, MEDLINE, and Google Scholar searches as well as preprint servers, given the rapidly evolving understanding of the COVID-19 pandemic.


Assuntos
COVID-19/epidemiologia , Registros Eletrônicos de Saúde , COVID-19/diagnóstico , COVID-19/prevenção & controle , Busca de Comunicante/métodos , Reposicionamento de Medicamentos , Monitoramento Epidemiológico , Humanos , SARS-CoV-2/genética
15.
PLoS One ; 16(6): e0252990, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34111199

RESUMO

The outbreak of the COVID-19 disease was first reported in Wuhan, China, in December 2019. Cases in the United States began appearing in late January. On March 11, the World Health Organization (WHO) declared a pandemic. By mid-March COVID-19 cases were spreading across the US with several hotspots appearing by April. Health officials point to the importance of surveillance of COVID-19 to better inform decision makers at various levels and efficiently manage distribution of human and technical resources to areas of need. The prospective space-time scan statistic has been used to help identify emerging COVID-19 disease clusters, but results from this approach can encounter strategic limitations imposed by constraints of the scanning window. This paper presents a different approach to COVID-19 surveillance based on a spatiotemporal event sequence (STES) similarity. In this STES based approach, adapted for this pandemic context we compute the similarity of evolving daily COVID-19 incidence rates by county and then cluster these sequences to identify counties with similarly trending COVID-19 case loads. We analyze four study periods and compare the sequence similarity-based clusters to prospective space-time scan statistic-based clusters. The sequence similarity-based clusters provide an alternate surveillance perspective by identifying locations that may not be spatially proximate but share a similar disease progression pattern. Results of the two approaches taken together can aid in tracking the progression of the pandemic to aid local or regional public health responses and policy actions taken to control or moderate the disease spread.


Assuntos
COVID-19/epidemiologia , Monitoramento Epidemiológico , Análise por Conglomerados , Surtos de Doenças , Humanos , Incidência , Saúde Pública , SARS-CoV-2/isolamento & purificação , Análise Espaço-Temporal , Fatores de Tempo , Estados Unidos/epidemiologia
16.
Nat Commun ; 12(1): 3903, 2021 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-34162869

RESUMO

While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.


Assuntos
COVID-19/genética , SARS-CoV-2/genética , Animais , COVID-19/sangue , COVID-19/economia , COVID-19/virologia , Células Cultivadas , Chlorocebus aethiops , Análise Custo-Benefício , Monitoramento Epidemiológico , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala/economia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Filogenia , SARS-CoV-2/isolamento & purificação , SARS-CoV-2/patogenicidade , Fluxo de Trabalho
18.
Mayo Clin Proc ; 96(6): 1592-1608, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-34088418

RESUMO

The coronavirus disease 2019 (COVID-19) pandemic continues its global spread. Coordinated effort on a vast scale is required to halt its progression and to save lives. Electronic health record (EHR) data are a valuable resource to mitigate the COVID-19 pandemic. We review how the EHR could be used for disease surveillance and contact tracing. When linked to "omics" data, the EHR could facilitate identification of genetic susceptibility variants, leading to insights into risk factors, disease complications, and drug repurposing. Real-time monitoring of patients could enable early detection of potential complications, informing appropriate interventions and therapy. We reviewed relevant articles from PubMed, MEDLINE, and Google Scholar searches as well as preprint servers, given the rapidly evolving understanding of the COVID-19 pandemic.


Assuntos
COVID-19/epidemiologia , Registros Eletrônicos de Saúde , COVID-19/diagnóstico , COVID-19/prevenção & controle , Busca de Comunicante/métodos , Reposicionamento de Medicamentos , Monitoramento Epidemiológico , Humanos , SARS-CoV-2/genética
19.
MMWR Morb Mortal Wkly Rep ; 70(23): 846-850, 2021 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-34111060

