Coinfection of SARS-CoV-2 with other respiratory pathogens in outpatients from Ecuador.

Worldwide, the COVID-19 pandemic caused by SARS-CoV-2 has enormously impacted healthcare systems, especially in low and middle-income countries. Coinfections with respiratory pathogens in COVID-19 patients may contribute to worse outcomes. This study identified the presence of 12 viral coinfections and pneumococcal carriers among individuals with SARS-CoV-2 infection in outpatient and community settings in Ecuador. From January 2020 to November 2021, 215 nasopharyngeal and nasal swabs were taken from individuals who reported symptoms of COVID-19 or had known exposure to someone with confirmed or suspected COVID-19. One hundred fifty-eight tested positive for SARS-CoV-2 by RT-qPCR and coinfections were detected in 12% (19/158) of SARS-CoV-2-positive patients; the most frequent coinfection was with influenza A virus at 4.4% (7/158; 95% CI: 1.2-7.6), followed by respiratory syncytial virus with 3.1% (5/158; 95% CI: 0.4-5.8), and finally rhinovirus and human coronavirus NL63 with 1.2% (2/158). Pneumococcal carriage was detected in 3.7% (6/158; 95% CI: 0.76-6.64) of SARS-CoV-2 cases. Influenza B, adenovirus, human metapneumovirus (HMPV), parainfluenza virus types 1, 2, and 3, and human coronavirus HKU1 were undetected. To our knowledge, this is the first study of coinfection of SARS-CoV-2 and respiratory pathogens performed on outpatients in Latin America. The high proportion of outpatients with viral coinfections reported in our cohort allows us to suggest that testing for SARS-CoV-2 and other common respiratory pathogens should be carried out to ensure accurate diagnoses, prompt patient treatment, and appropriate isolation.

High rates of SARS-CoV-2 infection in funeral home workers in Ecuador: Is it an occupational risk for COVID-19?

Aim: The COVID-19 outbreak has already caused more than 6.5 million deaths, overwhelming health systems worldwide. The unusual demand for funeral home services could make these workers a potential risk group for occupational exposure to SARS-CoV-2 associated with corpses management for COVID-19 patients. Methodology: This is a cross-sectional study aimed to describe the infection rate of SARS-CoV-2 in funeral home staff by testing them with RT-qPCR in Quito, Ecuador. A total of 232 funeral home workers, representing more than 40% of funeral home personnel in Quito, were included in the study, in June 2020, immediately after the population lockdown was lifted in Ecuador. Results: A total of 48 individuals tested positive for SARS-CoV-2, yielding an infection rate of 20.7%. The SARS-CoV-2 infection rate was 18.1 and 20.0% among personnel managing corpses or not managing corpses, respectively. Among the SARS-CoV-2 positive patients, 81.3% reported no symptoms related to COVID-19, and 3 individuals had high viral loads over 108 copies/ml. Conclusion: The high SARS-CoV-2 infection rate in funeral home staff suggested a potential occupational risk for COVID-19 but not related to corpses management. Public health guidelines for safe corpses management for COVID-19 victims and safe funeral services should be reinforced.

A comparative analysis of SARS-CoV-2 viral load across different altitudes.

SARS-CoV-2 has spread throughout the world, including areas located at high or very high altitudes. There is a debate about the role of high altitude hypoxia on viral transmission, incidence, and COVID-19 related mortality. This is the first comparison of SARS-CoV-2 viral load across elevations ranging from 0 to 4300 m. To describe the SARS-CoV-2 viral load across samples coming from 62 cities located at low, moderate, high, and very high altitudes in Ecuador. An observational analysis of viral loads among nasopharyngeal swap samples coming from a cohort of 4929 patients with a RT-qPCR test positive for SARS-CoV-2. The relationship between high and low altitude only considering our sample of 4929 persons is equal in both cases and not significative (p-value 0.19). In the case of low altitude, adding the sex variable to the analysis, it was possible to find a significative difference between men and women (p-value < 0.05). Considering initially sex and then altitude, it was possible to find a significative difference between high and low altitude for men (p-value 0.05). There is not enough evidence to state that viral load is affected directly by altitude range but adding a new variable as sex in the analysis shows that the presence of new variables influences the relationship of altitude range and viral load. There is no evidence that viral loads (Ct and copies/ml) differ at low or high altitude. Using sex as a co-factor, we found that men have higher viral loads than women at low and moderate altitude locations, while living at high altitude, no differences were found. When Ct values were aggregated by low, moderate, and high viral load, we found no significant differences when sex was excluded from the analysis. We conclude that viral load is not directly affected by altitude, but COVID-19 incidence and mortality are rather affected by socio-demographic and idiosyncratic dynamics.

