A first insight into seropositivity of Neospora caninum and associated risk factors in free-roaming dogs from Ecuador

Neosporosis is a worldwide parasitic disease caused by the protozoan Neospora caninum. It can cause economic losses to farmers due to its relationship with abortions and neonatal mortality in cows. Dogs play a key role in its spread as they are considered definitive hosts. In this study, we determined for the first time the seropositivity of N. caninum infection in dogs from Ecuador and evaluated potential risk factors. A total number of 339 free-roaming dogs from the three main regions of Ecuador (Coastal, Andean, and Amazonian regions) were included in the study and classified either as urban or rural dogs. Serum samples were collected from November 2018 to May 2019, and analyzed with a commercial ELISA test. An overall seropositivity of 6.8 % (CI: 95 %, 2.8 % - 11.7 %) was found in N. caninum infection with no statistical differences among regions or urban/rural dogs. This is the first surveillance of N. caninum in Ecuador, confirming a country-wide distribution of this pathogen. Considering the large populations of free-roaming dogs in Ecuador, a One Health approach for surveillance and managing N. caninum in dogs is needed to protect either livestock or wildlife.

Prevalence, drug resistance, and genotypic diversity of the RDRio subfamily of Mycobacterium tuberculosis in Ecuador: a retrospective analysis for years 2012-2016

Introduction

A major sublineage within the Mycobacterium tuberculosis (MTB) LAM family characterized by a new in-frame fusion gene Rv3346c/55c was discovered in Rio de Janeiro (Brazil) in 2007, called RDRio, associated to drug resistance. The few studies about prevalence of MTB RDRio strains in Latin America reported values ranging from 3% in Chile to 69.8% in Venezuela, although no information is available for countries like Ecuador.

Methods

A total of 814 MTB isolates from years 2012 to 2016 were screened by multiplex PCR for RDRio identification, followed by 24-loci MIRU-VNTR and spoligotyping.

Results

A total number of 17 MTB RDRio strains were identified, representing an overall prevalence of 2.09% among MTB strains in Ecuador. While 10.9% of the MTB isolates included in the study were multidrug resistance (MDR), 29.4% (5/17) of the RDRio strains were MDR.

Discussion

This is the first report of the prevalence of MTB RDRio in Ecuador, where a strong association with MDR was found, but also a very low prevalence compared to other countries in Latin America. It is important to improve molecular epidemiology tools as a part of MTB surveillance programs in Latin America to track the transmission of potentially dangerous MTB stains associated to MDR TB like MTB RDRio.

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.

A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that, since March 2020, has been responsible for a global and ongoing pandemic. Its rapid spread over the past nearly 3 years has caused novel variants to arise. To monitor the circulation and emergence of SARS-CoV-2 variants, surveillance systems based on nucleotide mutations are required. In this regard, we searched in the spike, ORF8, and nucleocapsid genes to detect variable sites among SARS-CoV-2 variants. We describe polymorphic genetic regions that enable us to differentiate between the Alpha, Beta, Gamma, Delta, and Omicron variants of concern (VoCs). We found 21 relevant mutations, 13 of which are unique for Omicron lineages BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5. This genetic profile enables the discrimination between VoCs using only four reverse transcription PCR fragments and Sanger sequencing, offering a cheaper and faster alternative to whole-genome sequencing for SARS-CoV-2 surveillance. IMPORTANCE Our work describes a new (Sanger sequencing-based) screening methodology for SARS-CoV-2, performing PCR amplifications of a few target regions to detect diagnostic mutations between virus variants. Using the methodology developed in this work, we were able to discriminate between the following VoCs: Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5). This becomes important, especially in low-income countries where current methodologies like next-generation sequencing have prohibitive costs. Furthermore, rapid detection would allow sanitary authorities to take rapid measures to limit the spread of the virus and therefore reduce the probability of new virus dispersion. With this methodological approach, 13 previously unreported diagnostic mutations among several Omicron lineages were found.

Massive testing in the Galapagos Islands and low positivity rate to control SARS-CoV-2 spread during the first semester of the COVID-19 pandemic: a story of success for Ecuador and South America

INTRODUCTION

During the first months of the COVID-19 pandemic in Latin America, countries like Ecuador, Peru and Colombia experienced chaotic scenarios with public health systems collapsing and lack of testing capacity to control the spread of the virus. In main cities like Guayaquil in Ecuador, dramatic situations such as corpses in the streets were internationally broadcasted.

