Genomic surveillance and sequencing of SARS-CoV-2 across South America.

After 2 years of the COVID-19 pandemic, the protocols used to control infection lack attention and analysis. We present data about deposits of complete genomic sequences of SARS-CoV-2 in the Global Initiative on Sharing All Influenza Data (GISAID) database made between January 2021 and May 31, 2022. We build the distribution profile of SARS-CoV-2 variants across South America, highlighting the contribution and influence of each variant over time. Monitoring the genomic sequences in GISAID illustrates negligence in the follow up of infected patients in South America and also the discrepancies between the number of complete genomes deposited throughout the pandemic by developed and developing countries. While Europe and North America account for more than 9 million of the genomes deposited in GISAID, Africa and South America deposited less than 400 000 genome sequences. Genomic surveillance is important for detecting early warning signs of new circulating viruses, assisting in the discovery of new variants and controlling pandemics.

Tras dos años de pandemia del COVID-19, los protocolos empleados para controlar la infección carecen de atención y análisis. En este artículo se presentan datos sobre depósitos de secuencias genómicas completas del SARS-CoV-2 en la base de datos de secuenciación GISAID, la Iniciativa mundial para intercambiar todos los datos sobre la gripe aviar, realizadas entre enero del 2021 y el 31 de mayo del 2022. Se creó el perfil de distribución de las variantes del SARS-CoV-2 en América del Sur, en el que se destacaron la contribución y la influencia de cada variante a lo largo del tiempo. El monitoreo de las secuencias genómicas en GISAID ilustra la negligencia en el seguimiento de los pacientes infectados en América del Sur, así como las discrepancias entre el número de genomas completos depositados a lo largo de la pandemia por parte de los países desarrollados y los países en desarrollo. Mientras que Europa y América del Norte han depositado más de 9 millones de genomas en GISAID, África y América del Sur han aportado menos de 400 000 secuencias genómicas. La vigilancia genómica es importante para detectar los primeros signos de alerta de virus nuevos en circulación, ayudar en el descubrimiento de nuevas variantes y controlar las pandemias.

Após 2 anos da pandemia de covid-19, os protocolos usados para controlar a infecção necessitam maior atenção e análise. Apresentamos dados sobre as sequências genômicas completas do SARS-CoV-2 depositadas no banco de dados do a iniciativa internacional para o intercâmbio de dados sobre os vírus da influenza (GISAID) entre janeiro de 2021 e 31 de maio de 2022. Construímos o perfil de distribuição das variantes do SARS-CoV-2 na América do Sul, destacando a contribuição e a influência de cada variante ao longo do tempo. O monitoramento das sequências genômicas do GISAID ilustra a negligência no acompanhamento de pacientes infectados na América do Sul e as discrepâncias entre os países desenvolvidos e em desenvolvimento com relação ao número de genomas completos depositados ao longo da pandemia. Enquanto a Europa e a América do Norte respondem por mais de 9 milhões dos genomas depositados no GISAID, a África e a América do Sul depositaram menos de 400 000 sequências genômicas. A vigilância genômica é importante para detectar sinais de alerta precoces de novos vírus circulantes, auxiliar na descoberta de novas variantes e controlar pandemias.

Genomic surveillance and sequencing of SARS-CoV-2 across South America Vigilancia genómica y secuenciación del SARS-CoV-2 en América del Sur Vigilância genômica e sequenciamento do SARS-CoV-2 na América do Sul

After 2 years of the COVID-19 pandemic, the protocols used to control infection lack attention and analysis. We present data about deposits of complete genomic sequences of SARS-CoV-2 in the Global Initiative on Sharing All Influenza Data (GISAID) database made between January 2021 and May 31, 2022. We build the distribution profile of SARS-CoV-2 variants across South America, highlighting the contribution and influence of each variant over time. Monitoring the genomic sequences in GISAID illustrates negligence in the follow up of infected patients in South America and also the discrepancies between the number of complete genomes deposited throughout the pandemic by developed and developing countries. While Europe and North America account for more than 9 million of the genomes deposited in GISAID, Africa and South America deposited less than 400 000 genome sequences. Genomic surveillance is important for detecting early warning signs of new circulating viruses, assisting in the discovery of new variants and controlling pandemics.

Schools reopening and the COVID-19 pandemic: a case study from Macaé, Rio de Janeiro, Brazil.

Since the first reported case of COVID-19 in Brazil, the public and private educational system started to close. Up to November 2020, scientific discussions about the return of schooling activities have been rarely performed by the national scientific community and police-makers. The great delay of school returning in Brazil contrasts with successful international strategies of school reopening worldwide and seems counterintuitive with the reopening of non-essential activities. Here, important issues to be considered before and during school reopening are reviewed and discussed. COVID-19 testing is essential to avoid disease spreading, but high cost of individual RT-qPCRs impairs an extensive testing strategy for school returning. To reduce costs and increase the speed of diagnosis, we tested the efficiency of a pooled-sample PCR strategy in a cohort of the educational staff in the city of Macaé/RJ, finding five asymptomatic individuals (0,66%) among the 754 people tested. Thus, a polled-sample PCR testing strategy of the educational staff might prevent infection spreading in schools at a reasonable cost. We discuss how our test strategy could be coupled with internationally recognized safety rules to allow for a safe school return and how countries from different world regions are dealing with educational activities during COVID-19 pandemic.

Molecular testing and analysis of disease spreading during the emergence of COVID-19 in Macaé, the Brazilian National Capital of Oil.

The Brazilian strategy to overcome the spread of COVID-19 has been particularly criticized due to the lack of a national coordinating effort and an appropriate testing program. Here, a successful approach to control the spread of COVID-19 transmission is described by the engagement of public (university and governance) and private sectors (hospitals and oil companies) in Macaé, state of Rio de Janeiro, Brazil, a city known as the National Oil Capital. In 2020 between the 17th and 38th epidemiological week, over two percent of the 206,728 citizens were subjected to symptom analysis and RT-qPCR testing by the Federal University of Rio de Janeiro, with positive individuals being notified up to 48 h after swab collection. Geocodification and spatial cluster analysis were used to limit COVID-19 spreading in Macaé. Within the first semester after the outbreak of COVID-19 in Brazil, Macaé recorded 1.8% of fatalities associated with COVID-19 up to the 38th epidemiological week, which was at least five times lower than the state capital (10.6%). Overall, considering the successful experience of this joint effort of private and public engagement in Macaé, our data suggest that the development of a similar strategy countrywise could have contributed to a better control of the COVID-19 spread in Brazil. Quarantine decree by the local administration, comprehensive molecular testing coupled to scientific analysis of COVID-19 spreading, prevented the catastrophic consequences of the pandemic as seen in other populous cities within the state of Rio de Janeiro and elsewhere in Brazil.