SARS-CoV-2 Viral Load Analysis at Low and High Altitude: A Case Study from Ecuador.

SARS-CoV-2 has spread throughout the world, including remote areas such as those located at high altitudes. There is a debate about the role of hypobaric hypoxia on viral transmission and COVID-19 incidence. A descriptive cross-sectional analysis of SARS-CoV-2 infection and viral load among patients living at low (230 m) and high altitude (3800 m) in Ecuador was completed. Within these two communities, the total number of infected people at the time of the study was 108 cases (40.3%). The COVID-19 incidence proportion at low altitude was 64% while at high altitude was 30.3%. The mean viral load from those patients who tested positive was 3,499,184 copies/mL (SD = 23,931,479 copies/mL). At low altitude (Limoncocha), the average viral load was 140,223.8 copies/mL (SD = 990,840.9 copies/mL), while for the high altitude group (Oyacachi), the mean viral load was 6,394,789 copies/mL (SD = 32,493,469 copies/mL). We found no statistically significant differences when both results were compared (p = 0.056). We found no significant differences across people living at low or high altitude; however, men and younger populations had higher viral load than women older populations, respectively.

Clinical Performance of Three Commercial SARS-CoV-2 Rapid Antigen Tests for Community-Dwelling Individuals in a Tropical Setting.

During the second year of the COVID-19 pandemic, the use of Rapid Diagnosis Antigen Tests (RDAgTs) for SARS-CoV-2 detection has substantially increased as some of the brands available in the market were certified for clinical use by international regulatory agencies. RDAgTs are a fast and cheap tool for SARS-CoV-2 surveillance with great potential to improve testing capacities in middle- and low-income countries compared to the gold standard RT-qPCR. However, as the clinical performance of RDAgTs has been shown to vary greatly between the commercial brands available, evaluation studies are necessary. Moreover, the available evaluation has been done in high-income countries while SARS-CoV-2 transmission is also actively happening in developing countries, many of which are located in tropical latitudes where cross-reactivity with other infectious agents is highly prevalent, which could compromise RDAgT specificity. Moreover, unreported mutations and/or new SARS-CoV-2 variants may compromise RDAgT sensitivity as genomic surveillance is limited in these settings. Here we describe a multicenter and manufacturer-independent evaluation of the clinical performance and analytical sensitivity of three different RDAgTs brands available in South America from three companies, Rapigen (South Korea), SD-Biosensor (South Korea), and Certest (Spain), compared to the gold standard RT-qPCR. A total number of 1,646 nasopharyngeal swabs from community-dwelling individuals were included in the study, and 379 of them were SARS-CoV-2 positive by RT-qPCR. The overall sensitivity for each RDAgT was 79% (IC95%: 72 - 86.2), 64.2% (IC95%: 56.7 - 71.6), and 45.8% (IC95%: 35.8 - 55.8) for SD-Biosensor, Certest, and Rapigen, respectively. The overall specificity for each RDAgT was 100%, 97.7% (IC95%: 96.8 - 98.6), and 100% for SD-Biosensor, Certest, and Rapigen, respectively. However, the limit of detection (LoD) to achieve a sensitivity over 90% was substantially lower for Certest RDAgT (102 copies/uL) compared to SD-Biosensor (103 copies/uL) or Rapigen (106 copies/uL) RDAgTs, considering that the gold standard RT-qPCR method used in this study has a high sensitivity of 97.7% and low LoD of 5 copies/uL. Additionally, the Certest RDAgT also showed an improved sensitivity up to 79.7% (IC95%: 70.2 - 89.2) for symptomatic individuals. Finally, the slight reduction in specificity for Certest RDAgTs was only associated with one of the laboratories performing this study, pointing out the need for locally assessed evaluation for RDAgTs like this one carried out in Ecuador. In conclusion, two of the three the RDAgTs tested in this study are a fast, cheap, and point of care tool for SARS-CoV-2 surveillance and reliable enough to detect SARS-CoV-2 infectious individuals.