RESUMO

SARS-CoV-2, the virus that causes COVID-19, is constantly mutating, leading to new variants (1). Variants have the potential to affect transmission, disease severity, diagnostics, therapeutics, and natural and vaccine-induced immunity. In November 2020, CDC established national surveillance for SARS-CoV-2 variants using genomic sequencing. As of May 6, 2021, sequences from 177,044 SARS-CoV-2-positive specimens collected during December 20, 2020-May 6, 2021, from 55 U.S. jurisdictions had been generated by or reported to CDC. These included 3,275 sequences for the 2-week period ending January 2, 2021, compared with 25,000 sequences for the 2-week period ending April 24, 2021 (0.1% and 3.1% of reported positive SARS-CoV-2 tests, respectively). Because sequences might be generated by multiple laboratories and sequence availability varies both geographically and over time, CDC developed statistical weighting and variance estimation methods to generate population-based estimates of the proportions of identified variants among SARS-CoV-2 infections circulating nationwide and in each of the 10 U.S. Department of Health and Human Services (HHS) geographic regions.* During the 2-week period ending April 24, 2021, the B.1.1.7 and P.1 variants represented an estimated 66.0% and 5.0% of U.S. SARS-CoV-2 infections, respectively, demonstrating the rise to predominance of the B.1.1.7 variant of concern† (VOC) and emergence of the P.1 VOC in the United States. Using SARS-CoV-2 genomic surveillance methods to analyze surveillance data produces timely population-based estimates of the proportions of variants circulating nationally and regionally. Surveillance findings demonstrate the potential for new variants to emerge and become predominant, and the importance of robust genomic surveillance. Along with efforts to characterize the clinical and public health impact of SARS-CoV-2 variants, surveillance can help guide interventions to control the COVID-19 pandemic in the United States.


Assuntos
COVID-19/virologia , SARS-CoV-2/genética , COVID-19/epidemiologia , Monitoramento Epidemiológico , Humanos , SARS-CoV-2/isolamento & purificação , Estados Unidos/epidemiologia
20.
Rev. cuba. inform. méd ; 13(1): e401, ene.-jun. 2021.
Artigo em Espanhol | LILACS, CUMED | ID: biblio-1251736

RESUMO

La COVID-19 ha desatado una emergencia internacional en Salud Pública al afectar millones de personas, provocar muertes, y causar una crisis humanitaria nunca antes vista. Esto ha saturado los sistemas de información en salud de los países afectados, donde resultan de utilidad las herramientas informáticas para el manejo de un gran número de casos, al menor costo económico posible. En este contexto resalta el paquete de programas epidemiológicos Epi InfoTM, que permite crear formularios electrónicos para la recolección de datos. La presente investigación tiene como objetivo describir las ventajas y facilidades de implementar Epi InfoTM para los casos de COVID-19. Con módulos para analizar la información mediante cálculos y representaciones de medidas epidemiológicas, además de crear mapas de casos sospechosos o confirmados, Epi InfoTM cuenta también con complementos para dispositivos móviles y la web; todos con experiencias probadas en situaciones de epidemias como la del Ébola, VIH y el MERS. Por lo que Epi InfoTM es una aplicación robusta y libre de costo muy útil para su implementación en los sistemas de información en salud para el manejo adecuado de casos de COVID-19(AU)


COVID-19 has unleashed an international Public Health emergency by affecting millions of people, causing deaths, and a humanitarian crisis never seen before. This has saturated the health information systems of the affected countries, where computer tools are useful for managing a large number of cases, at the lowest possible economic cost. In this context, the Epi InfoTM package of epidemiological programs which allows creating electronic forms for data collections, stands out in addition with modules to analyze the information through calculations and representations of epidemiological measures. It also allows creating maps of suspected or confirmed cases and has applications for mobile devices and web; all with proven experiences in epidemic situations such as Ebola, HIV, and the previous outbreaks of Coronavirus. Therefore, Epi InfoTM is a robust and free of cost application, very useful for its implementation in health information systems for the adequate management of COVID-19 cases(AU)


Assuntos
Humanos , Sistemas de Informação Geográfica/normas , Epidemias/história , Monitoramento Epidemiológico , Sistemas de Informação em Saúde/organização & administração , COVID-19/transmissão
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