key: cord-0801218-o87vx3xr
authors: Loyola, Steev; Torres‐Pacheco, Jaison; Malambo‐García, Dacia; Gómez‐Camargo, Doris
title: SARS‐CoV‐2 Delta variant in Cartagena de Indias, Colombia, August 2021
date: 2022-01-23
journal: Health Sci Rep
DOI: 10.1002/hsr2.480
sha: 1a3fbda997ec14c70abf75857f72afba40247af7
doc_id: 801218
cord_uid: o87vx3xr

nan

Participants were recruited by an ongoing surveillance study conducted by Unidad de Investigaci on Molecular (UNIMOL) that enrolls individuals with acute respiratory symptoms since 2014 under an institutional review board-approved protocol (UDC2014-70). Epidemiological information, including demographic characteristics, co-morbidities, vaccination status, and clinical data, were collected at the time of enrollment using a standard form provided by the National Institute of Health of Colombia. Nasopharyngeal swabs were routinely collected, and real-time reverse-transcriptase polymerase chain reaction (RT-PCR) 3 

Device) tests were performed to detect SARS-CoV-2 RNA and protein, respectively.

The SARS-CoV-2 spike gene was sequenced using a targeted amplification approach of overlapping segments. Briefly, previously described sets of 12 PCR primers (SC2M1-54 to SC2M1-65) and a set of primers (SC2M1-55_ LEFT and SC2M1-56_RIGHT) were selected for the entire and partial gene sequencing, respectively. 4 Viral RNA was extracted from swabs using the QIAamp Viral RNA Mini kit (QIAGEN; 52906), and cDNA and amplicons were generated as previously described 4 in a one-step RT-PCR using 20 μL reaction volume that contained 1.5 μL nuclease-free water, 10 μL 2X buffer, 0.5 μL enzyme mix (Invitrogen; 12574026), 1.5 μL 10 μM of forward and reverse primers, and 5 μL of RNA. Amplicon products were purified 

On 9 August 2021, Subject A was enrolled and tested positive for SARS-CoV-2 (Table 1) . Subject A was a 53-year-old female who reported no co-morbidities, being fully vaccinated with a two-dose mRNA COVID-19 vaccine 2.9 months prior to enrollment. She did report of a headache since 6 August. Additionally, Subject A reported to have attended a work-related social event on August 4. Subject A reported no suspected cases of COVID-19 among her close contacts.

On 10 August 2021, Subject B was enrolled and tested positive for SARS-CoV-2 (Table 1) Figure 1B ).

Since its initial report in October 2020, the Delta variant has evolved and become the most dominant variant in several locations worldwide. [6] [7] [8] However, it was not until July 2021 that the Delta variant increased exponentially in the Americas. 9 In Colombia, Delta variant reports increased similarly to those observed in the rest of the Americas. August was the month in which these reports specifically increased (https://covariants.org/per-country). Sanger sequencing of the spike gene is a rapid and low-cost strategy that allows it to identify signature mutations, and to distinguish and monitor circulating variants. 10, 11 In this study, the mutation calling and Nextstrain clade assignment were successfully performed using 

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The authors declare no conflict of interest. All authors had full access to the data and takes complete responsibility for the integrity of the data and the accuracy of the data analysis.

https://orcid.org/0000-0001-5455-2423