Diagnostic Performance of Seven Commercial COVID-19 Serology Tests Available in South America.

BACKGROUND: Although RT-qPCR remains the gold-standard for COVID-19 diagnosis, anti-SARS-CoV-2 serology-based assays have been widely used during 2020 as an alternative for individual and mass testing, and are currently used for seroprevalence studies. OBJECTIVE: To study the clinical performance of seven commercial serological tests for COVID-19 diagnosis available in South America. METHODS: We conducted a blind evaluation of five lateral-flow immunoassays (LFIA) and two enzyme-linked immunosorbent assays (ELISAs) for detecting anti-SARS-CoV-2 antibodies. RESULTS: We found no statistically significant differences among ELISA kits and LFIAs for anti-SARS-CoV-2 IgG sensitivity (values ranging from 76.4% to 83.5%) and specificity (100% for the seven serological assays). For anti-SARS-CoV-2 IgM, the five LFIAs have a significantly higher sensitivity for samples collected 15 days after the first time RT-qPCR positive test, with values ranging from 47.1% to 88.2%; moreover, the specificity varied from 85% to 100%, but the only LFIA brand with a 100% specificity had the lowest sensitivity. CONCLUSION: The diagnostic performance of the seven serological tests was acceptable for the seven brands tested for anti-SARS-CoV-2 IgG detection for seroprevalence screening purposes. On the other hand, our results show the lack of accuracy of anti-SARS-CoV-2 IgM detection in LFIAs as a tool for SARS-CoV-2 acute-phase infection diagnosis.

COVID-19 Community Transmission and Super Spreaders in Rural Villages from Manabi Province in the Coastal Region of Ecuador Assessed by Massive Testing of Community-Dwelling Population.

Neglected rural communities in Latin America are highly vulnerable to COVID-19 due to a poor health infrastructure and limited access to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis. Manabí is a province of the Coastal Region of Ecuador characterized by a high prevalence of rural population living under poverty conditions. In the current study, we present the retrospective analysis of the results of a massive SARS-CoV-2 testing operation in nonhospitalized populations from Manabí carried out from August to September 2020. A total of 4,003 people from 15 cantons were tested for SARS-CoV-2 by reverse-transcriptase quantitative polymerase chain reaction, resulting in an overall infection rate of 16.13% for SARS-CoV-2, with several communities > 30%. Moreover, 29 SARS-CoV-2 super-spreader community-dwelling individuals with viral loads above 108 copies/mL were found. These results support that uncontrolled COVID-19 community transmission was happening in Manabí during the first semester of COVID-19 pandemic. This report endorses the utility of massive SARS-CoV-2 testing among asymptomatic population for control and surveillance of COVID-19.

Pneumococcal Carriage Among Indigenous Kichwa Children From the Ecuadorian Andes After the 10-Valent Pneumococcal Vaccine Introduction.

BACKGROUND: We assessed nasopharyngeal pneumococcal carriage in Andean Kichwa children, the largest Amerindian indigenous population in the Ecuadorian Andes. All children in our study had been vaccinated with the 10-valent pneumococcal vaccine (PCV10). METHODS: Nasopharyngeal swabs from 63 families, 100 children <10 years old including 38 children under 5 years and 63 adult caregivers, from 5 different communities, were cultivated for Streptococcus pneumoniae and isolates were serotyped and antibiotic susceptibility testing was performed. RESULTS: Respectively, 67% of the 38 children under 5 years old, 49% of the 62 children between 6 and 10 years old and 16% of the 100 adults were colonized with S. pneumoniae. Of these, 30.9% carried a vaccine serotype, 5.4% a serotype shared by the PCV10/13-valent pneumococcal vaccine (PCV13) vaccine and 25.5% a PCV13 serotype or PCV13 vaccine-related serotype, with 19A (10.9%) and 6C (10.9%) as the most prominent. Drug susceptibility testing revealed that 46% of the S. pneumoniae strains were susceptible to 6 tested antibiotics. However, 20.3% of the strains were multidrug-resistant or extensively drug-resistant strains, including 82% of the vaccine (-related) serotype 19A and 6C strains. CONCLUSIONS: Kichwa children, vaccinated with PCV10, were highly colonized with pneumococci and should be considered a high-risk group for pneumococcal disease. Twenty-five percent of the colonizing S. pneumoniae strains were PCV13-only vaccine-targeted serotypes, and in addition to that, most were multidrug-resistant or extensively drug-resistant strains. The vaccine benefits for this population possibly will significantly increase with the introduction of PCV13.

