Routes of importation and spatial dynamics of SARS-CoV-2 variants during localised interventions in Chile (preprint)

South America suffered large SARS-CoV-2 epidemics between 2020 and 2022 caused by multiple variants of interest and concern, some causing substantial morbidity and mortality. However, their transmission dynamics are poorly characterised. The epidemic situation in Chile enables us to investigate differences in the distribution and spread of variants Alpha, Gamma, Lambda, Mu and Delta. Chile implemented non-pharmaceutical interventions and an integrated genomic and epidemiological surveillance system that included airport and community surveillance to track SARS-CoV-2 variants. Here we combine viral genomic data and anonymised human mobility data from mobile phones to characterise the routes of importation of different variants into Chile, the relative contributions of airport-based importations to viral diversity versus land border crossings and test the impact of the mobility network on the diffusion of viral lineages within the country. We find that Alpha, Lambda and Mu were identified in Chile via airport surveillance six, four and five weeks ahead of their detection via community surveillance, respectively. Further, some variants that originated in South America were imported into Chile via land rather than international air travel, most notably Gamma. Different variants exhibited similar trends of viral dissemination throughout the country following their importation, and we show that the mobility network predicts the time of arrival of imported lineages to different Chilean comunas. Higher stringency of local NPIs was also associated with fewer domestic viral importations. Our results show how genomic surveillance combined with high resolution mobility data can help predict the multi-scale geographic expansion of emerging infectious diseases. Significance statementGlobal preparedness for pandemic threats requires an understanding of the global variations of spatiotemporal transmission dynamics. Regional differences are important because the local context sets the conditions for the unfolding of local epidemics, which in turn affect transmission dynamics at a broader scale. Knowledge gaps from the SARS-CoV-2 pandemic remain for regions like South America, where distinct sets of viral variants emerged and spread from late 2020 onwards, and where changes in human behaviour resulted in epidemics which differed from those observed in other regions. Our interdisciplinary analysis of the SARS-CoV-2 epidemic in Chile provides insights into the spatiotemporal trends of viral diffusion in the region which shed light on the drivers that can influence future epidemic waves and pandemics.

Effectiveness and duration of a second COVID-19 vaccine booster (preprint)

Using a prospective national cohort of 3.75 million individuals aged 20 or older, we evaluated the effectiveness against COVID-19 related ICU admissions and death of mRNA-based second vaccine boosters for four different three-dose background regimes: BNT162b2 primary series plus a homologous booster, and CoronaVac primary series plus an mRNA booster, a homologous booster, and a ChAdOx-1 booster. We estimated the vaccine effectiveness weekly from February 14 to August 15, 2022, by estimating hazard ratios of immunization over non-vaccination, accounting for relevant confounders. The overall adjusted effectiveness of a second mRNA booster shot was 88.2% (95%CI, 86.2-89.9) and 90.5% (95%CI 89.4-91.4) against ICU admissions and death, respectively. Vaccine effectiveness showed a mild decrease for all regimens and outcomes, probably associated with the introduction of BA.4 and BA.5 Omicron sub-lineages and immunity waning. The duration of effectiveness suggests that no additional boosters are needed six months following a second booster shot.

Effectiveness of CoronaVac in children 3 to 5 years during the omicron SARS-CoV-2 outbreak (preprint)

The outbreak of the B.1.1.529 lineage of SARS-CoV-2 (omicron) has caused an unprecedented number of Covid-19 cases, including pediatric hospital admissions. Policymakers urgently need evidence of vaccine effectiveness in children to balance the costs and benefits of vaccination campaigns, but the evidence is sparse or non-existing. Leveraging a population-based cohort of 490,694 children aged 3–5 years, we estimated the effectiveness of administering a two-dose schedule, 28 days apart, of CoronaVac using inverse probability-weighted survival regression models to estimate hazard ratios of complete immunization over non-vaccination, accounting for time-varying vaccination exposure and relevant confounders. The study was conducted between December 6, 2021, and February 26, 2022, during the omicron outbreak in Chile. The estimated vaccine effectiveness was 38.2% (95%CI, 36.5–39.9) against Covid-19, 64.6% (95%CI, 49.6–75.2) against hospitalization, and 69.0% (95%CI, 18.6–88.2) to prevent intensive care unit admission. The effectiveness was modest; however, protection against severe disease remained high.