METHODS

While the COVID-19 pandemic was devastating South America, SARS-CoV-2 transmission was successfully managed in the Galapagos Islands due to the implementation of a massive screening strategy including hospitalized and community-dwelling populations, and travel restrictions facilitated by its geographical location (972 km from the Ecuadorian continental territory). Floreana Island was one of the few locations in the world that remained COVID-19 free during 2020.

RESULTS

In this study, we retrospectively analyzed the data related to SARS-CoV-2 massive testing campaigns from April to September 2020 in the Galapagos Islands, and found this territory to have the lowest positivity rate in South America (4.8-6.7%) and the highest testing ratio among Ecuadorian provinces (9.87% of the population, which is 2480 out of 25 124 inhabitants) during the first wave of the COVID-19 pandemic.

CONCLUSION

This story of success was possible because of the interinstitutional collaboration between the regional government of Galapagos Islands (Consejo de Gobierno), the local authorities (Gobiernos Autonomos Descentralizados de Santa Cruz, San Cristobal and Isabela), the regional authorities from Ecuadorian Ministry of Health, the Agencia de Regulación y Control de la Bioseguridad y Cuarentena para Galápagos and Universidad de Las Américas.

Dog bites as a zoonotic risk in Ecuador: Need for the implementation of a One Health approach

Rabies is a viral zoonotic disease that can infect all mammals and the main route of transmission to human is attributed to dog bites. Due to the limited information available about the rabies vaccination coverage, although Ecuador is supposed to be free of rabies, we conducted a retrospective study of the epidemiological surveillance records on the notification of dog attacks to humans in Guayaquil, the most populated city in Ecuador. The results showed an annual incidence rate of 105.6 dog bites per 100,000 inhabitants, where the most affected anatomical parts are the lower extremities; individuals from 1 to 14 years of age were the most affected age group (IC95% 1.42-1.92; p < 0.001). As for the severity of the wounds, most of them (65%) were mild. Moreover, 25% of the dogs were free roaming ones, and only 43% of the dogs with owner had a complete vaccination scheme against rabies virus. We found a important dog attack rate in Guayaquil city and more than half of the dogs involved were not vaccinated against rabies. Under a potential scenario of rabies circulation in canine population, there would be a serious risk for rabies transmission to humans. Hence, it is important to reinforce rabies surveillance and vaccination programs aligned to the One Health concept to manage this public health issue.

A recent distemper virus outbreak in the growing canine populations of Galapagos Islands: a persistent threat for the endangered Galapagos Sea Lion

Canine Distemper Virus (CDV) is a highly contagious virus that can cross mammalian species barriers and has widespread impacts on both domestic animals and wildlife populations. This study describes a recent outbreak of CDV in the Galapagos Islands in 2019. A total number of 125 dogs with clinical signs compatible with CDV were included in this study. Nasal swabs were taken and analyzed by RT-qPCR for the detection of CDV, resulting in a positivity rate of 74.4% (IC95%, 66-81%). Among the CDV positive dogs, 82.2% presented with respiratory signs, 48.8% neurological signs, and 28.9% gastrointestinal signs. CDV has been previously reported in the domestic canine population of the Galapagos Islands in 2001 and 2004. The current study shows how CDV is still a threat for the endemic and endangered Galapagos sea lion, despite recent policies for dog population control and CDV vaccination.

Macro and microplastic intake in seafood variates by the marine organism's feeding behaviour: Is it a concern to human health?

Seafood is considered one of the healthiest sources of food intake for humans, mainly because of its high protein content. However, oceans are among the most polluted environments, and microplastics have been widely reported to be ingested, absorbed or bioaccumulated by marine organisms. The different feeding behaviour may contribute to infer the amounts of microplastic particles accidently intake by marine organisms. We investigated the putative levels of microplastics in different edible species of fish, molluscs, and crustaceans. Plastic fragments larger than 200 μm were detected in the digestive tract of 277 out of 390 specimens (71.5 ± 22.2%) of the 26 different species analysed. There was no evidence of microplastic translocation or bioaccumulation in the muscle tissue of fish, molluscs, and crustaceans. Organisms with carnivorous feeding habits had the highest prevalence of plastic ingestion (79 ± 9.4%), followed by planktivorous species (74 ± 15.5%), and detritivorous species (38 ± 36.9%), suggesting a transfer through the food chain. Moreover, we found evidence that species with less selective feeding habits may be the most affected by the ingestion of large microplastic particles. Our results provide further evidence to the ubiquitous presence of microplastics in marine organisms representing a direct threat to marine wildlife, and to human health with potential consequences for future generations according to the One Health initiatives approach.

