Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama

Abstract

Background With more than 50000 accumulated cases, Panama has one of the highest incidences of SARS-CoV-2 in Central America, despite the fast implementation of disease control strategies. We investigated the early transmission patterns of the virus and the outcomes of mitigation measures in the country. Methods We collected information from epidemiological surveillance, including contact tracing, and genetic data from SARS-CoV-2 whole genomes, of the first five weeks of the outbreak. These data were used to estimate the exponential growth rate, doubling time and the time-varying effective reproductive number (Rt) using date of symptom onset in a Bayesian framework. The time of most recent ancestor for the introduced and circulating lineages was estimated by Bayesian analysis. Findings A total of 4210 subjects were SARS-CoV-2 positive during the period evaluated, of them we sequenced 313 cases, detecting the circulation of 10 SARS-CoV-2 lineages. Whole genomes analysis identified the local transmission of one cryptic lineage as early as 2 weeks before it was detected by surveillance systems. Analysis of transmission dynamics showed that lockdown reduced Rt and increased the doubling time, however, these measures did not stop the circulation of this lineage in the country. Interpretation These results demonstrate the value of epidemiological modeling and genome surveillance to assess mitigation strategies. At the same time, an active search for cryptic transmission clusters is crucial to interrupt local transmission of SARS-CoV-2 in a region.

Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil

“…A maximum of three sublevels is allowed (e.g., A.1.1.1); after that, new descendent lineages are given a letter. The SARS-CoV-2 lineage B.1 was initially identified as the most common variant in Europe and is currently also the predominant viral lineage in the Americas ( Candido et al, 2020 ; Deng et al, 2020 ; Fauver et al, 2020 ; Franco et al, 2020 ; Gonzalez-Reiche et al, 2020 ; Laiton-Donato et al, 2020 ; Paiva et al, 2020 ; Paniz-Mondolfi et al, 2020 ; Ramirez et al, 2020 ; Salazar et al, 2020 ; Taboada et al, 2020 ; Xavier et al, 2020 ).…”

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

“…Insights from regions sampled at very high intensities, such as the United Kingdom, show that the majority of introductions lead to small, transient, dead-end transmission lineages, whereas a smaller number of introductions lead to larger and longer-lasting transmission lineages ( 15 ). If this phenomenon is a general property of the first wave of SARS-CoV-2 transmission, as appears to be the case given similar early observations in Brazil ( 5 ), Panama ( 48 ), Uruguay ( 49 ), Spain ( 50 ) and the Netherlands ( 51 ), we can expect that many of the introductions to Guayas led to few new cases, and that most of the ongoing transmission was derived from only a few introductions.…”

Severe acute respiratory syndrome coronavirus 2 detected in placentas of 2 coronavirus disease 2019–positive asymptomatic pregnant women—case report

“… 16 However, the virus was successfully sequenced from the nasopharyngeal swab of the mother. The whole genome indicated that the virus was from the A2 lineage, the main lineage circulating in Panama 17 ( Figure 1 ). A histopathologic examination of the maternal side of the placenta showed hemorrhagic necrosis and hematomas with no inflammatory cell infiltration.…”

“…At the time of detection, the lineages in case 1 (A2) and case 2 (B1) had a local prevalence of around 53.4% and 14.4%, respectively. 17 Further studies should be done in pregnant women to determine the possible association between specific lineages and vertical transmission, and to evaluate whether the A23403G (D614G) 18 and G11803T 19 mutations, both potential signals of viral adaptation, are associated with a viral mechanism for vertical transplacental transmission.…”