Crucial contribution of the universities to SARS-CoV-2 surveillance in Ecuador: Lessons for developing countries.

COVID-19 pandemic has challenged public health systems worldwide, particularly affecting developing countries in Latin America like Ecuador. In this report, we exposed the fundamental role of the Ecuadorian universities to improve COVID-19 surveillance in the country, with an overall contribution over 15% of the total SARS-CoV-2 RT-PCR tests done. We highlight the role of our university during the first semester of the COVID-19 pandemic, contributing to a massive free SARS-CoV-2 testing up to almost 10% of the total diagnosis completed in the country, mainly focus on underserved urban, rural and indigenous communities. Finally, we described our contribution to a high quality and low-cost SARS-CoV-2 RT-PCR diagnostic in Ecuador.

Testing for SARS-CoV-2 at the core of voluntary collective isolation: Lessons from the indigenous populations living in the Amazon region in Ecuador.

Voluntary collective isolation has been proposed to be the best response to COVID-19 for indigenous populations. While the potential value of voluntary collective isolation is appealing, the feasibility of this approach needs empirical evidence to support it as the best response to protect indigenous communities from COVID-19. This paper describes our experience during SARS-CoV-2 surveillance among Waorani communities in the Ecuadorian Amazonian region, from June to September 2020. We found that self-isolation strategies failed to contain the spread of SARS-CoV-2 from main urban areas to remote and isolated comunities.

Massive SARS-CoV-2 RT-PCR Testing on Rural Communities in Manabi Province (Ecuador) Reveals Severe COVID-19 Outbreaks.

Rural communities from Latin America are particularly susceptible to develop serious outbreaks of infectious diseases. Inadequate diagnosis and poor health infrastructure jeopardize proper contact tracing and other actions to reduce the impact of COVID-19 in the region. We herein describe the preliminary data of our ongoing fieldwork of massive testing among nonhospitalized rural population in Manabi Province of the coastal region of Ecuador. A total of 1,479 people from six different rural communities were tested for SARS-CoV-2 by RT-qPCR following the CDC protocol; 350 individuals tested positive, resulting in an overall attack rate of 23.7% for SARS-CoV-2 infection. This ultrahigh prevalence must urge to the public health authorities from Ecuador to take immediate actions to counteract this dramatic scenario in Manabi Province and to improve SARS-CoV-2 testing countrywide.

High prevalence of SARS-CoV-2 infection among food delivery riders. A case study from Quito, Ecuador.

AIM: COVID-19 pandemic has posed an unprecedented pressure on health systems and economies worldwide. Delivery services have grown as an alternative source of revenue for many people. Consumers generally perceive that delivery services are safer than going into a restaurant, because they reduce exposure to other people and their risk of SARS-CoV-2 contagion. There are no studies analyzing viral load or the burden of COID-19 within this population. This study aims to describe the presence of SARS-CoV-2 among food delivery riders in the city of Quito, Ecuador. STUDY DESIGN: From July and August 2020, bike and motorbike riders self-employed in two of the main online delivery services in Quito, Ecuador, were invited for RT-PCR testing for SARS-CoV-2 detection during the compulsory lockdown due to the COVID-19 pandemic. The Center for Disease Control (CDC) 2019-Novel Coronavirus (2019-nCoV) RT-qPCR Diagnostic Panel was used to identify the presence of SARS-CoV-2 in nasopharyngeal swabs. All samples were processed in the BSL2 certified molecular biology laboratory at Universidad de Las Americas. RESULTS: A total of 22 out of 145 delivery workers (15.2%) tested positive for SARS-CoV-2. The majority of workers were men (n = 138), the average age of male workers was 32 years-old (±7.3) and 38 years-old (± 10.6) for females. The presence of mild symptoms was reported in only 9 subjects (6%). The calculated viral load was higher among males with 1.31E+08 copies/mL vs 2.30E+06 in females, although this difference was not statistically significant (p value: 0.68, [CI: -53 to -79]). CONCLUSIONS: The self-employed food delivery riders have a high incidence rate of SARS-CoV-2 infection in relation to the national average. It is important to point out that this is the first study of its kind in Latin-American and probably one of the very few in the world. The results emphasize the need for policy makers to look at the pandemic from as many population's sub-groups as possible. Delivery riders are a highly moving population that offer their services to a wide range of clients, including vulnerable populations such as the elderly or those less likely to leave their house for basic needs stoking.