Phylogenetic analysis reveals that the H5N1 avian influenza A outbreak in poultry in Ecuador in November 2022 is associated to the highly pathogenic clade 2.3.4.4b

The ongoing H5N1 outbreak in the Americas caused by clade 2.3.4.4, is causing unprecedented impact in poultry and wild birds. In November 2022, a highly pathogenic avian influenza A outbreak was declared in poultry in Ecuador, affecting more than 1.1 million head of poultry in two farms by February 2023. Phylogenetic analysis shows that the virus clade is 2.3.4.4b, and to the best of our knowledge this is the first scientific publication reporting this clade in South America.

Leptospirosis in Ecuador: Current Status and Future Prospects

The location of Ecuador-an equatorial nation-favors the multiplication and dispersal of the Leptospira genus both on the Pacific Coast and in the Amazon tropical ecoregions. Nevertheless, leptospirosis epidemiology has not been fully addressed, even though the disease has been recognized as a significant public health problem in the country. The purpose of this literature review is to update knowledge on the epidemiology and geographical distribution of Leptospira spp. and leptospirosis in Ecuador to target future research and develop a national control strategy. A retrospective literature search using five international, regional, and national databases on Leptospira and leptospirosis including humans, animals, and environmental isolations of the bacteria and the disease incidence in Ecuador published between 1919 and 2022 (103 years) with no restriction on language or publication date was performed. We found and analyzed 47 publications including 22 of humans, 19 of animals, and two of the environments; three of these covered more than one of these topics, and one covered all three (i.e., One Health). Most (60%) of the studies were conducted in the Coastal ecoregion. Twenty-four (51%) were published in international journals, and 27 (57%) were in Spanish. A total of 7342 human and 6314 other animal cases were studied. Leptospirosis was a frequent cause of acute undifferentiated febrile illness in the Coast and Amazon and was associated with rainfall. All three major clusters of Leptospira-pathogenic, intermediate, and saprophytic-were identified from both healthy and febrile humans, the environment, and animals; moreover, nine species and 29 serovars were recorded over the three Ecuadorian ecoregions. Leptospira infections were diagnosed in livestock, companion, and wild animals from the Amazon and the Coast regions along with sea lions from the Galápagos Islands. Microscopic-agglutination test was the diagnostic tool most widely used. Three reviews covering national data on outpatients and inpatients determined the varied annual incidence and mortality rate, with males being more commonly affected. No human cases have been reported in the Galápagos Islands. Genomic sequences of three pathogenic Leptospira were reported. No studies on clinical ground, antibiotic resistance, or treatment were reported, nor were control programs or clinical-practice guidelines found. The published literature demonstrated that leptospirosis was and still is an endemic disease with active transmission in the four geoclimatic regions of Ecuador including the Galápagos Islands. Animal infections, distributed in mainland and insular Ecuador, pose a significant health risk for humans. Nationwide epidemiological surveys-encouraging more research on the fauna and environment with appropriate sampling design on risk factors for human and animal leptospirosis, Leptospira genotyping, increased laboratory capability, and readily available official data-are required to improve our understanding of transmission patterns and to develop effective national intervention strategies with the intention of applying One Health approaches.

Fast, cheap and sensitive: Homogenizer-based RNA extraction free method for SARS-CoV-2 detection by RT-qPCR

Background

The SARS-CoV-2 gold standard detection method is an RT-qPCR with a previous step of viral RNA extraction from the patient sample either by using commercial automatized or manual extraction kits. This RNA extraction step is expensive and time demanding.

Objective

The aim of our study was to evaluate the clinical performance of a simple SARS-CoV-2 detection protocol based on a fast and intense sample homogenization followed by direct RT-qPCR.

