Evaluation and comparison of the sensitivity of three commercial RT-qPCR kits used for the detection of SARS-CoV-2 in Santiago, Chile.

Introduction: The COVID-19 pandemic is still in force, causing global public health challenges and threats. Although vaccination and herd immunity have proven to be the most efficient way to control the pandemic, massive and early testing of patients using the RT-qPCR technique is crucial for constant genomic surveillance. The appearance of variants of SARS-CoV-2 with new mutations can reduce the efficiency of diagnostic detection. In this sense, several commercial RT-qPCR kits have been the target of extensive analysis because low assay performance could lead to false-negative diagnoses. Methods: In this study, we evaluated the performance of three commercial RT-qPCR kits; Thermo Fisher (TaqMan 2019-nCoV Assay Kit v1), BGI and Roche (LightCycler® Multiplex RNA Virus Master) used for the diagnosis of COVID-19 throughout the pandemic in Santiago de Chile. Results: Under our best assay conditions, we found significant differences in Cq amplification values for control and viral probes, against the same nasopharyngeal swab samples (NPSs). In addition, in some cases, the sensitivity of the RT-qPCR kits decreased against viral variants. Conclusion: Our study suggests evaluating the RT-qPCR kits used to detect SARS-CoV-2 because variants such as Omicron, which has several mutations, can compromise their detection and underestimate viral circulation.

Genomic Evidence Suggests Viral Persistence of SARS-CoV-2 for 386 Days in Health Worker: A Case Report from Santiago of Chile.

The COVID-19 pandemic continues to affect several countries. One of the best ways to control its spread is the timely identification of infected patients for isolation and quarantine. While an episode of infection lasts an average of 8-10 days from the onset of symptoms, there is literature describing long-lasting viral persistence events. Here, we report a case of persistence of SARS-CoV-2 for 386 days in a health worker from Santiago de Chile. Our study could be one of the longest reported viral persistence events. RNA sequencing analyses indicated that the first positive diagnosis (8 June 2020) corresponded to a SARS-CoV-2 variant belonging to Clade Nextstrain 20A. Three hundred eighty-six days later (23 September 2021), the second positive result reached the same viral variant (Clade 20A) but without presence or circulation in Chile since May 2021. Both sequencing coverages showed an identity of 99.21%, with some mutations related to the severity of the disease (ORF1b:P314L) and more infectivity (S:D614G). This work reinforces the idea of implementing an RT-qPCR or rapid antigen test once the quarantine is fulfilled to ensure viral absence, identify potential persistence, and, consequently, minimize the risk of local outbreaks of SARS-CoV-2 infection.

Epidemiological characteristics of Omicron and Delta SARS-CoV-2 variant infection in Santiago, Chile.

The variant of concern (VOC) SARS-CoV-2 Omicron (B.1.1529) has been described as a highly contagious variant but less virulent than the current variant being monitored (VBM) Delta (B.1.617.2), causing fewer cases of hospitalizations, symptomatology, and deaths associated with COVID-19 disease. Although the epidemiological comparison of both variants has been previously reported in other countries, no report indicates their behavior and severity of infection in Chile. In this work, we report for the first time the effect of the Omicron and Delta variants in a cohort of 588 patients from the Hospital de Urgencia Asistencia pública (HUAP), a high-complexity health center in Santiago, Chile. This report is framed at the beginning of Chile's third wave of the COVID-19 pandemic, with a marked increase in the Omicron variant and a decrease in the circulating Delta variant. Our results indicated a similar proportion of patients with a complete vaccination schedule for both variants. However, the Delta variant was associated with a higher prevalence of hospitalization and more significant symptomatology associated with respiratory distress. On the other hand, our data suggest that vaccination is less effective in preventing infection by the Omicron variant. This antecedent, with a low severity but high contagiousness, suggests that the Omicron variant could even collapse the primary health care service due to the high demand for health care.

Sensitivity analysis of rapid antigen tests for the Omicron SARS-CoV-2 variant detection from nasopharyngeal swab samples collected in Santiago of Chile.