Duration of Effectiveness of Vaccines Against SARS-CoV-2 Infection and COVID-19 Disease: Results of a Systematic Review and Meta-Regression (preprint)

Background: Knowing whether and to what extent COVID-19 vaccine effectiveness wanes is critical to informing vaccine policy, such as the need for and timing of booster doses. Methods: We performed a systematic review from June 17 to October 27, 2021, using a structured search strategy of multiple databases. Studies with vaccine efficacy or effectiveness (VE) estimates for any WHO Emergency-Use-Listed COVID-19 vaccine at discrete time intervals after full vaccination and meeting pre-defined screening criteria underwent full-text review and risk of bias assessment. Random effects meta-regression was used to estimate the average change in VE from one to six months after full vaccination. Findings: Of 9,261 studies screened, 217 underwent full text review, and 14 were included in analyses. Vaccines evaluated were Pfizer/BioNTech-Comirnaty (n=11), Moderna-mRNA-1273 (n=8), Janssen-Ad26.COV2.S (n=3), and AstraZeneca-Vaxzevria (n=2). On average, VE against SARS-CoV-2 infection decreased between 1 and 6 months after full vaccination by 18·5 percentage points (95% CI 8·4-33·4, p=0·0006) among persons of all ages and 19·9 percentage points (95% CI 9·2-36·7, p=0·0007) among older persons; for symptomatic COVID-19 disease, VE decreased by 25·4 (95% CI 13·7-42·5) and 32·0 percentage points (95% CI 11·0-69·0), respectively; and for severe COVID-19 disease, VE decreased by 8·0 (95% CI 3·6-15·2) and 9·7 percentage points (95% CI 5·9-14·7), respectively. The majority of VE estimates against severe disease remained over 70% for all time points. Interpretation: COVID-19 vaccine efficacy or effectiveness against COVID-19 severe disease remained high (>70%) in most studies in the six months after full vaccination, although it did decrease some (on average, 8-10 percentage points) between one and six months after full vaccination. In contrast, VE against SARS-CoV-2 infection and symptomatic COVID-19 disease decreased approximately 20-30 percentage points during the six months after vaccination. The decrease in VE is likely due, at least in part, to waning immunity, although we cannot rule out the effect of bias. Continued follow-up of VE beyond six months is critical for updating COVID-19 vaccine policy. . Funding Information: Coalition for Epidemic Preparedness Innovations (CEPI)Declaration of Interests: MMH reports research grants from World Health Organization (WHO, Coalition for Epidemic Preparedness Innovations (CEPI), Asian Development Bank (ADB), Bill & Melinda Gates Foundation (BMGF), and Pfizer (all paid to the institution). RA reports a contract from the United States Centers for Disease Control and Prevention, a grant from the Chile Ministry of Science, and consulting fees from Mayo Clinic and Chile Ministry of Health. YG reports research grants from the United States-Israel Binational Science Foundation (BSF) and Israel Science Foundation. MJG reports research grants from South African Medical Research Council and BMGF (all paid to the institution) and participation on a data safety monitoring board for a study on the effectiveness of COVID-19 vaccination against SARS-CoV-2-associated hospitalization and death. AH reports research grants from United States-Israel BSF. KLO serves as the Secretariat for the WHO Strategic Advisory Group of Experts on Immunization. MDK reports research grants from WHO, CEPI, ADB, and Pfizer (all paid to the institution) and consultancy fees from Merck. All other authors have nothing to declare.

Tool for estimating the probability of having COVID-19 with one or more negative RT-PCR results (preprint)

Early case detection and isolation of infected individuals are critical to controlling COVID-19. RT-PCR is considered the diagnosis gold standard, but false-negatives occur. Based on previous work, we built a user-friendly online tool to estimate the probability of having COVID-19 with negative RT-PCR results and thus avoid preventable SARS-CoV-2 transmission.

