We detected Leishmania RNA virus 1 (LRV1) in 11 isolates of Leishmania (Viannia) panamensis collected during 2014-2019 from patients from different geographic areas in Panama. The distribution suggested a spread of LRV1 in L. (V.) panamensis parasites. We found no association between LRV1 and an increase in clinical pathology.

Background: Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections and hospitalization in infants and children. Whole genome sequencing (WGS) plays a critical role in understanding the evolution and epidemiology of RSV. Limited studies have been conducted in Central America and the Caribbean, and none have specifically focused on lineages involved in recent outbreaks. Furthermore, no assays currently exist to evaluate the sensitivity of the RSV fusion protein to monoclonal antibodies. Methods: In Panama, an epidemiological surveillance system tracks RSV activity through the collection of nasopharyngeal samples from patients with acute respiratory infections. Between January 2018 and July 2024, 303 RSV‐positive samples were analyzed by RT‐qPCR. RSV‐B was the dominant subgroup in 2018, but following years had alternating dominance between RSV‐A and RSV‐B. Of the 303 samples, 115 underwent WGS. Additionally, neutralization assays were done using different Anti‐F Monoclonal Antibodies. Results: In RSV‐A, 11 lineages were identified, with 3 to 5 cocirculating during each annual outbreak, and a shift in predominance from A.D .1 (2019) to A.D .5.2 (2023–2024). In RSV‐B, two lineages circulated: B.D.4.1.1 (2018–2020) and its descendant B.D.E.1, which predominated from 2021 onward. Several monoclonal antibodies, including nirsevimab's precursor MEDI8897*, effectively neutralized the RSV strains in neutralization assays. Conclusions: Although Panama has not yet implemented a preventive therapy for RSV, this step could modify outbreak dynamics. The findings from this study provide a baseline reference prior to the implementation of preventive therapies against RSV in Panama and the region, facilitating the assessment of potential changes in the evolutionary dynamics of the virus.

Leishmania (Viannia) spp. can harbor a double-stranded RNA virus known as Leishmania RNA virus 1 (LRV-1), whose presence has been reported in nine countries across the Americas and seven Leishmania species. Here, we studied 100 Leishmania (Viannia) isolates from patients with cutaneous leishmaniasis collected from different endemic areas in Panama from 2016 to 2022. We identified L. (V.) panamensis, L. (V.) guyanensis, L. (V.) braziliensis/guyanensis hybrid, and L. (V.) panamensis sp.1. (genetic variant). LRV-1 was detected by RT-PCR in 9% of L. (Viannia) isolates (eight cases in L. (V.) panamensis, and one in L. (V.) guyanensis). Phylogenetic analysis based on sequencing data classified all LRV-1 isolates within genotype A, suggesting that LRV phylogenetic proximity is closely aligned with geographical distribution or to the phylogenetic proximity of the Leishmania host in the case of the L. (V.) panamensis and L. (V.) guyanensis in Panama.

Summary: 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. Funding: Ministry of Health, Contribution from private donors and Secretaría Nacional de Ciencia y Tecnología. Research in Context: Evidence before this study: In May 2020, we searched for published studies in PubMed and web of Science related to genetic variability and dynamics of SARS-CoV-2 transmission in Latin America, and there was none. On July 2020, there was one study of this type on SARS-CoV-2 transmission in Brazil and none in Central America. We were particularly interested in SARS-CoV-2 cryptic transmission that could allow the virus spread through locals without being detected by respiratory health system surveillance, and no publication was reported. On July 2020, seven papers (five in preprint) were about SARS-CoV-2 cryptic transmission, one in China, another in UK and five in the US. None in Central America. All of them showed the importance of genomic surveillance to detect different lineage introductions, cryptic transmission and its role in early spread in a region or in health-care setting. Added value of this study: We integrate data collected from tested individual during national surveillance of COVID19 suspected cases or contact of cases, as part of the National COVID19 Laboratory network. This data was used to estimate epidemiological parameters of the outbreak as well as the effect of mitigation measures on the epidemic dynamic. We sequence the whole genome of SARS-COV-2 of 7.4% of RT-PCR confirmed cases at the national level, and with phylogenetic analysis we identified SARS-CoV-2 lineages introduced in the country and estimate date of their introductions. Epidemiological and genetic data was compared and we observed the cryptic transmission of one introduced lineage and the rise of a local lineage that was not detected by the active contact tracing implemented by the health system surveillance. This cryptic lineage could explain the fact that early implementation measures decreased the transmission rate and the increased the doubling time, however they were not able to eliminate totally the virus spread. Implications of all the available evidence: This is the first study that analyzed the epidemiology and transmission dynamics of the early COVID19 epidemic in a Central American country using both epidemiological and genomic surveillance. Our findings suggest that strict containment measures and movement restrictions in Panama might have contributed to decrease the early spread of the virus, but that cryptic local transmission allowed a continual basal virus diffusion that could explain, in part, the high incidence of cases in the country. More broadly, our findings are crucial to inform intervention policy in real-time, for countries in similar situations and the importance of constant monitoring of SARS-CoV-2 lineages to understand its transmission in a region.