No abstract

No abstract

The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem unprecedented in the recent history of humanity. Different in-house real-time RT-PCR (rRT-PCR) methods for SARS-CoV-2 diagnosis and the appearance of genomes with mutations in primer regions have been reported. Hence, whole-genome data from locally-circulating SARS-CoV-2 strains contribute to the knowledge of its global variability and the development and fine tuning of diagnostic protocols. To describe the genetic variability of Colombian SARS-CoV-2 genomes in hybridization regions of oligonucleotides of the main in-house methods for SARS-CoV-2 detection, RNA samples with confirmed SARS-CoV-2 molecular diagnosis were processed through next-generation sequencing. Primers/ probes sequences from 13 target regions for SARS-CoV-2 detection suggested by 7 institutions and consolidated by WHO during the early stage of the pandemic were aligned with Muscle tool to assess the genetic variability potentially affecting their performance. Finally, the corresponding codon positions at the 3′ end of each primer, the open reading frame inspection was identified for each gene/protein product. Complete SARS-CoV-2 genomes were obtained from 30 COVID-19 cases, representative of the current epidemiology in the country. Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP and N genes were observed. The 3′ end of 4 primers aligned to the third codon position, showed high risk of nucleotide substitution and potential mismatches at this critical position. Genetic variability was detected in Colombian SARS-CoV-2 sequences in some of the primer/probe regions for in-house rRT-PCR diagnostic tests available at WHO COVID-19 technical guidelines; its impact on the performance and rates of false-negative results should be experimentally evaluated. The genomic surveillance of SARS-CoV-2 is highly recommended for the early identification of mutations in critical regions and to issue recommendations on specific diagnostic tests to ensure the coverage of locally-circulating genetic variants.

C oronavirus disease (COVID-19) is a life-threatening respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an emerging zoonotic virus first identified in Wuhan, China (1). The first confirmed cases of COVID-19 were reported on January 12, 2020, from patients who had respiratory symptoms during December 8, 2019-January 2, 2020 (2). Despite early containment and mitigation measures (3), the high infectiousness, presymptomatic transmission, and prolonged transmissibility of SARS-CoV-2 (4,5) combined with other factors, such as globalization, led to the rapid spread of COVID-19 across the world. Rigorous contact-tracing and physical distancing measures implemented in different countries have been effective in delaying the epidemic during the contention phase (6-9). However, ensuing lockdowns and travel restrictions to minimize the burden on healthcare systems have led to a decline in wellbeing and an economic downturn and have had profound impacts in low-to-middle income countries (10). The contention phase in Colombia started on March 6, 2020, when the Instituto Nacional de Salud (INS; National Institute of Health) confirmed the first case of COVID-19 from a person returning to Colombia from Italy on February 26, 2020 (11). On March 23, a total 314 cases had been confirmed, which prompted the closure of all the country borders to contain the outbreak. On March 31, >10% of confirmed cases were among persons with no known exposure to a COV-ID-19 patient (12), presumably due to extensive community transmission. Colombia then implemented the mitigation phase, which included physical distancing as the main strategy to limit virus spread. By June 18, a total of 57,046 confirmed cases and 1,864 deaths had been reported in Colombia (13). The unprecedented global health and societal emergency posed by the COVID-19 pandemic urged data sharing and faster-than-ever outbreak research developments that are reflected in the >37,000 complete SARS-CoV-2 genomes made available through

During 2014, cutaneous lesions were reported in dairy cattle and farmworkers in the Amazon Region of western Colombia. Samples from 6 patients were analyzed by serologic and PCR testing, and results demonstrated the presence of vaccinia virus and pseudocowpox virus. These findings highlight the need for increased poxvirus surveillance in Colombia.