Results

388 nasopharyngeal swabs were analyzed in this study. 222 of them tested positive for SARS-CoV-2 by the gold standard RNA extraction and RT-qPCR method, while 166 tested negative. 197 of those 222 positive samples were also positive for the homogenization protocol, yielding a sensitivity of 88.74% (95% IC; 83.83 – 92.58). 166 of those negative samples were also negative for the homogenization protocol, so the specificity obtained was 97% (95% IC; 93.11 – 99.01). For Ct values below 30, meaning a viral load of 103 copies/uL, only 4 SARS-CoV-2 positive samples failed for the RNA extraction free method; for that limit of detection, the homogenizer-based method had a sensitivity of 97.92% (95% CI; 96.01 – 99.83).

Conclusions

Our results show that this fast and cheap homogenization method for the SARS-CoV-2 detection by RT-qPCR is a reliable alternative of high sensitivity for potentially infectious SARS-CoV-2 positive patients. This RNA extraction free protocol would help to reduce diagnosis time and cost, and to overcome the RNA extraction kits shortage experienced during COVID-19 pandemic.

High SARS-CoV-2 infection rates and viral loads in community-dwelling individuals from rural indigenous and mestizo communities from the Andes during the first wave of the COVID-19 pandemic in Ecuador

Background

Neglected indigenous groups and underserved rural populations in Latin America are highly vulnerable to COVID-19 due to poor health infrastructure and limited access to SARS-CoV-2 diagnosis. The Andean region in Ecuador includes a large number of isolated rural mestizo and indigenous communities living under poverty conditions.

Objective

We herein present a retrospective analysis of the surveillance SARS-CoV-2 testing in community-dwelling populations from four provinces in the Ecuadorian Andes, carried out during the first weeks after the national lockdown was lifted in June 2020.

Results

A total number of 1,021 people were tested for SARS-CoV-2 by RT-qPCR, resulting in an overall high infection rate of 26.2% (268/1,021, 95% CI: 23.6-29%), which was over 50% in several communities. Interestingly, community-dwelling super spreaders with viral loads over 10⁸ copies/mL represented 7.46% (20/268, 95% CI: 4.8-11.1%) of the SARS-CoV-2 infected population.

Conclusion

These results support that COVID-19 community transmission in rural communities from the Andean region was happening at the early stages of the COVID-19 pandemic in Ecuador and point out the weakness of the COVID-19 control program. Community-dwelling individuals in neglected rural and indigenous communities should be considered for a successful control and surveillance program in future pandemics in low- and middle-income countries.

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.

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.

Leptospirosis: Morbidity, mortality, and spatial distribution of hospitalized cases in Ecuador. A nationwide study 2000-2020

Background

In Ecuador, leptospirosis surveillance involves a mandatory notification of all cases and a hospitalization for severe illness. Morbidity and mortality are, nevertheless, underestimated and contribute directly to the status of leptospirosis as a neglected disease. Leptospira spp. is zoonotic in Ecuador with established endemic transmission in the Tropics. Here, we review retrospective national data within the country to aid in control strategies.

Methodology/Principal findings

In a population-based nationwide study, we analysed morbidity, mortality, and spatial distribution on confirmed hospital-discharged leptospirosis cases from 2000–2020 from a publicly accesible National Database, including males and females of all ages. We computed data for the 24 provinces across the four-geoclimatic regions of Ecuador based on seasonal and monthly variations and calculated rates according to age and sex. The spatial distribution was estimated at the level of ecoregions, provinces, and cantons. A total of 2,584 hospitalizations were recorded over all three continental regions in 22 provinces, except Carchi province and the Galapagos Islands. The annual incidence varied from 0.27 to 2.45 cases per 100,000 inhabitants with ages ranging from 1 to 98 years-old and an overall male/female ratio of 1.92:1. Most hospitalizations and deaths occurred in males ages 25–34 years. We registered 79 fatalities (3.06%); the highest mortality rate was 0.05 per 100,000 inhabitants. More cases clustered in the tropical cantons of central and north of the Coast and in the southern Amazon when compared to the Andes.

Conclusions and significance

Our findings evidence leptospirosis endemicity and pinpoint the highest incidence within resource-poor tropical settings. The highest incidence occurred in males of adult age, with those also exhibiting the highest mortality. The national incidence rate was stable, but peaks occurred intermittently during the rainy seasons. Thus, strategies aimed at leptospirosis monitoring and control involving the application of preventive measures should consider this season and the aforementioned high-risk groups.