The COVID-19 pandemic continues to be a concern and keeps global health authorities on alert. The RT-PCR technique has been the gold-standard assay for detecting the SARS-CoV-2 virus. However, rapid antigen tests (RATs) have been widely used to increase the number of tests faster and more efficiently in the population. Nevertheless, the appearance of new viral variants, with genomic mutations associated with greater contagiousness and immune evasion, highlights the need to evaluate the sensitivity of these RATs. This report evaluates the sensitivity of SD Biosensor-Roche, Panbio™, and Clinitest® RATs widely used in Santiago de Chile in the detection of the Omicron variant from Nasopharyngeal samples (NPSs), the most predominant SARS-CoV-2 variant in Chile and the world. SD Biosensor-Roche shows a detection sensitivity of 95.7% in the viral amplification range of 20 ≤ Cq < 25, while Panbio™ and Clinitest® show 100% and 91.3%, respectively. In the viral amplification ranges of 25 ≤ Cq < 30, the detection sensitivity decreased to 28% for SD Biosensor-Roche, 32% for Panbio™, and 72% for Clinitest®. This study indicates that the tested RATs have high sensitivity in detecting the Omicron variant of concern (VOC) at high viral loads. By contrast, its sensitivity decreases at low viral loads. Therefore, it is suggested to limit the use of RATs as an active search method, considering that infections in patients are increasingly associated with lower viral loads of SARS-CoV-2. These antecedents could prevent contagion outbreaks and reduce the underestimation of the current Omicron variant circulation at the local level.

Comparison of the First and Second Wave of Infections by SARS-CoV-2: A Retrospective and Longitudinal Study From a Primary Health Care Center in Santiago of Chile

The current COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Many countries have reported the experience of at least two contagion waves, describing associated mortality rates and population behavior. The analysis of the effect of this pandemic in different localities can provide valuable information on the key factors to consider in the face of future massive infectious diseases. This work describes the first retrospective and comparative study about behavior during the first and second waves of the COVID-19 pandemic in Chile from a primary Healthcare Center. From 19,313 real-time quantitative PCR (RT-qPCR) tests assessed, the selected 1,694 positive diagnostics showed a decrease in mortality rate in the second wave (0.6%) compared with the first (4.6%). In addition, we observed that infections in the second wave were mainly in young patients with reduced comorbidities. The population with a complete vaccination schedule shows a decrease in the duration of symptoms related to the disease, and patients with more comorbidities tend to develop severe illness. This report provides evidence to partially understand the behavior and critical factors in the severity of the COVID-19 pandemic in the population of Santiago of Chile.

The Comparative Analysis of Two RT-qPCR Kits for Detecting SARS-CoV-2 Reveals a Higher Risk of False-Negative Diagnosis in Samples with High Quantification Cycles for Viral and Internal Genes.

The early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using the real-time quantitative polymerase chain reaction (RT-qPCR) as a gold-standard molecular tool has allowed to test and trace the viral spread and the isolation of COVID-19-infected patients. The detection capacity of viral and internal genes is an essential parameter to consider and analyze during the assay. In this study, we analyze the performance of the two commercial RT-qPCR kits used in Chile, TaqMan™ 2019-nCoV Control Kit v1 (Thermo Fisher) and MaxCov19 (TAAG Genetics), for the COVID-19 diagnosis from nasopharyngeal swab samples (NPSs). Our results show a lower sensitivity of the TAAG kit compared to the Thermo Fisher kit, even in the detection of SARS-CoV-2 mutations associated with its variants. This study reinforces the relevance of evaluating the performance of RT-qPCR kits before being used massively since those with lower sensitivity can generate false negatives and produce outbreaks of local infections.

[Disruption of health services for pregnant women, newborns, children, adolescents, and women during the COVID-19 pandemic: ISLAC 2020 ProjectInterrupção dos serviços de saúde para grávidas, recém-nascidos, crianças, adolescentes e mulheres durante a pandemia de COVID-19: projeto ISLAC 2020]. / Interrupción de servicios de salud para embarazadas, recién nacidos, niños y niñas, adolescentes y mujeres durante la pandemia de COVID-19: proyecto ISLAC 2020.

