SARS-CoV-2 in a tropical area of Colombia, a remarkable conversion of presymptomatic to symptomatic people impacts public health.

BACKGROUND: The ability of SARS-CoV-2 to remain in asymptomatic individuals facilitates its dissemination and makes its control difficult. OBJECTIVE: To establish a cohort of asymptomatic individuals, change to the symptomatic status, and determine the most frequent clinical manifestations.  METHODS: Between April 9 and August 9, 2020, molecular diagnosis of SARS-CoV-2 infection was confirmed in 154 asymptomatic people in contact with subjects diagnosed with COVID-19. Nasopharyngeal swabs were performed on these people in different hospitals in Córdoba, the Caribbean area of Colombia. The genes E, RdRp, and N were amplified with RT-qPCR. Based on the molecular results and the Cq values, the patients were subsequently followed up through telephone calls to verify their health conditions. RESULTS: Overall, of 154 asymptomatic individuals, 103 (66.9%) remained asymptomatic, and 51 (33.1%) changed to symptomatic. The most frequent clinical manifestations in young people were anosmia and arthralgia. Adults showed cough, ageusia, and odynophagia; in the elderly were epigastralgia, dyspnea, and headache. Mortality was 8%. CONCLUSIONS: A proportion of 33% of presymptomatic individuals was found, of which four of them died. This high rate could indicate a silent transmission, contributing significantly to the epidemic associated with SARS-CoV-2.

Epidemiological and viral features of a cohort of SARS-CoV-2 symptomatic and asymptomatic individuals in an area of the Colombian Caribbean.

BACKGROUND: Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is an emerging viral pandemic disease. In the last 6 months, SARS-CoV-2 has caused millions of reported cases and hundreds of thousands of deaths. As other world regions, South America has not contained the pandemic's advance since it lacks the hospital and economic capacities. Public health implications of transmission, while the asymptomatic/presymptomatic infection is a critical concern at the current pandemic. OBJECTIVE: Describe the socio-demographic, clinical, and viral features of a cohort of SARS-CoV-2 infected individuals from the Colombian Caribbean. METHODS: Six hundred eighty-six clinical samples of suspected SARS-CoV-2 infection cases and contacts individuals from several hospital centers in the department of Córdoba, Colombia, were received at our laboratory between April 9th and May 16th, 2020. RNA was extracted using lysis buffers and spin columns. The samples were tested for SARS-CoV-2 by reverse transcription real-time polymerase chain reaction (RT-qPCR) using commercially available multiplex real-time PCR assay for simultaneous detection of 3 target genes of SARS-CoV-2 (Allplex™, 2019-nCoV assay, Korea). Viral copies quantification was done using a standard curve constructed from seriated dilutions of a SARS-CoV-2 positive control. Statics descriptive methods were used. RESULTS: Thirty-five nasopharyngeal samples were positive for SARS-CoV-2 infection; the average age was 43 (range, 1-95 years). Seventeen of 35 (49%) of the patients showed symptoms. Most of them had a cough, fever, and odynophagia; three of the patients reported having arthralgia. Only two patients required hospitalization. None of the patients had known co-morbidities. RT-qPCR results show that two of the symptomatic patients had significantly higher RNA copies than the rest. Eighteen of 35 (51%) individuals were asymptomatic, and the average age was 30 (range, 6-61 years). Four asymptomatic individuals showed a higher copy than some symptomatic patients; nonetheless, the average of RNA copies 8.26 × 1010 was lower than the symptomatic. CONCLUSIONS: This study shows that asymptomatic patients may develop infections with a high number of RNA copies. Since a considerable percentage of infections may be asymptomatic/presymptomatic, enhanced testing approaches may be needed to detect these persons. Due the occurrence of a large proportion of infections being a result from transmission originated in asymptomatic/presymptomatic individuals, public health interventions in Colombia should be based on two steps: a massive molecular screening, and viral load quantification. Finally, a remarkable issue in our study is the average age of symptomatic and asymptomatic groups (43 and 30 respectively) which may be important because of the economic impact that has been caused by the coronavirus pandemic and may be probably the cause of the reduced lethality observed in the country and the department at the time of this study.

Hard ticks (Ixodida: Ixodidae) in the Colombian Caribbean harbor the Jingmen tick virus: an emerging arbovirus of public health concern.