Leptospirosis is a neglected tropical disease poorly characterized in Latin American countries like Ecuador. Although this zoonotic disease is considered by the Epidemiology Department of the Ministry of Public Health to be of mandatory notification, an updated document on the patterns of morbidity and mortality or a control strategy do not yet exist. In the present study, we carried out a retrospective analysis of Ecuadorian national data (INEC) on hospitalized cases and deaths from 2000 through 2020 to estimate the trends of morbidity and mortality, and the spatial distribution of this disease throughout its four geoclimatic regions (Pacific coastal, Andes, Amazon, and the Galapagos Islands). The INEC recorded only hospitalized cases, meaning those with severe illness. The spatial distribution was estimated at the ecoregion, province, and canton levels. With a total number of 2,584 hospitalizations, an annual incidence ranging from 0.27 to 2.45 cases per 100,000 inhabitants, and a fatality rate of 3.06% during the period of study. Our findings evidence the endemicity of leptospirosis, particularly within the neglected tropical settings in the Ecuadorian Coast and Amazon regions. Despite the wide geographic distribution of leptospirosis and its severity in terms of incidence, morbidity, and mortality, leptospirosis is not yet considered a “tool-ready” disease for control/elimination and research initiatives.

Analytical sensitivity and clinical performance of "COVID-19 RT-PCR Real TM FAST (CY5) (ATGen, Uruguay) and "ECUGEN SARS-CoV-2 RT-qPCR" (UDLA-STARNEWCORP, Ecuador)": High quality-low cost local SARS-CoV-2 tests for South America

BACKGROUND

Dozens of commercial RT-qPCR kits for SARS-CoV-2 detection are available with or without Emergency Use Authorization (EUA) by FDA or other regulatory agencies.

OBJECTIVE

We evaluated the clinical performance of two SARS-CoV-2 RT-PCR kits designed and produced in South America, "COVID-19 RT-PCR Real TM FAST (CY5)" (ATGen, Uruguay) and "ECUGEN SARS-CoV-2 RT-qPCR" (UDLA-STARNEWCORP, Ecuador), for RT-qPCR SARS-CoV2 detection using "TaqMan 2019-nCoV Assay Kit v1" (Thermofisher, USA) as a gold standard technique.

RESULTS

We report a great clinical performance and analytical sensitivity for the two South American kits with sensitivity values of 96.4 and 100%, specificity of 100% and limit of detection in the range of 10 copies/uL of RNA extraction.

CONCLUSIONS

"COVID-19 RT-PCR Real TM FAST (CY5)" and "ECUGEN SARS-CoV-2 RT-qPCR" kits are reliable SARS-CoV-2 tests made in South America that have been extensively used in Uruguay, Argentina, Brazil, Bolivia and Ecuador. These locally produced SARS-CoV-2 tests have contributed to overcome supply shortages and reduce diagnosis cost, while maintaining the high quality standards of FDA EUA commercially available kits. This approach could be extended for other diagnostic products to improve infectious diseases surveillance at middle and low income countries beyond COVID-19 pandemic.

SARS-CoV-2 infection in free roaming dogs from the Amazonian jungle

During the ongoing COVID-19 pandemic, there were several reports of SARS-CoV-2 transmission from human to animals, mostly to companion cats and dogs but also to free ranging wild species like minks and deers. Under this scenario, SARS-CoV-2 surveillance in domestic animals to assess the risk of transmission between species have been suggested by the OIE. Here we present a case report of SARS-CoV-2 infection in free roaming dogs, found at a rural indigenous community from the Ecuadorian Amazonia. Oral and nasal swabs samples were collected from three dogs found during a COVID-19 surveillance intervention in Amazonian indigenous communities where severe COVID-19 outbreaks were suspected. Total RNA was extracted from dog samples and detection of SARS-CoV-2 gene targets N, ORF1ab and S was performed. The three dogs tested positive for at least two SARS-CoV-2 viral targets. Moreover, there was a high SARS-CoV-2 infection rate of 87.2% within this community. Given that 17.1% of SARS-CoV-2 positive individuals had an ultra high load greater than 10⁸ copies/ml, transmission from humans to dogs likely occurred. To our knowledge, this study is the first report of SARS-CoV-2 positive free roaming dogs. Also, as those animals were found in the Amazonian forest, SARS-CoV-2 transmission to wild mammals is a potential concern. Given the high presence of free roaming dogs associated to rural and indigenous communities in South America, the potential role of these domestic animals on COVID-19 spread would deserve further surveillance studies involving SARS-CoV-2 detection by PCR and molecular epidemiology based on genome sequencing to confirm human to dog transmission.

