Ineffectiveness of international travel restrictions to contain spread of the SARS-CoV-2 Omicron BA.1 variant: a continent-wide laboratory-based observational study from Africa (preprint)

Background: In mid-November 2021, the SARS-CoV-2 Omicron BA.1 variant was detected in Southern Africa, prompting international travel restrictions of unclear effectiveness that exacted a substantial economic toll. Methods: Amidst the BA.1 wave, we tested 13,294 COVID-19 patients in 24 African countries between mid-2021 to early 2022 for BA.1 and Delta variants using real-time reverse transcription-PCR tests. The diagnostic precision of the assays was evaluated by high-throughput sequencing in four countries. The observed BA.1 spread was compared to mobility-based mathematical simulations. Findings: By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a median Rt of 2.4 up to 30 days before BA.1 became predominant. PCR-based South-North spread was in agreement with phylogeographic reconstructions relying on 939 SARS-CoV-2 genomes from GISAID. PCR-based reconstructions of country-level BA.1 predominance correlated significantly in time with the emergence of BA.1 genomic sequences on GISAID (p=0.0035, cor=0.70). First BA.1 detections in affluent settings beyond Africa were predicted adequately in time by mobility-based mathematical simulations (p<0.0001). BA.1-infected inbound travelers departing from five continents were identified in five Western countries and one Northern African country by late November/early December 2021, highlighting fast global BA.1 spread aided by international travel. Interpretation: Unilateral travel bans were poorly effective because by the time they came into effect, BA.1 was already widespread in Africa and beyond. PCR-based variant typing combined with mobility-based mathematical modelling can inform rapidly and cost-efficiently on Rt, spread to inform non-pharmaceutical interventions.

[Evidence of the validity of a Brazilian version of the Fear of COVID-19 Scale]. / Evidências de validade de uma versão brasileira da Fear of COVID-19 Scale.

This study sought to analyze the evidence of the validity of a Brazilian version of the Fear of COVID-19 Scale (FCV-19S), based on indicators relating to: (1) the internal structure; (2) the internal consistency; (3) the relation with external variables; and (4) the content. The instrument was culturally adapted, focusing on semantic and specifically Brazilian linguistic aspects. The Brazilian version of the FCV-19S was then applied, in a virtual environment, to 211 participants (72.98% female) with an average age of 37.07 years (SD=13.03), together with the Self-Perception Questionnaire on Mental Health in Pandemics and the Sociodemographic and Functional Questionnaire. The confirmatory factor analysis revealed one-dimensionality. The internal consistency indices obtained (Cronbach's alpha =0.921; McDonald's omega =0.926) can be considered high. The correlation between fear and obsessive thinking of the disease, generalized anxiety, generalized stress, phobic-avoidant behavior and bereavement due to the pandemic was found to be statistically significant. Evidence of the validity related to content, derived from a qualitative approach, were satisfactory. The conclusion drawn is that the Brazilian version of the FCV-19S proved to be adequate regarding the evidence of the expected validity.

O presente estudo teve como objetivo analisar evidências de validade de uma versão brasileira da Fear of COVID-19 Scale (FCV-19S), com base em indicadores concernentes: (1) à estrutura interna; (2) à consistência interna; (3) à relação com variáveis externas; e (4) ao conteúdo. Procedeu-se a adaptação cultural do instrumento, com foco em aspectos semânticos e linguísticos próprios do Brasil. A seguir, esta versão brasileira da FCV-19S foi aplicada, em um ambiente virtual, em 211 participantes (72,98% do sexo feminino), com idade média de 37,07 anos (DP=13,03), juntamente com o Questionário de Autopercepção de Saúde Mental em Pandemia e o Questionário Sociodemográfico e Funcional. A análise fatorial confirmatória atestou unidimensionalidade. Os índices de consistência interna obtidos (alfa de Cronbach =0,921; ômega de McDonald =0,926) podem ser considerados elevados. Constatou-se correlação estatisticamente significativa entre medo e pensamento obsessivo, ansiedade generalizada, estresse generalizado, comportamento fóbico-evitativo e vivência de luto pela pandemia. As evidências de validade relativas ao conteúdo, oriundas de uma abordagem qualitativa, foram satisfatórias. Conclui-se que esta versão brasileira da FCV-19S mostrou-se adequada quanto às evidências de validade contempladas.

A novel variant of interest of SARS-CoV-2 with multiple spike mutations is identified from travel surveillance in Africa (preprint)