BACKGROUND: Ticks are obligate hematophagous ectoparasites involved in transmitting viruses of public health importance. The objective of this work was to identify the Jingmen tick virus in hard ticks from the Colombian Caribbean, an arbovirus of importance for public health. METHODS: Ticks were collected in rural areas of Córdoba and Cesar, Colombia. Taxonomic identification of ticks was carried out, and pools of 13 individuals were formed. RNA extraction was performed. Library preparation was performed with the MGIEasy kit, and next-generation sequencing (NGS) with MGI equipment. Bioinformatic analyses and taxonomic assignments were performed using the Galaxy platform, and phylogenetic analyses were done using IQ-TREE2. RESULTS: A total of 766 ticks were collected, of which 87.33% (669/766) were Rhipicephalus microplus, 5.4% (42/766) Dermacentor nitens, 4.2% (32/766) Rhipicephalus linnaei, and 3.0% (23/766) Amblyomma dissimile. Complete and partial segments 1, 2, 3, and 4 of Jingmen tick virus (JMTV) were detected in the metatranscriptome of the species R. microplus, D. nitens, and A. dissimile. The JMTVs detected are phylogenetically related to JMTVs detected in Aedes albopictus in France, JMTVs detected in R. microplus in Trinidad and Tobago, JMTVs in R. microplus and A. variegatum in the French Antilles, and JMTVs detected in R. microplus in Colombia. Interestingly, our sequences clustered closely with JMTV detected in humans from Kosovo. CONCLUSIONS: JMTV was detected in R. microplus, D. nitens, and A. dissimile. JMTV could pose a risk to humans. Therefore, it is vital to establish epidemiological surveillance measures to better understand the possible role of JMTV in tropical diseases.

Molecular evidence of Borrelia spp. in bats from Córdoba Department, northwest Colombia.

BACKGROUND: The genus Borrelia is composed of two well-defined monophyletic groups, the Borrelia burgdorferi sensu lato complex (Bb) and the relapsing fever (RF) group borreliae. Recently, a third group, associated with reptiles and echidnas, has been described. In general, RF group borreliae use rodents as reservoir hosts; although neotropical bats may also be involved as important hosts, with scarce knowledge regarding this association. The objective of this study was to detect the presence of Borrelia spp. DNA in bats from the department of Córdoba in northwest Colombia. METHODS: During September 2020 and June 2021, 205 bats were captured in six municipalities of Córdoba department, Colombia. Specimens were identified using taxonomic keys and DNA was extracted from spleen samples. A Borrelia-specific real-time PCR was performed for the 16S rRNA gene. Fragments of the 16S rRNA and flaB genes were amplified in the positive samples by conventional PCR. The detected amplicons were sequenced by the Sanger method. Phylogenetic reconstruction was performed in IQ-TREE with maximum likelihood based on the substitution model TPM3+F+I+G4 with bootstrap values deduced from 1000 replicates. RESULTS: Overall, 10.2% (21/205) of the samples were found positive by qPCR; of these, 81% (17/21) and 66.6% (14/21) amplified 16S rRNA and flaB genes, respectively. qPCR-positive samples were then subjected to conventional nested and semi-nested PCR to amplify 16S rRNA and flaB gene fragments. Nine positive samples for both genes were sequenced, and seven and six sequences were of good quality for the 16S rRNA and flaB genes, respectively. The DNA of Borrelia spp. was detected in the insectivorous and fruit bats Artibeus lituratus, Carollia perspicillata, Glossophaga soricina, Phyllostomus discolor, and Uroderma sp. The 16S rRNA gene sequences showed 97.66-98.47% identity with "Borrelia sp. clone Omi3," "Borrelia sp. RT1S," and Borrelia sp. 2374; the closest identities for the flaB gene were 94.02-98.04% with "Borrelia sp. Macaregua." For the 16S rRNA gene, the phylogenetic analysis showed a grouping with "Candidatus Borrelia ivorensis" and "Ca. Borrelia africana," and for the flaB gene showed a grouping with Borrelia sp. Macaregua and Borrelia sp. Potiretama. The pathogenic role of the Borrelia detected in this study is unknown. CONCLUSIONS: We describe the first molecular evidence of Borrelia spp. in the department of Córdoba, Colombia, highlighting that several bat species harbor Borrelia spirochetes.

Effectiveness of the CoronaVac® vaccine in a region of the Colombian Amazon, was herd immunity achieved?

