Detection and Molecular Characterization of Zoonotic Poxviruses Circulating in the Amazon Region of Colombia, 2014.

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.

SARS-CoV-2 infection in newborn infants: descriptive epidemiological analysis of cases reported to the Colombian national surveillance system during the first pandemic year, March 2020-February 2021.

OBJECTIVE: To describe the clinical and epidemiological characteristics of newborn infants with SARS-CoV-2 infection notified in the Colombian Public Health Surveillance System. DESIGN: This epidemiological descriptive analysis was conducted using the data of all cases of newborn infants with confirmed SARS-CoV-2 infection notified in the surveillance system. Absolute frequencies and central tendency measures were calculated and a bivariate analysis comparing variables of interest with symptomatic and asymptomatic disease was performed. SETTING: Population-based descriptive analysis. PATIENTS: Laboratory-confirmed COVID-19 cases in newborn infants (aged ≤28 days of life) reported to the surveillance system from 1 March 2020 to 28 February 2021. RESULTS: 879 newborns were identified, corresponding to 0.04% of all reported cases in the country. The mean age at diagnosis was 13 days (range 0-28 days), 55.1% were male and most (57.6%) were classified as symptomatic. Preterm birth and low birth weight were identified in 24.0% and 24.4% of the cases, respectively. Common symptoms were fever (58.3%), cough (48.3%) and respiratory distress (34.9%). A higher prevalence of symptomatic newborns was seen in individuals with low birth weight for gestational age (prevalence ratio (PR): 1.51, 95% CI: 1.44 to 1.59) and newborns with underlying conditions (PR: 1.33, 95% CI: 1.13 to 1.55). CONCLUSIONS: There were a low proportion of confirmed COVID-19 cases in the newborn population. A substantial number of newborns were classified as symptomatic, having low birth weight and being preterm. Clinicians caring for COVID-19-infected newborns should be aware of population characteristics that potentially contribute to disease manifestations and severity.

Estimating Zika virus attack rates and risk of Zika virus-associated neurological complications in Colombian capital cities with a Bayesian model.

Zika virus (ZIKV) is a mosquito-borne pathogen that caused a major epidemic in the Americas in 2015-2017. Although the majority of ZIKV infections are asymptomatic, the virus has been associated with congenital birth defects and neurological complications (NC) in adults. We combined multiple data sources to improve estimates of ZIKV infection attack rates (IARs), reporting rates of Zika virus disease (ZVD) and the risk of ZIKV-associated NC for 28 capital cities in Colombia. ZVD surveillance data were combined with post-epidemic seroprevalence data and a dataset on ZIKV-associated NC in a Bayesian hierarchical model. We found substantial heterogeneity in ZIKV IARs across cities. The overall estimated ZIKV IAR across the 28 cities was 0.38 (95% CrI: 0.17-0.92). The estimated ZVD reporting rate was 0.013 (95% CrI: 0.004-0.024), and 0.51 (95% CrI: 0.17-0.92) cases of ZIKV-associated NC were estimated to be reported per 10 000 ZIKV infections. When we assumed the same ZIKV IAR across sex or age group, we found important spatial heterogeneities in ZVD reporting rates and the risk of being reported as a ZVD case with NC. Our results highlight how additional data sources can be used to overcome biases in surveillance data and estimate key epidemiological parameters.

Clinical outcomes associated with Mu variant infection during the third epidemic peak of COVID-19 in Colombia.

BACKGROUND: The higher number of cases and deaths caused by COVID-19 in Colombia occurred during the third epidemic peak, where the Mu variant was associated with 50% of the cases. OBJECTIVE: To evaluate the association between the clinical outcome of COVID-19 with health conditions and SARS-CoV-2 lineages. METHODS: In this study, clinical metadata and SARS-CoV-2 lineages from 535 patients with different degrees of COVID-19 severity were obtained after the SARS-CoV-2 genomic surveillance in Colombia. Then, the associations between these variables were determined using a multidimensional unfolding analysis. RESULTS: Asymptomatic, symptomatic, severe, and deceased outcomes represented 15.2%, 29.7%, 7.3%, and 47.8% of the cases, respectively. Males tend to develop more serious COVID-19, and severe or fatal outcomes were typically observed in patients aged >60 years with comorbidities, including chronic obstructive pulmonary disease, heart disease, kidney disease, obesity, asthma, and smoking history. The SARS-CoV-2 Mu and Gamma variants dominated the third epidemic peak and accounted for most fatal cases with odd ratio values of 128.2 (CI 53.0-310.1) and 18.6 (CI 8.294-41.917). CONCLUSION: This study shows the high impact of SARS-CoV-2 lineages with higher prevalence on public health and the importance of monitoring COVID-19 risk factors to control the associated mortality.

Descriptive analysis of surveillance data for Zika virus disease and Zika virus-associated neurological complications in Colombia, 2015-2017.

Zika virus (ZIKV) is a mosquito-borne pathogen that recently caused a major epidemic in the Americas. Although the majority of ZIKV infections are asymptomatic, the virus has been associated with birth defects in fetuses and newborns of infected mothers as well as neurological complications in adults. We performed a descriptive analysis on approximately 106,000 suspected and laboratory-confirmed cases of Zika virus disease (ZVD) that were reported during the 2015-2017 epidemic in Colombia. We also analyzed a dataset containing patients with neurological complications and recent febrile illness compatible with ZVD. Females had higher cumulative incidence of ZVD than males. Compared to the general population, cases were more likely to be reported in young adults (20 to 39 years of age). We estimated the cumulative incidence of ZVD in pregnant females at 3,120 reported cases per 100,000 population (95% CI: 3,077-3,164), which was considerably higher than the incidence in both males and non-pregnant females. ZVD cases were reported in all 32 departments. Four-hundred and eighteen patients suffered from ZIKV-associated neurological complications, of which 85% were diagnosed with Guillain-Barré syndrome. The median age of ZIKV cases with neurological complications was 12 years older than that of ZVD cases. ZIKV-associated neurological complications increased with age, and the highest incidence was reported among individuals aged 75 and older. Even though neurological complications and deaths due to ZIKV were rare in this epidemic, better risk communication is needed for people living in or traveling to ZIKV-affected areas.

Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America.

SARS-CoV-2 is a new member of the genus Betacoronavirus, responsible for the COVID-19 pandemic. The virus crossed the species barrier and established in the human population taking advantage of the spike protein high affinity for the ACE receptor to infect the lower respiratory tract. The Nucleocapsid (N) and Spike (S) are highly immunogenic structural proteins and most commercial COVID-19 diagnostic assays target these proteins. In an unpredictable epidemic, it is essential to know about their genetic variability. The objective of this study was to describe the substitution frequency of the S and N proteins of SARS-CoV-2 in South America. A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm. Forty-three sequences from 13 Colombian departments were obtained in this study using the Oxford Nanopore and Illumina MiSeq technologies, following the amplicon-based ARTIC network protocol. The substitutions D614G in S and R203K/G204R in N were the most frequent in South America, observed in 83% and 34% of the sequences respectively. Strikingly, genomes with the conserved position D614 were almost completely replaced by genomes with the G614 substitution between March to April 2020. A similar replacement pattern was observed with R203K/G204R although more marked in Chile, Argentina and Brazil, suggesting similar introduction history and/or control strategies of SARS-CoV-2 in these countries. It is necessary to continue with the genomic surveillance of S and N proteins during the SARS-CoV-2 pandemic as this information can be useful for developing vaccines, therapeutics and diagnostic tests.

Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia.

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.

Long-term outcomes of Guillain-Barré syndrome possibly associated with Zika virus infection.

BACKGROUND: This prospective cohort investigation analyzed the long-term functional and neurologic outcomes of patients with Zika virus-associated Guillain-Barré syndrome (GBS) in Barranquilla, Colombia. METHODS: Thirty-four Zika virus-associated GBS cases were assessed a median of 17 months following acute GBS illness. We assessed demographics, results of Overall Disability Sum Scores (ODSS), Hughes Disability Score (HDS), Zung Depression Scale (ZDS), and Health Related Quality of Life (HRQL) questionnaires; and compared outcomes indices with a normative sample of neighborhood-selected control subjects in Barranquilla without GBS. RESULTS: Median age at time of acute neurologic onset was 49 years (range, 10-80); 17 (50%) were male. No deaths occurred. At long-term follow-up, 25 (73%) patients had a HDS 0-1, indicating complete / near complete recovery. Among the group, HDS (mean 1.4, range 0-4), ODSS (mean 1.9, range 0-9) and ZDS score (mean 34.4, range 20-56) indicated mild / moderate ongoing disability. Adjusting for age and sex, Zika virus-associated GBS cases were similar to a population comparison group (n = 368) in Barranquilla without GBS in terms of prevalence of physical or mental health complaints, though GBS patients were more likely to have an ODSS of ≥ 1 (OR 8.8, 95% CI 3.2-24.5) and to suffer from moderate / moderate-severe depression (OR 3.89, 95% CI 1.23-11.17) than the comparison group. CONCLUSIONS: Long-term outcomes of Zika virus-associated GBS are consistent with those associated with other antecedent antigenic stimuli in terms of mortality and ongoing long-term morbidity, as published in the literature. Persons with Zika virus-associated GBS more frequently reported disability and depression after approximately one year compared with those without GBS.

Zika virus disease-associated Guillain-Barré syndrome-Barranquilla, Colombia 2015-2016.

BACKGROUND: An outbreak of Guillain-Barré syndrome (GBS), a disorder characterized by acute, symmetric limb weakness with decreased or absent deep-tendon reflexes, was reported in Barranquilla, Colombia, after the introduction of Zika virus in 2015. We reviewed clinical data for GBS cases in Barranquilla and performed a case-control investigation to assess the association of suspect and probable Zika virus disease with GBS. METHODS: We used the Brighton Collaboration Criteria to confirm reported GBS patients in Barranquilla during October 2015-April 2016. In April 2016, two neighborhood and age range-matched controls were selected for each confirmed GBS case-patient. We obtained demographics and antecedent symptoms in the 2-month period before GBS onset for case-patients and the same period for controls. Sera were collected for Zika virus antibody testing. Suspected Zika virus disease was defined as a history of rash and ≥2 other Zika-related symptoms (fever, arthralgia, myalgia, or conjunctivitis). Probable Zika virus disease was defined as suspected Zika virus disease with laboratory evidence of a recent Zika virus or flavivirus infection. Conditional logistic regression adjusted for sex and race/ethnicity was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs). RESULTS: We confirmed 47 GBS cases. Incidence increased with age (10-fold higher in those ≥60years versus those <20years). We interviewed 40 case-patients and 79 controls. There was no significant difference in laboratory evidence of recent Zika virus or flavivirus infection between case-patients and controls (OR: 2.2; 95% CI: 0.9-5.1). GBS was associated with having suspected (OR: 3.0, 95% CI: 1.1-8.6) or probable Zika virus disease (OR: 4.6, CI: 1.1-19.0). CONCLUSIONS: Older individuals and those with suspected and probable Zika virus disease had higher odds of developing GBS. KEY POINTS: We confirmed a Guillain-Barré syndrome (GBS) outbreak in Barranquilla, Colombia, during October 2015-April 2016. A case-control investigation using neighborhood controls showed an association of suspected and probable Zika virus disease with GBS.