Implementation of a COVID-19 Genomic Surveillance Regional Network for Latin America and Caribbean region

Leite, Juliana Almeida; Vicari, Andrea; Gutiérrez, Enrique Pérez; Siqueira, Marilda Agudo Mendonça Teixeira de; Resende, Paola Cristina; Motta, Fernando Couto; Freitas, Lucas; Fernández, Jorge Onrubia; Parra, Bárbara; Castillo, Andrés; Fasce, Rodrigo; Caballero, Alexander Augusto Martinez; Gresh, Lionel; Aldighieri, Sylvain; Gabastou, Jean-Marc; Franco, Leticia; Méndez‐Rico, Jairo

doi:10.1371/journal.pone.0252526

Cited by 21 publications

(24 citation statements)

References 21 publications

(24 reference statements)

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“…In the present study, SARS-CoV-2 variates were not sequenced, but SARS-CoV-2 B.1 clade, subclade B.1.1.33, was reported as the most prevalent genetic group circulating in the Latin America and Caribbean region until January 2021 ( 26 ). So, we can admit that, at least for the Brazil series, most of the patients were infected with the SARS-CoV-2 B.1 clade.…”

Section: Discussionmentioning

confidence: 70%

Detection of SARS-CoV-2 infection in thyroid follicular cells from a COVID-19 autopsy series

Macedo

Pestana

Santos

et al. 2022

European Thyroid Journal

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Objective: To understand whether thyroid cells can be directly infected by the SARS-CoV-2 virus and to establish a putative correlation with the expression of the host entry machinery: ACE-2, TMPRSS2, and Furin. Methods: We assessed the presence of SARS-CoV-2 virus at the gene level by RT-PCR, viral RNA transcripts localization by in situ hybridization, and by detecting viral proteins by immunohistochemistry for the nucleocapsid and the spike proteins. Furthermore, we also describe the immunoexpression of key host factors for virus entry in the COVID-19 thyroid samples. Results: We performed RT-PCR for SARS-CoV-2 in all autopsy specimens and detected viral genome positivity in 13 of 15 thyroid tissues and in a lung specimen. In nine of the 14 positive samples, we were also able to confirm SARS-CoV-2 signal by in situ hybridization. Immunohistochemistry for the viral nucleocapsid and spike protein was also positive for 10 and nine of the RT-PCR positive cases, respectively, but revealed a lower sensitivity. We also described, for the first time in a COVID-19 series, the immunohistochemical expression of ACE-2, TMPRSS2, and Furin in the thyroid. Conclusions: Our results obtained in thyroid specimens from deceased COVID-19 patients indicate that thyrocytes can be directly infected by SARS-CoV-2, since we detected the presence of SARS-CoV-2 genome in follicular cells. Nevertheless, we did not find a clear correlation between the presence of viral genome and the expression of the host factors for virus entry, namely ACE-2, TMPRSS2, and Furin.

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Section: Discussionmentioning

confidence: 70%

Detection of SARS-CoV-2 infection in thyroid follicular cells from a COVID-19 autopsy series

Macedo

Pestana

Santos

et al. 2022

European Thyroid Journal

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“…Consequently, we did not observe frequent clustering of Puerto Rican sequences with sequences from regions other than the United States. This is further supported by the difference in lineages circulating in the Americas and Puerto Rico 42 . The frequent mixing of viruses between Puerto Rico and the United States, the lineage diversity circulating in the island, and the low density of sampling at the location of origin generated phylogenetic uncertainty, limiting the capacity to resolve the precise origin of some local clusters and specific transmission chains 43 .…”

Section: Discussionmentioning

confidence: 77%

“…Similar patterns have been observed in the United States, where variant emergence and spread potentially affect Puerto Rico 51 . Travel restrictions could have blocked the introduction of additional variants directly to Puerto Rico through international travel as seen in the difference in lineages detected between Puerto Rico and the rest of the Americas and Caribbean region 42 . However, our results suggest that lineage turn-over was in part driven by domestic travel in the United States.…”