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.

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.

First Report of SARS-CoV-2 Lineage B.1.1.7 (Alpha Variant) in Ecuador, January 2021

On January 5 2021, Ecuadorian COVID-19 genomic surveillance program detected a suspicious case of the B.1.1.7 lineage (alpha variant) of SARS-CoV-2 in Los Rios province, later confirmed by genome sequencing. The patient travelled from the UK by the end of December 2020. By contact tracing, several new cases were detected confirming B.1.1.7 transmission and spreading in Ecuador.

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.

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.

High sensitivity-low cost detection of SARS-CoV-2 by two steps end point RT-PCR with agarose gel electrophoresis visualization

More than one year since Coronavirus disease 2019 (COVID-19) pandemic outbreak, the gold standard technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is still the RT-qPCR. This is a limitation to increase testing capacities, particularly at developing countries, as expensive reagents and equipment are required. We developed a two steps end point RT-PCR reaction with SARS-CoV-2 Nucleocapsid (N) gene and Ribonuclease P (RNase P) specific primers where viral amplicons were verified by agarose gel electrophoresis. We carried out a clinical performance and analytical sensitivity evaluation for this two-steps end point RT-PCR method with 242 nasopharyngeal samples using the CDC RT-qPCR protocol as a gold standard technique. With a specificity of 95.8%, a sensitivity of 95.1%, and a limit of detection of 20 viral RNA copies/uL, this two steps end point RT-PCR assay is an affordable and reliable method for SARS-CoV-2 detection. This protocol would allow to extend COVID-19 diagnosis to basic molecular biology laboratories with a potential positive impact in surveillance programs at developing countries.

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.

COVID-19 outbreaks at shelters for women who are victims of gender-based violence from Ecuador

BACKGROUND

One of the constraints in containing the impact of the COVID-19 pandemic in Ecuador is limited testing capacity, especially in high-risk populations such as people living in humanitarian shelters.

OBJECTIVES

The "United Nations High Commissioner for Refugees" office in Ecuador in collaboration with "Universidad de Las Américas" performed surveillance screening at shelters for women victims of gender-based violence. They had been granted access to RT-qPCR tests for SARS-CoV-2 diagnosis since July 2020, a few weeks after the general population lockdown was lifted.

RESULTS

From 411 people tested, 52 tests were SARS-CoV-2 positive, yielding an overall high attack rate of 12.65%. Moreover, COVID-19 outbreaks were found in nine of 11 shelters that were included in the study. While attacks rates varied among shelters, no association was found with occupancy.

CONCLUSION

This study is key to clarifying the epidemiological situation in this highly vulnerable population in Latin America. It highlights the importance of mass testing beyond the symptomatic population to prevent the spread of COVID-19.

Analytical and clinical evaluation of a heat shock SARS-CoV-2 detection method without RNA extraction for N and E genes RT-qPCR

Background

The COVID-19 pandemic has caused significant supply shortages worldwide for SARS-CoV-2 molecular diagnosis, like RNA extraction kits.

Objective

The aim of our study was to evaluate the clinical performance and analytical sensitivity of a simple SARS-CoV-2 diagnosis protocol based on heat shock without RNA extraction using both "CDC" (N gene) and "Charite" (E gene) RT-qPCR protocols.

Results

1,036 nasopharyngeal samples, 543 of them SARS-CoV-2 positive, were analyzed. The heat shock method correctly identified 68.8% (232/337) and 89.4% (202/226) of SARS-CoV-2 positive samples for N gene and E gene, respectively. Analytical sensitivity was assessed for heat shock method using the CDC RT-qPCR protocol, obtaining sensitivity values of 98.6%, 93.3% and 84.8% for limit of detection of 100.000, 50.000 and 20.000 viral RNA copies/mL of sample.

Conclusions

Our findings show that a simple heat shock SARS-CoV-2 RT-qPCR diagnosis method without RNA extraction is a reliable alternative for potentially infectious SARS-CoV-2 positive patients at the time of testing. This affordable protocol can help overcome the cost and supply shortages for SARS-CoV-2 diagnosis, especially in developing countries. In Ecuador, it has been used already by laboratories in the public health system for more than 100.000 specimens.