OBJECTIVE: Describe the perceptions of key actors regarding the disruption of health services for populations that ceased to be prioritized because of the COVID-19 pandemic-pregnant women, newborn, children, adolescents, and women-in countries of Latin America and the Caribbean (LAC) during the first stage of the pandemic. METHODS: In this cross-sectional study, a 35-question survey was administered to key actors in 19 LAC countries between July and September 2020. The respondents were asked for their personal perceptions regarding the situation of social and health services in their country before and during the pandemic. They were also asked for a projection of the situation during the post-pandemic period. RESULTS: In the 691 responses received, the main perception was that coverage in the services analyzed had been high before the pandemic, although their quality was not as highly rated. Both the coverage and quality of services were thought to have declined for adolescents and women. The majority of respondents predicted that all services will continue to function at lower than usual coverage levels for another three months (53.1%) and another 12 months (41.3%). Guaranteeing coverage and access to health services was considered the main policy challenge going forward. The next most needed initiatives noted were financing for actions to support women, children, and adolescents, and protection against violence and promotion of measures to combat it. CONCLUSIONS: Although the pandemic has struck all countries, its effect on the delivery of services in the populations analyzed differs from country to country and according to the types of service. It is essential to invest in national information systems that will make it possible to monitor the different services and identify the populations that need to be prioritized.

OBJETIVOS: Descrever a percepção de atores-chave na interrupção dos serviços de saúde para populações não priorizadas na pandemia ­ grávidas, recém-nascidos, crianças, adolescentes e mulheres ­ em países da América Latina e do Caribe (ALC) durante a primeira fase da pandemia de COVID-19. MÉTODOS: Estudo transversal. Foi realizada uma pesquisa com atores relevantes de 19 países da ALC entre julho e setembro de 2020, com 35 perguntas sobre a percepção pessoal do estado dos serviços sociais e de saúde em seus países antes e durante a pandemia, bem como uma projeção para depois dela. RESULTADOS: Nas 691 respostas, predominou a percepção de que a cobertura dos serviços analisados era alta antes da pandemia, embora a qualidade fosse vista como mais baixa. Notou-se uma redução na cobertura e na qualidade dos serviços a adolescentes e mulheres. A maioria estimou que todos os serviços seguiriam com uma menor cobertura tanto em 3 como em 12 meses (53,1% e 41,3%, respectivamente). Garantir a cobertura e o acesso aos serviços de saúde é o principal desafio político para o futuro, seguido do financiamento de iniciativas para mulheres, crianças e adolescentes, e da proteção e promoção contra a violência. CONCLUSÕES: Embora a pandemia tenha afetado todos os países, o abalo na provisão de serviços para as populações analisadas é heterogêneo entre os países e os tipos de serviço. É preciso investir em sistemas de informação nacionais que permitam monitorar os distintos serviços e identificar as populações que não foram priorizadas.

Factors associated with change in adherence to COVID-19 personal protection measures in the Metropolitan Region, Chile.

Personal protective measures such use of face masks, hand washing and physical distancing have proven to be effective in controlling the spread of the Covid-19 pandemic. However, adherence to these measures may have been relaxed over time. The objective of this work is to assess the change in adherence to these measures and to find factors that explain the change For this purpose, we conducted a survey in the Metropolitan Region of Chile in which we asked the adherence to these measures in August-September 2021 and retrospectively for 2020. With the answers obtained we fit a logistic regression model in which the response variable is the relaxation of each of the self-care preventive actions. The explanatory variables used are socio-demographic characteristics such as the age, sex, income, and vaccination status of the respondents. The results obtained show that there has been a significant decrease in adherence to the three personal protection measures in the Metropolitan Region of Chile. In addition, it was observed that younger people are more likely to relax these measures. The results show the importance of generating new incentives for maintaining adherence to personal protection measures.

First Identification of Reinfection by a Genetically Different Variant of SARS-CoV-2 in a Homeless Person from the Metropolitan Area of Santiago, Chile.

The identification and tracking of SARS-CoV-2 infected patients in the general population are essential components of the global strategy to limit the COVID-19 viral spread, specifically for maintaining traceability and suppressing the resurgence of local outbreaks. Public health programs that include continuous RT-qPCR testing for COVID-19 in the general population, viral sequencing, and genomic surveillance for highly contagious forms of the virus have allowed for the identification of SARS-CoV-2 infections and reinfections. This work identified SARS-CoV-2 reinfection in a homeless person, which occurred 58 days after the first COVID-19 diagnosis. Genomic sequencing identified a different Nextstrain classification clade (20A and 20B) and PANGO lineage, with a divergence of 4 single nucleotide variants (SNVs) in S and ORF1ab genes, suggesting reinfection by different viral variants. This study is the first from the great metropolitan area of Santiago, Chile, one of the top ten countries in the world to live during the COVID-19 pandemic. We support the importance of performing intensive genomic surveillance programs in the whole population and high-risk groups, such as homeless people, nearly 20 thousand people in Chile, and have limited access to health care services and poor viral traceability.