At the end of 2020, the Network for Genomic Surveillance in South Africa (NGS-SA) detected a SARS-CoV-2 variant of concern (VOC) in South Africa (501Y.V2 or PANGO lineage B.1.351)1. 501Y.V2 is associated with increased transmissibility and resistance to neutralizing antibodies elicited by natural infection and vaccination2,3. 501Y.V2 has since spread to over 50 countries around the world and has contributed to a significant resurgence of the epidemic in southern Africa. In order to rapidly characterize the spread of this and other emerging VOCs and variants of interest (VOIs), NGS-SA partnered with the Africa Centres for Disease Control and Prevention and the African Society of Laboratory Medicine through the Africa Pathogen Genomics Initiative to strengthen SARS-CoV-2 genomic surveillance across the region. Here, we report the first genomic surveillance results from Angola, which has had 21 500 reported cases and around 500 deaths from COVID-19 up to March 2021 (Supplemental Fig S1). On 15 January 2021, in response to the international spread of VOCs, the government instituted compulsory rapid antigen testing of all passengers arriving at the main international airport, in addition to the existing requirement to present a negative PCR test taken within 72 hours of travel. All individuals with a positive antigen test are isolated in a government facility for a minimum of 14 days and require two negative RT-PCR tests at least 48 hours apart for de-isolation, whilst all travelers with a negative test on arrival proceed to mandatory self-quarantine for 10 days followed by a repeat test. In March 2021, we received 118 nasopharyngeal swab samples collected between June 2020 and February 2021, a number of which were from incoming air travelers (Supplemental Fig S1). From these, we produced 73 high quality genomes (>80% coverage), 14 of which were known VOCs/VOIs (seven 501Y.V2/B.1.351, six B.1.1.7, one B.1.525), 44 of which were C.16 (a common lineage circulating in Portugal), and twelve of which were other lineages (Supplemental Fig S2). In addition, we detected a new VOI in three incoming travelers from Tanzania who were tested together at the airport in mid-February. The three genomes from these passengers were almost identical and presented highly divergent sequences within the A lineage (Figure 1A & 1B). The GISAID database contains nine other sequences reported to be sampled from cases involving travel from Tanzania, two of which are basal to the three sampled in Angola (Figure 1A, Supplemental Table S1). This new VOI, temporarily designated A.VOI.V2, has 31 amino acid substitutions (11 in spike) and three deletions (all in spike) (Figure 1C & 1D). The spike mutations include three substitutions in the receptor-binding domain (R346K, T478R and E484K); five substitutions and three deletions in the N-terminal domain, some of which are within the antigenic supersite (Y144{Delta}, R246M, SYL247-249{Delta} and W258L)4; and two substitutions adjacent to the S1/S2 cleavage site (H655Y and P681H). Several of these mutations are present in other VOCs/VOIs and are evolving under positive selection.

Plano de [contingência] municipal para Covid-19: Pedro Afonso - TO

Orienta na campanha para ações de combate ao Coronavírus (Covid-19) no município de Pedro Afonso no Tocantins. Apresenta quais as definições de casos de infecção humana pelo COVID-19. Orientações de como notificar ao Centro de Informações Estratégicas de Vigilância em Saúde (CIEVS). Quais os períodos de incubação da doença. Fatores sobre a transmissão e tratamento. Investigação epidemiológica. Quais atribuições da Vigilância em Saúde. Orientações para a coleta de amostras no Laboratório Central de Saúde Pública do Tocantins (LACEN-TO) bem como a técnica de coleta de Swabde nasofaringe e orofaringe (swabs combinados), o acondicionamento, transporte e envio das amostras. Traz as recomendações para a coleta de amostras em situação de óbito. Mostra as medidas de prevenção e controle Precauções padrão, as medidas de isolamento. Transporte do paciente. Como se dá a Limpeza e desinfecção de superfícies. He guides in the campaign for actions to combat the Coronavirus (Covid-19) in the municipality of Pedro Afonso in Tocantins. It presents the definitions of cases of human infection by COVID-19. Guidelines on how to notify the Health Surveillance Strategic Information Center (CIEVS). What are the disease incubation periods. Factors about transmission and treatment. Epidemiological investigation. Which attributions of Health Surveillance. Guidelines for the collection of samples at the Central Laboratory of Public Health of Tocantins (LACEN-TO) as well as the technique of collecting Swabde nasopharynx and oropharynx (combined swabs), packaging, transport and sending of samples . It provides recommendations for the collection of samples in situations of death. Shows prevention and control measures Standard precautions, isolation measures. Transporting the patient. How to clean and disinfect surfaces. Orienta en la campaña de acciones de combate al Coronavirus (Covid-19) en el municipio de Pedro Afonso en Tocantins. Presenta las definiciones de casos de infección humana por COVID-19. Directrices sobre cómo notificar al Centro de Información Estratégica de Vigilancia Sanitaria (CIEVS). Cuáles son los períodos de incubación de la enfermedad. Factores de transmisión y tratamiento. Investigación epidemiológica. Qué atribuciones de la Vigilancia Sanitaria. Lineamientos para la recolección de muestras en el Laboratorio Central de Salud Pública de Tocantins (LACEN-TO) así como la técnica de recolección de Swabde nasofaringe y orofaringe (hisopos combinados), el empaque, transporte y envío de las muestras . Proporciona recomendaciones para la recolección de muestras en situaciones de muerte. Muestra medidas de prevención y control Precauciones estándar, medidas de aislamiento. Transporte del paciente. Cómo limpiar y desinfectar superficies. Il guide dans la campagne d'actions de lutte contre le Coronavirus (Covid-19) dans la commune de Pedro Afonso à Tocantins. Il présente les définitions des cas d'infection humaine par COVID-19. Lignes directrices sur la manière de notifier le Centre d'information stratégique de surveillance sanitaire (CIEVS). Quelles sont les périodes d'incubation de la maladie. Facteurs de transmission et de traitement. Enquête épidémiologique. Quelles attributions de la Surveillance de la Santé. Directives pour le prélèvement d'échantillons au Laboratoire Central de Santé Publique de Tocantins (LACEN-TO) ainsi que la technique de prélèvement de Swabde nasopharynx et oropharynx (écouvillons combinés), l'emballage, le transport et l'envoi des échantillons . Il fournit des recommandations pour le prélèvement d'échantillons en cas de décès. Affiche les mesures de prévention et de contrôle. Transport du patient. Comment nettoyer et désinfecter les surfaces.