Analytical and Clinical Evaluation of "AccuPower SARS-CoV-2 Multiplex RT-PCR kit (Bioneer, South Korea)" and "Allplex 2019-nCoV Assay (Seegene, South Korea)" for SARS-CoV-2 RT-PCR Diagnosis: Korean CDC EUA as a Quality Control Proxy for Developing Countries

Background

Multiple RT-qPCR kits are available in the market for SARS-CoV-2 diagnosis, some of them with Emergency Use Authorization (EUA) by FDA or their country of origin agency, but many of them lack of proper clinical evaluation.

Objective

We evaluated the clinical performance of two Korean SARS-CoV-2 RT-PCR kits available in South America, AccuPower SARS-CoV-2 Multiplex RT-PCR kit (Bioneer, South Korea) and Allplex 2019-nCoV Assay (Seegene, South Korea), for RT-qPCR SARS-CoV-2 diagnosis using the CDC protocol as a gold standard.

Results

We found strong differences among both kits clinical performance and analytical sensitivity; while the Allplex 2019-nCoV Assay has sensitivity of 96.5% and an estimated limit of detection of 4,000 copies/ml, the AccuPower SARS-CoV-2 Multiplex RT-PCR kit has a sensitivity of 75.5% and limit of detection estimated to be bigger than 20,000 copies/ml.

Conclusions

AccuPower SARS-CoV-2 Multiplex RT-PCR kit and Allplex 2019-nCoV Assay are both made in South Korea but EUA by Korean CDC was only granted to the later. Our results support that Korean CDC EUA should be considered as a quality control proxy for Korean SARS-CoV-2 RT-PCR kits prior to importation by developing countries to guarantee high sensitivity diagnosis.

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.

Analytical and Clinical Evaluation of Two RT-qPCR SARS-CoV-2 Diagnostic Tests with Emergency Use Authorization in Ecuador

Dozens of RT-qPCR kits are available in the market for SARS-CoV-2 diagnosis, some of them with Emergency Use Authorization (EUA) by the Food and Drug Administration (FDA) or at least by a responsible agency of their country of origin, but many of them lack proper evaluation studies because of COVID-19 pandemic emergency. We evaluated the clinical performance of two commercially available kits in South America, the 2019-nCoV kit (Da An Gene, Guangzhou, China) and GenomeCoV19 kit (ABM, Richmond, Canada), for RT-qPCR SARS-CoV-2 diagnosis using the FDA EUA 2019-nCoV CDC kit (IDT, Coralville, IA) as gold standard. We found striking differences among clinical performance and analytical sensitivity in both kits; whereas the 2019-nCoV kit (Da An Gene) has a limit of detection of 2,000 copies/mL and 100% of sensitivity, the GenomeCoV19 kit (ABM) has a poor sensitivity of 75% and a limit of detection estimated to be over 8.000 copies/mL. The GenomeCoV19 kit (ABM) lacks clinical use authorization in Canada; however, the 2019-nCoV kit (Da An Gene) is authorized by the Chinese CDC. Our results support that only SARS-CoV-2 diagnosis kits with clinical use authorization from their country of origin should be exported to developing countries lacking proper evaluation agencies to avoid a deep impact of the COVID-19 pandemic due to unreliable diagnosis.

Clinical Performance and Analytical Sensitivity of Three SARS-CoV-2 Nucleic Acid Diagnostic Tests

Hundreds of RT-qPCR kits are available in the market for SARS-CoV-2 diagnosis, some of them with emergency use authorization (EUA) by the Food Drug Administration (FDA) or their country of origin agency, but also many of them without any independent clinical performance evaluation. We performed a clinical evaluation for two Chinese SARS-CoV-2 RT-PCR kits available in South America, COVID-19 Nucleic Acid Test Kit (eDiagnosis Biomedicine, Wuhan, China) and 2019-nCoV Nucleic Acid Diagnostic Kit (Sansure Biotech, Changsha, China), for RT-qPCR SARS-CoV-2 diagnosis using the FDA EUA 2019-nCoV CDC kit (IDT, Coralville, IA) as gold standard. We found an excellent clinical performance and analytical sensitivity for both kits with sensitivity values of 100% and 95.3% and estimated limit of detection of 500 copies/mL and 1,000 copies/mL, for eDiagnosis and Sansure Biotech kits, respectively. COVID-19 Nucleic Acid Test Kit (eDiagnosis) and 2019-nCoV Nucleic Acid Diagnostic Kit (Sansure Biotech) are both made in China and hold EUA by the Chinese CDC. Also, Sansure Biotech kit has EUA by the FDA. In conclusion, our results endorse the use of these two commercially available kits imported to Ecuador for SARS-CoV-2 diagnosis, as they had the similar clinical performance as the gold standard from the CDC.