Description of Symptoms Caused by the Infection of the SARS-CoV-2 B.1.621 (Mu) Variant in Patients With Complete CoronaVac Vaccination Scheme: First Case Report From Santiago of Chile.

Vaccine administration is one of the most efficient ways to control the current coronavirus disease 2019 (COVID-19) pandemic. However, the appearance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants can avoid the immunity generated by vaccines. Thus, in patients with a complete vaccine schedule, the infection by SARS-CoV-2 may cause severe, mild, and asymptomatic manifestations of the disease. In this case report, we describe for the first time the clinical symptoms of four patients (three symptomatic; one asymptomatic) from Santiago of Chile, with a complete vaccination schedule with two doses of CoronaVac (Sinovac Life Science) infected with the variant of interest (VOI) B.1.621 (Mu). They were compared with four unvaccinated patients, who had a higher prevalence of symptoms after infection compared to vaccinated patients. In the CoronaVac-vaccinated group, an 80-year-old patient who registered various comorbidities required Invasive mechanical ventilation for 28 days with current home medical recovery discharge. By contrast, in the unvaccinated group, a 71-year-old presented more symptoms with more than 45 days of Invasive mechanical ventilation, which continues to date, presenting greater lung damage than the vaccinated hospitalized patient. This first report evidence differences in the clinical symptomatology of patients vaccinated and non-vaccinated infected with the VOI B.1.621 (Mu) and suggest the protective effects of CoronaVac against this variant.

Analysis by real-time PCR of five transport and conservation mediums of nasopharyngeal swab samples to COVID-19 diagnosis in Santiago of Chile.

Due to the COVID-19 pandemic, many transport kits have been manufactured to preserve and transport nasopharyngeal swab samples (NPSs) from patients. However, there is no information on the performance of the different virus transport media (VTM) used in COVID-19 diagnosis in the population of Santiago de Chile. We compared the RT-qPCR amplification profile of five different viral transport kit mediums, including DNA/RNA Shield™, NAT, VTM-N, Ezmedlab™, and phosphate-buffered saline (PBS), for NPSs from Central Metropolitan Health Service, Santiago, Chile. The DNA/RNA Shield™ medium showed a better performance in terms of Cq and RFU values for the internal reference RNase P and viral ORF1ab probes. By contrast, the PBS transport medium registered higher Cq values for the viral and reference gene, compared to the other VTM. DNA/RNA Shield™ shows higher relative fluorescence units (RFUs) and lower Cq values for the reference gene. Collectively, our results suggest that the PBS medium could compromise the sample diagnosis because of its lower RT-qPCR performance. The NAT, Ezmedlab and VTM-N, and DNA/RNA Shield™ media show acceptable RT-qPCR parameters and, consequently, seem suitable for use in COVID-19 diagnosis.

Evaluation of the Immune Response Induced by CoronaVac 28-Day Schedule Vaccination in a Healthy Population Group

CoronaVac vaccine from Sinovac Life Science is currently being used in several countries. In Chile, the effectiveness of preventing hospitalization is higher than 80% with a vaccination schedule. However, to date, there are no data about immune response induction or specific memory. For this reason, we recruited 15 volunteers without previous suspected/diagnosed COVID-19 and with negative PCR over time to evaluate the immune response to CoronaVac 28 and 90 days after the second immunization (dpi). The CoronaVac administration induces total and neutralizing anti-spike antibodies in all vaccinated volunteers at 28 and 90 dpi. Furthermore, using ELISpot analysis to assay cellular immune responses against SARS-CoV-2 spike protein, we found an increase in IFN-gamma- and Granzyme B-producing cells in vaccinated volunteers at 28 and 90 dpi. Together, our results indicate that CoronaVac induces a robust humoral immune response and cellular immune memory of at least 90 dpi.

The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants.

