Early Transmission Dynamics, Spread, and Genomic Characterization of SARS-CoV-2 in Panama

Franco, Danilo; González, Claudia; Ábrego, Leyda; Carrera, Jean-Paul; Díaz, Yamilka; Caicedo, Yaset; Moreno, Ambar; Chavarria, Oris; Góndola, Jessica; Castillo, Marlene; Valdespino, Elimelec; Gaitán, Melissa; Martínez-Mandiche, Jose; Hayer, Lizbeth; González, Pablo A.; Lange, Carmen; Moltó, Yadira; Mojica, Dalis; Ramos, Rubén; Mastelari, Maria; Cerezo, Lizbeth; Moreno, Lourdes; Donnelly, Christl A.; Pascale, Juan Miguel; Faria, Nuno Rodrigues; López‐Vergès, Sandra; Martínez, Alexander A.

doi:10.3201/eid2702.203767

Cited by 27 publications

(24 citation statements)

References 15 publications

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“…Furthermore, this suggests that untracked SARS-CoV-2 community transmission occurred prior to the first confirmed case (April 7, 2020) (Fig 3). Such transmission dynamics has been reported in other countries like the US (e.g., Washington State [20], California [21]) and Panama [26] where viral circulation was reported weeks prior to the first confirmed cases. Interestingly, all isolates in this study encode the D614G spike variant which has been associated with higher viral loads and increased infectivity and transmissibility [46,55].…”

Section: Plos Neglected Tropical Diseasessupporting

confidence: 65%

“…Genomic epidemiology studies have enabled not only the characterization and spread of the VOCs and other viral lineages, but also has been widely implemented to decipher regional transmission dynamics [18], introduction events, and the high-resolution reconstruction of transmission patterns of SARS-CoV-2 in several countries, including China [19], the US (Washington [20], California [21], New York [22]), Chile [23], Colombia [24], Brazil [25], Panama [26], among others.…”

Section: Introductionmentioning

confidence: 99%

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Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin

et al. 2021

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Background The SARS-CoV-2 pandemic has forced health authorities across the world to take important decisions to curtail its spread. Genomic epidemiology has emerged as a valuable tool to understand introductions and spread of the virus in a specific geographic location. Methodology/Principal findings Here, we report the sequences of 59 SARS-CoV-2 samples from inhabitants of the Colombian Amazonas department. The viral genomes were distributed in two robust clusters within the distinct GISAID clades GH and G. Spatial-temporal analyses revealed two independent introductions of SARS-CoV-2 in the region, one around April 1, 2020 associated with a local transmission, and one around April 2, 2020 associated with other South American genomes (Uruguay and Brazil). We also identified ten lineages circulating in the Amazonas department including the P.1 variant of concern (VOC). Conclusions/Significance This study represents the first genomic epidemiology investigation of SARS-CoV-2 in one of the territories with the highest report of indigenous community of the country. Such findings are essential to decipher viral transmission, inform on global spread and to direct implementation of infection prevention and control measures for this vulnerable population, especially, due to the recent circulation of one of the variants of concern (P.1) associated with major transmissibility and possible reinfections.

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Section: Plos Neglected Tropical Diseasessupporting

confidence: 65%

Section: Introductionmentioning

confidence: 99%

Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin

et al. 2021

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“…Whole genome sequencing showed that both viruses belong to two endemic lineages ( Figure 1 B, Supplementary Figure 1): GMI-PA376271 (EPI_ISL_1001457) being A.2.4, previously named A.2.1. ( Franco et al, 2020 ). The second genome GMI-PA584303 accumulated 33 nucleotide (nt) mutations compared with reference MN908947.3 and 23 (21 nt substitutions, 1 deletion, 1 insertion) compared to first sample GMI-PA376271 ( Figure 1 C, Supplementary Table 1).…”

Section: Resultsmentioning

confidence: 99%

“…SARS-CoV-2 genome analysis showed that both infections were induced by viruses from Panamanian endemic lineages, A.2.4 ( Franco et al, 2020 ) for the first, and A.2.5., containing Spike mutations D614 G and L452R, for the second. Most of the fifthteen induced a.a. changes in the second virus, like the ones in ORF1a, have not been previously described.…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama

Díaz

Ortiz

Weeden

et al. 2021

International Journal of Infectious Diseases

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“…It is also worth noting that B.1.214.2 displays a large deletion (10 codons) in the N-terminal region of ORF3a, which is not found in other relevant SARS-CoV-2 lineages (Figure 3). Context for the emergence of A.2.5 A.2.5 stems from A.2.4, the dominant lineage in the Panama pandemics during the first half of 2020 [46]. This lineage started spreading very early in the region, with the first detections in oropharyngeal swabs sampled in late February 2020.…”

Section: Resultsmentioning

confidence: 99%

Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein

Gerdol

2021

Preprint

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Tracking the evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through genomic surveillance programs is undoubtedly one of the key priorities in the current pandemic situation. Although the genome of SARS-CoV-2 acquires mutations at a slower rate compared with other RNA viruses, evolutionary pressures derived from the widespread circulation of SARS-CoV-2 in the human population have progressively favored the global emergence though natural selection of several variants of concern that carry multiple non-synonymous mutations in the spike glycoprotein. Such mutations are often placed in key sites within major antibody epitopes and may therefore confer resistance to neutralizing antibodies, leading to partial immune escape, or otherwise compensate minor infectivity deficits associated with other mutations. As previously shown by other authors, several emerging variants carry recurrent deletion regions (RDRs) that display a partial overlap with antibody epitopes located in the spike N-terminal domain. Comparatively, very little attention has been directed towards spike insertion mutations, which often go unnoticed due to the use of insertion-unaware bioinformatics analysis pipelines. This manuscript describe a single recurrent insertion region (RIR1) in the N-terminal domain of SARS-CoV-2 spike protein, characterized by the independent acquisition of 3-4 additional codons between Arg214 and Asp215 in different viral lineages. Even though RIR1 is unlikely to confer antibody escape, its progressive increase in frequency and its association with two distinct emerging lineages (A.2.5 and B.1.214.2) warrant further investigation concerning its effects on spike structure and viral infectivity.

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Early Transmission Dynamics, Spread, and Genomic Characterization of SARS-CoV-2 in Panama

Cited by 27 publications

References 15 publications

Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin

Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin

SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama

Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein

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