High SARS-CoV-2 Infection Rates Among Special Forces Police Units During the Early Phase of the COVID-19 Pandemic in Ecuador.

Background: At the beginning of the COVID-19 pandemic, health workers and first-responders, such as police officers, were in charge of trying to contain a disease that was unknown at that time. The lack of information and the tremendous need to contain new outbreaks put police officers at higher risk. Methodology: A cross-sectional study was conducted to describe SARS-CoV-2 infection rates among Police Special Forces Officers in Quito, Ecuador. In this study, 163 community-dwelling police officers from elite divisions voluntarily participated in our SARS-CoV-2 detection program using reverse transcription quantitative real-time PCR (RT-qPCR). Results: A total of 20 out of 163 police officers tested positive for SARS-CoV-2, yielding an infection rate of 12.3%. Within this cohort, 10% (2/20) of SARS-CoV-2 positive individuals were potentially super spreaders with viral loads over 108 copies/ul. About 85% of the SARS-CoV-2 positive individuals were asymptomatic and 15% reported mild symptoms related to COVID-19. Conclusions: We found a high SARS-CoV-2 infection rate within the special forces police officers that, beyond a high health risk for themselves, their families, and coworkers. Our results point out the need for permanent SARS-CoV-2 testing among asymptomatic essential workers and first-responders to avoid local outbreaks and to prevent work-place absenteeism among police special units.

Nasopharyngeal Microbiota Profiles in Rural Venezuelan Children Are Associated With Respiratory and Gastrointestinal Infections.

BACKGROUND: Recent research suggests that the microbiota affects susceptibility to both respiratory tract infections (RTIs) and gastrointestinal infections (GIIs). In order to optimize global treatment options, it is important to characterize microbiota profiles across different niches and geographic/socioeconomic areas where RTI and GII prevalences are high. METHODS: We performed 16S sequencing of nasopharyngeal swabs from 209 Venezuelan Amerindian children aged 6 weeks-59 months who were participating in a 13-valent pneumococcal conjugate vaccine (PCV13) study. Using random forest models, differential abundance testing, and regression analysis, we determined whether specific bacteria were associated with RTIs or GIIs and variation in PCV13 response. RESULTS: Microbiota compositions differed between children with or without RTIs (P = .018) or GIIs (P = .001). Several species were associated with the absence of infections. Some of these health-associated bacteria are also observed in developed regions, such as Corynebacterium (log2(fold change [FC]) = 3.30 for RTIs and log2(FC) = 1.71 for GIIs), while others are not commonly observed in developed regions, such as Acinetobacter (log2(FC) = 2.82 and log2(FC) = 5.06, respectively). Klebsiella spp. presence was associated with both RTIs (log2(FC) = 5.48) and GIIs (log2(FC) = 7.20). CONCLUSIONS: The nasopharyngeal microbiota of rural Venezuelan children included several bacteria that thrive in tropical humid climates. Interestingly, nasopharyngeal microbiota composition not only differed in children with an RTI but also in those with a GII, which suggests a reciprocal interplay between the 2 environments. Knowledge of region-specific microbiota patterns enables tailoring of preventive and therapeutic approaches.

Fast, Simple, and Cheap: the Kudoh-Ogawa Swab Method as an Alternative to the Petroff-Lowenstein-Jensen Method for Culturing of Mycobacterium tuberculosis.