Timely detection of severe acute respiratory syndrome due to coronavirus 2 (SARS-CoV-2) by reverse transcription quantitative polymerase chain reaction (RT-qPCR) has been the gold- strategy for identifying positive cases during the current pandemic. However, faster and less expensive methodologies are also applied for the massive diagnosis of COVID-19. In this way, the rapid antigen test (RAT) is widely used. However, it is necessary to evaluate its detection efficiency considering the current pandemic context with the circulation of new viral variants. In this study, we evaluated the sensitivity and specificity of RAT (SD BIOSENSOR, South Korea), widely used for testing and SARS-CoV-2 diagnosis in Santiago of Chile. The RAT showed a 90% (amplification range of 20 ≤ Cq <25) and 10% (amplification range of 25 ≤ Cq <30) of positive SARS-CoV-2 cases identified previously by RT-qPCR. Importantly, a 0% detection was obtained for samples within a Cq value>30. In SARS-CoV-2 variant detection, RAT had a 42.8% detection sensitivity in samples with RT-qPCR amplification range 20 ≤ Cq <25 containing the single nucleotide polymorphisms (SNP) K417N/T, N501Y and E484K, associated with beta or gamma SARS-CoV-2 variants. This study alerts for the special attention that must be paid for the use of RAT at a massive diagnosis level, especially in the current scenario of appearance of several new SARS-CoV-2 variants which could generate false negatives and the compromise of possible viral outbreaks.

Identification of COVID-19 Waves: Considerations for Research and Policy.

The identification of COVID-19 waves is a matter of the utmost importance, both for research and decision making. This study uses COVID-19 information from the 52 municipalities of the Metropolitan Region, Chile, and presents a quantitative method-based on weekly accumulated incidence rates-to define COVID-19 waves. We explore three different criteria to define the duration of a wave, and performed a sensitivity analysis using multivariate linear models to show their commonalities and differences. The results show that, compared to a benchmark definition (a 100-day wave), the estimations using longer periods of study are worse in terms of the model's overall fit (adjusted R2). The article shows that defining a COVID-19 wave is not necessarily simple, and has consequences when performing data analysis. The results highlight the need to adopt well-defined and well-justified definitions for COVID-19 waves, since these methodological choices can have an impact in research and policy making.

The successful COVID-19 vaccine rollout in Chile: Factors and challenges.

As the COVID-19 pandemic continues causing problems around the world, Chile is facing a new episode of increasing cases and deaths. However, at the same time, the country has succeeded in providing vaccines for an important part of its population over a short period. What are the factors behind this successful process? What are the challenges faced by the country today? This article explores potential explanations for the "Chilean paradigm", regarding the COVID-19 vaccine rollout. Borrowing from implementation science frameworks, the analysis proposed an alternative explanation-based on multiple actors, approaches, and history-as opposed to one in which the outcome is due mainly to the government's performance. The rapid and extensive coverage of vaccination can be explained by the role played by the government and the academia in securing vaccines through a pragmatic approach; the capacity built at local level, as well as the coordination between the health system and local authorities; and favorable vaccine culture, developed through the implementation of the National Immunization Program. Short and long-term elements (such as investment in infrastructure and relationships between stakeholders, and actions carried out during the pandemic), as well as contextual factors (such as the political and socioeconomic context), provide a more complex story to explain the observed outcomes. While other countries could try to follow the Chilean example, the article shows that short-term actions are necessary but might not be sufficient to achieve results. At a global level, the situation calls for rethinking how countries will face these global challenges, including issues such as international cooperation and global health governance.

COVID-19 incidence and mortality in the Metropolitan Region, Chile: Time, space, and structural factors.

Demographic, health, and socioeconomic factors significantly inform COVID-19 outcomes. This article analyzes the association of these factors and outcomes in Chile during the first five months of the pandemic. Using the municipalities Metropolitan Region's municipalities as the unit of analysis, the study looks at the role of time dynamics, space, and place in cases and deaths over a 100-day period between March and July 2020. As a result, common and idiosyncratic elements explain the prevalence and dynamics of infections and mortality. Social determinants of health, particularly multidimensional poverty index and use of public transportation play an important role in explaining differences in outcomes. The article contributes to the understanding of the determinants of COVID-19 highlighting the need to consider time-space dynamics and social determinants as key in the analysis. Structural factors are important to identify at-risk populations and to select policy strategies to prevent and mitigate the effects of COVID-19. The results are especially relevant for similar research in unequal settings.