Section: Discussionmentioning

confidence: 99%

Genomic surveillance of SARS-CoV-2 in Puerto Rico enabled early detection and tracking of variants

et al. 2022

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Background Puerto Rico has experienced the full impact of the COVID-19 pandemic. Since SARS-CoV-2, the virus that causes COVID-19, was first detected on the island in March of 2020, it spread rapidly though the island’s population and became a critical threat to public health. Methods We conducted a genomic surveillance study through a partnership with health agencies and academic institutions to understand the emergence and molecular epidemiology of the virus on the island. We sampled COVID-19 cases monthly over 19 months and sequenced a total of 753 SARS-CoV-2 genomes between March 2020 and September 2021 to reconstruct the local epidemic in a regional context using phylogenetic inference. Results Our analyses reveal that multiple importation events propelled the emergence and spread of the virus throughout the study period, including the introduction and spread of most SARS-CoV-2 variants detected world-wide. Lineage turnover cycles through various phases of the local epidemic were observed, where the predominant lineage was replaced by the next competing lineage or variant after ~4 months of circulation locally. We also identified the emergence of lineage B.1.588, an autochthonous lineage that predominated in Puerto Rico from September to December 2020 and subsequently spread to the United States. Conclusions The results of this collaborative approach highlight the importance of timely collection and analysis of SARS-CoV-2 genomic surveillance data to inform public health responses.

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“…Expanding genomic sequencing capabilities, especially in LMICs, is a global priority 26 and current investments in sequencing must continue. 27,28 Simultaneously, sustained investments in public health systems are required to expand access to, and availability of, diagnostic testing to underpin SARS-CoV-2 surveillance programs. Here, we primarily focused on LMICs but our findings on the impact of testing rates and representativeness on genomic surveillance programs are equally important for HICs as they consider dismantling parts of their testing and surveillance infrastructure in the post-crisis phase of the pandemic.…”

Section: Discussionmentioning

confidence: 99%

“…Over time, especially after the emergence of VOCs, SARS-CoV-2 genomic surveillance gradually expanded to include community surveillance as many LMICs enhanced their sequencing capacities 4,[28][29][30] . This was done either by establishing regional sequencing networks to maximize available resources, investing in local sequencing capacities or partnering with global collaborators [30][31][32] . Sequencing turnaround time has also improved from an average of ~170 days in 2020 to ~30 days in 2021 across the African continent, albeit with substantial variation among countries 30 .…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs

Han

Toporowski

Sacks

et al. 2022

Preprint

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Background Genomic surveillance is essential for monitoring the emergence and spread of SARS-CoV-2 variants. SARS-CoV-2 diagnostic testing is the starting point for SARS-CoV-2 genomic sequencing. However, testing rates in many low- and middle-income countries (LMICs) are low (mean = 27 tests/100,000 people/day) and global testing rates are falling in the post-crisis phase of the pandemic, leading to spatiotemporal biases in sample collection. Various public health agencies and academic groups have produced recommendations on sample sizes and sequencing strategies for effective genomic surveillance. However, these recommendations assume very high volumes of diagnostic testing that are currently well beyond reach in most LMICs. Methods To investigate how testing rates, sequencing strategies and the degree of spatiotemporal bias in sample collection impact variant detection and monitoring outcomes, we used an individual-based model to simulate COVID-19 epidemics in a prototypical LMIC. Within the model, we simulated a range of testing rates, accounted for likely testing demand and applied various genomic surveillance strategies, including sentinel surveillance. Findings Diagnostic testing rates play a substantially larger role in monitoring the prevalence and emergence of new variants than the proportion of samples sequenced. To enable timely detection and monitoring of emerging variants, programs should achieve average testing rates of at least 100 tests/100,000 people/day and sequence 5-10% of test-positive specimens, which may be accomplished through sentinel or other routine surveillance systems. Under realistic assumptions, this averages to ~10 samples for sequencing/1,000,000 people/week. Interpretation For countries where testing capacities are low and sample collection is spatiotemporally biased, surveillance programs should prioritize investments in wider access to diagnostic testing to enable more representative sampling, ahead of simply increasing quantities of sequenced samples. Funding European Research Council, the Rockefeller Foundation, and the Governments of Germany, Canada, UK, Australia, Norway, Saudi Arabia, Kuwait, Netherlands and Portugal.

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Implementation of a COVID-19 Genomic Surveillance Regional Network for Latin America and Caribbean region

Cited by 21 publications

References 21 publications

Detection of SARS-CoV-2 infection in thyroid follicular cells from a COVID-19 autopsy series

Detection of SARS-CoV-2 infection in thyroid follicular cells from a COVID-19 autopsy series

Genomic surveillance of SARS-CoV-2 in Puerto Rico enabled early detection and tracking of variants

SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs

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