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 seroprevalence of anti-Leptospira spp. antibodies in domestic and wild mammals from a mixed use rescue center in Ecuador: Lessons for "One Health" based conservation strategies

Leptospirosis is a zoonotic disease of worldwide distribution that affects humans, domestic and wild animals. This study evaluates the frequency of anti- Leptospira spp. antibodies in companion, livestock and wild mammals from a mixed use rescue center on Guayaquil, the main city of Ecuador. Sera were collected from 23 domestic and 6 wild mammals. All animals tested were seropositive for Leptospira spp. using Microscopic Agglutination Test (MAT), most of them for multiple serovars. Leptospira interrogans serovars Canicola, Hardjo and Icterohaemorrhagiae were the most frequent ones. We conclude that the presence of domestic animals at this mixed use rescue center may cause the exposure of wild animals, considering the high frequency of Leptospira spp. seropositivity already reported for livestock and companion animals in Ecuador. This is the first serological survey for leptospirosis including wild animals rescued from illegal traffic in Ecuador and point out the urgent need of exclusive rescue and conservation units for wild species and the potential role as Leptospira spp. reservoir for wild mammals.

Analytical and clinical comparison of Viasure (CerTest Biotec) and 2019-nCoV CDC (IDT) RT-qPCR kits for SARS-CoV2 diagnosis

Background

Several RT-qPCR kits are available for SARS-CoV-2 diagnosis, some of them with Emergency Use Authorization (EUA) by FDA, but most of them lacking of proper evaluation studies due to covid19 emergency.

Objective

We evaluated Viasure RT-qPCR kit (CerTest Biotec, Spain) for SARS-CoV-2 diagnosis using FDA EUA 2019-nCoV CDC kit (IDT, USA) as a gold standard.

Results

Although we found the lack of RNA quality control probe as the main limitation for the Viasure kit, the sensitivity was 91.9% and the specificity was 100%. The limit of detection (LOD) was 2000 copies/mL and 1000 copies/mL for Viasure and IDT kits, respectively.

Conclusions

Viasure RT-qPCR kit is a reliable tool for SARS-CoV-2 diagnosis but improvement of an alternative RT-qPCR reaction for RNA extraction quality control as RNaseP is recommended.

Poor sensitivity of "AccuPower SARS-CoV-2 real time RT-PCR kit (Bioneer, South Korea)"

BACKGROUND

Several molecular kits are available for SARS-CoV-2 diagnosis, mostly lacking of proper clinical evaluation due to the emergency caused by COVID19 pandemia, particularly at developing countries like Ecuador.

OBJECTIVE

We carried out an evaluation of the clinical performance of "AccuPower SARS-CoV-2 Real Time RT-PCR kit" (Bioneer, South Korea) for SARS-CoV-2 diagnosis using 2019-nCoV CDC EUA kit (IDT, USA) as a gold standard.

RESULTS

48 clinical specimens were included on the study, 38 tested SARS-CoV-2 positive and 10 SARS-CoV-2 negative for 2019-nCoV CDC EUA kit. For "AccuPower SARS-CoV-2 Real Time RT-PCR kit", only 30 were SARS-CoV-2 positive, indicating a low clinical performance with sensitivity of 78.9%. Moreover, the limit of detection for "AccuPower SARS-CoV-2 Real Time RT-PCR kit" was estimated to be higher than 40,000 viral RNA copies/mL of sample.

CONCLUSIONS

Proper clinical performance evaluation studies from government agencies at developing countries should be mandatory prior to clinical use authorization of SARS-CoV-2 diagnosis kits, particularly when those kits lack of either FDA or its country of origin clinical use authorization, to prevent the distribution of low quality products that may have a negative impact of COVID19 surveillance at developing countries.