INTRODUCTION: Currently, more than 4.5 billion doses of SARS-CoV-2 vaccines have been applied worldwide. However, some developing countries are still a long way from achieving herd immunity through vaccination. In some territories, such as the Colombian Amazon, mass immunization strategies have been implemented with the CoronaVac® vaccine. Due to its proximity to Brazil, where one of the variants of interest of SARS-CoV-2 circulates. OBJECTIVE: To determine the effectiveness of the CoronaVac® vaccine in a population of the Colombian Amazon. METHODS: Between February 24, 2021, and August 10, 2021, a descriptive observational study was carried out in which a population of individuals over 18 years of age immunized with two doses of the CoronaVac® vaccine was evaluated. The study site was in the municipality of Mitú, Vaupés, in southeastern Colombia, a region located in the Amazon bordering Brazil. RESULTS: 99% of the urban population of the Mitú municipality were vaccinated with CoronaVac®. To date, 5.7% of vaccinated individuals have become ill, and only 0.1% of these require hospitalization. One death was attributable to COVID-19 has been reported among vaccinated individuals, and the vaccine has shown 94.3% effectiveness against mild disease and 99.9% against severe infection. CONCLUSIONS: The herd immunity achieved through mass vaccination in this population has made it possible to reduce the rate of complicated cases and mortality from COVID-19 in this region of the Colombian Amazon. HIGHLIGHTS: CoronaVac® has shown 94.3% effectiveness against mild disease and 99.9% against severe infection in this indigenous population. CoronaVac® reduces the mortality rate from 2.2% in 2020 to 0.22% in 2021. The herd immunity was achieved through mass vaccination in this region of the Colombian Amazon.

SARS-CoV-2 in eight municipalities of the Colombian tropics: high immunity, clinical and sociodemographic outcomes.

BACKGROUND: Serological evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an alternative that allows us to determine the prevalence and dynamics of this infection in populations. The goal of this study was to determine the clinical and sociodemographic dynamics of SARS-CoV-2 infection in a region of the Colombian Caribbean. METHODS: Between July and November 2020, a cross-sectional observational study was carried out in Córdoba, located in northeast Colombia in the Caribbean area. Eight municipalities with the largest populations were chosen and 2564 blood samples were taken. A commercial enzyme-linked immunosorbent assay was used with the recombinant protein antigen N of SARS-CoV-2. The people included in the study were asked for sociodemographic and clinical data, which were analysed by statistical methods. RESULTS: A seroprevalence of 40.8% was obtained for SARS-CoV-2 in the Córdoba region. In the bivariate analysis, no differences were observed in seropositivity against SARS-CoV-2 for gender or age range (p>0.05). Higher seropositivity was found in low socio-economic status and symptomatic patients (p<0.0001). A total of 30.7% of the asymptomatic patients were seropositive for SARS-CoV-2, which could be linked to the spread of this infection. In the multivariate analysis, seroconversion was related to poverty and clinical manifestations such as anosmia and ageusia (p<0.05). CONCLUSIONS: The high seropositivity in Córdoba is due to widespread SARS-CoV-2 in this population. The relationship between seropositivity and socio-economic status suggests a higher exposure risk to the virus caused by informal economic activities in low-income groups. Clinical manifestations such as anosmia and ageusia could be clinical predictors of infection by the new emergent coronavirus.

Severe Acute Respiratory Syndrome Coronavirus 2 Seroprevalence Among Adults in a Tropical City of the Caribbean Area, Colombia: Are We Much Closer to Herd Immunity Than Developed Countries?

A serological survey was carried out in Monteria (500 000 population), a mid-size city in Colombia. An overall prevalence of 55.3% (95% confidence interval, 52.5%-57.8%) was found among a sample of 1.368 people randomly selected from the population. Test positivity was related to economic characteristics with the highest prevalence found in the most impoverished areas, representing 83.8% of the city's population. We found a prevalence that might be associated with some important level of population immunity.

Serological cross-reactivity using a SARS-CoV-2 ELISA test in acute Zika virus infection, Colombia.

OBJECTIVES: We investigated seroreactivity by using a commercial SARS-CoV-2 ELISA test in samples collected from different groups of individuals, including patients diagnosed to have Dengue, Zika, and Chikungunya infection between 2015 and 2019, from an endemic area in the Caribbean Colombian region. METHODS: A total of 127 sera samples obtained from six different groups of individuals were included in this study: Group A: patients with confirmed SARS-CoV-2 infection; Group B: patients with symptoms suggestive of COVID-19 or asymptomatic contacts with confirmed patients; Group C: patients with acute or recent dengue virus infection; Group D: patients with acute Zika virus infection; Group E: patients with previous Chikungunya virus infection; and Group F: individuals with exposure to spotted fever group rickettsiae. RESULTS: Overall, group A, group B, and group D showed seroreactivity to SARS-CoV-2 in 92%, 75%, and 26% of samples, respectively; furthermore, group C, group E, and group F showed 100% seronegativity. CONCLUSIONS: We found 26% of serological cross-reactivity in patients with acute Zika virus infection by using a commercial SARS-CoV-2 ELISA test. Further studies are needed to evaluate whether serological cross-reaction is maintained with time in nonacute patients with previous exposure to the Zika virus and its effect in SARS-CoV-2 serosurveys in endemic areas for this arbovirus.