The objective of this study was to compare the diagnostic yield of the Kudoh-Ogawa (K-O) swab method for the culturing of Mycobacterium tuberculosis from clinical samples with the standard Petroff-Lowenstein-Jensen (P-LJ) procedure. A total of 2,287 sputum samples and 685 extrapulmonary clinical specimens were processed with both decontamination methods and compared for M. tuberculosis detection rate, recovery of M. tuberculosis colonies, and culture contamination. Overall, 23.9% and 23.5% of the samples, processed with, respectively, the K-O swab method and the P-LJ procedure, yielded M. tuberculosis after 8 weeks of incubation. The K-O swab method and the P-LJ procedure provided comparable diagnostic yields for extrapulmonary clinical specimens (P = 0.688), but the K-O method showed a slightly but statistically significantly higher diagnostic yield for pulmonary samples (P = 0.002). No significant difference for culture contamination or colony recovery was found for either method. The turnaround time for the isolation of M. tuberculosis was significantly shorter for the K-O swab method, with 77% of the M. tuberculosis cultures being positive within 3 weeks of incubation, and only 6.1% positivity for the P-LJ method. Concerning the workload, the K-O swab method needs a minimum sample manipulation and takes less than 4 min per sample, as the samples are not centrifuged in this procedure. The K-O swab method is an efficient and fast (in terms of sample processing and culture growth) alternative for culturing M. tuberculosis from either pulmonary or extrapulmonary clinical specimens. The method is particularly suitable for laboratories with a high workload and for laboratories lacking a special infrastructure.

Methicillin resistant Staphylococcus aureus carriage among guinea pigs raised as livestock in Ecuador.

Antimicrobial resistance is a growing problem in human and veterinary medicine. Here we show that 6.25% of the guinea pigs studied in Ecuador, raised as livestock, carry methicillin resistant Staphylococcus aureus (MRSA) in the nasopharynx and therefore may potentially play a role in the transmission of MRSA in the Andean Region of South America.

Serology for Neosporosis, Q fever and Brucellosis to assess the cause of abortion in two dairy cattle herds in Ecuador.

BACKGROUND: Determining the infectious cause of abortion in cattle is difficult. This case-control study was set up to investigate the infectious causes of abortion by determining the seroprevalence of three reproductive pathogens in dairy cattle in Ecuador and their association with abortion: Brucella abortus, Neospora caninum and Coxiella burnetii. RESULTS: Ninety-five blood samples were obtained from cows that had experienced a mid- or late gestation abortion of their first calf and seventy-seven samples from a control group of cows with the same age that did not experience abortion problems. No antibodies were detected for B. abortus in any of the serum samples, but a high seroprevalence for both C. burnetii (52.9%) and N. caninum infection (21.5%) was found in group of cows. The seroprevalence of N. caninum infection in cattle that had experienced abortions was significantly higher (p < 0.05) than the seroprevalence in the control cows on one of the cattle farms, but no association between abortion and seropositivity for C. burnetii was found. CONCLUSION: We conclude that Neosporosis plays an important role in the epidemiology of abortion on one cattle farm, but that Q fever is apparently not an important cause for abortion in this setting.

Nasopharyngeal carriage of respiratory pathogens in Warao Amerindians: significant relationship with stunting.

OBJECTIVE: To assess risk factors for nasopharyngeal carriage of potential pathogens in geographically isolated Warao Amerindians in Venezuela. METHODS: In this point prevalence survey, nasopharyngeal swabs were obtained from 1064 Warao Amerindians: 504 children aged 0-4 years, 227 children aged 5-10 years and 333 caregivers. Written questionnaires were completed to obtain information on demographics and environmental risk factors. Anthropometric measurements were performed in children aged 0-4 years. RESULTS: Carriage rates of Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae and Moraxella catarrhalis were 51%, 7%, 1% and 13%, respectively. Crowding index, method of cooking and tobacco exposure were not associated with increased carriage. In multivariable analysis, an increase in height-for-age Z score (i.e. improved chronic nutritional status) was associated with decreased odds of S. pneumoniae colonisation (OR 0.76, 95% CI 0.70-0.83) in children aged 0-4 years. CONCLUSIONS: Better knowledge of demographic and environmental risk factors facilitates better understanding of the dynamics of colonisation with respiratory bacteria in an Amerindian population. Poor chronic nutritional status was associated with increased pathogen carriage in children <5 years of age. The high rates of stunting generally observed in indigenous children may fuel the acquisition of respiratory bacteria that can lead to respiratory and invasive disease.