Covid-19 in South America: Clinical and epidemiological characteristics among 381 patients during the early phase of the pandemic in Santiago, Chile (preprint)

Background: Understanding the characteristics of the Covid-19 pandemic in different geographical regions, ethnic and socioeconomic settings are of emerging importance. This study presents the demographic and clinical features of SARS-CoV-2 infected patients in a large private healthcare center in Santiago, Chile, during the first month of the pandemic. Methods: : We analyzed the demographics, laboratory and clinical characteristics including severity and outcome of all patients diagnosed with Covid-19 during the first month of the pandemic. SARS-2-CoV infection was confirmed by RT-PCR in nosopharyngeal samples. The primary outcome was a composite of ICU admission or all-cause, in-hospital mortality. Clinical and laboratory parameters of hospitalized patients were analyzed regarding their association with the primary outcome. Results: : From March 3 to April 4, 2020, 3679 individuals were tested for SARS-CoV-2 in our hospital. Of those, 381 had Covid-19 and were included into this analysis. Most patients (99.2%) were Chileans, 12% returning from recent travel. The median age was 39 years (IQR 31-49) and 52% were female. A total of 88 patients (23.1%) were hospitalized; 18 (3.7%) required ICU and/or died. The overall mortality was 0.7%. Increased body mass index (BMI) and elevated C-reactive protein (CRP) were independently associated with ICU care or death. Conclusion: During the first weeks of the pandemic in Chile, most Covid-19 patients were young, with low rates of hospitalization, ICU requirement, and fatality. BMI and CRP on admission were predictors for severity. Our data provide important information on the clinical course and outcome of Covid-19 in a Latin American setting.

Rapid SARS-CoV-2 antigen detection by immunofluorescence - a new tool to detect infectivity (preprint)

The evaluated SARS-CoV-2 antigen rapid fluorescence immunoassays reliably identified patients within the first 5 days of symptom onset, when respiratory secretions carried high viral loads. This high performance suggests that these tests might play an important role for future PCR-independent strategies to detect early or infective cases.

Clinical and Epidemiological Characteristics of the First Month of the Covid-19 Pandemic in Chile (preprint)

Introduction: Understanding the clinical course and outcomes of patients with Covid-19 in underrepresented populations like Latin America is paramount. In this study, we report the clinical characteristics of Covid-19 in Chile, with a focus on subjects requiring hospitalization during the initial phases of the SARS-CoV-2 pandemic. Methods: This is a single center study including all consecutive patients diagnosed with Covid-19 during the first month of the pandemic. Demographics, clinical characteristics and laboratory data were collected within 24 hours of admission. The primary outcome was a composite of ICU admission or all-cause, in-hospital mortality. Results: During the first month of the pandemic, 381 patients were confirmed as positive for SARS- CoV-2 by molecular testing; 88 (23.1%) of them eventually required hospitalization. Median age of the cohort was 39 years (IQR 31-49). Overall mortality was 0.7% and 18 (3.7%) out of the 88 subjects who required hospitalization either died and/or required ICU. Increased body mass index (BMI), C-reactive protein levels (CRP) and the SaTO2/FiO2 index on admission were independently associated with a higher risk of ICU care or death. Discussion: The lower mortality observed in our prospective cohort during the first month of SARS-Cov-2 pandemic was lower than previously reported. This finding could be due to a lower threshold for admission, a healthcare system not yet overburdened and a younger population, among other factors. BMI, CRP on admission were strong predictors for ICU care or all-cause, in- hospital mortality. Our data provide important information regarding the clinical course of Covid- 19 in Latin America.

Head-to-head comparison of four antigen-based rapid detection tests for the diagnosis of SARS-CoV-2 in respiratory samples (preprint)

In the context of the Covid-19 pandemic, the development and validation of rapid and easy-to-perform diagnostic methods are of high priority. We compared the performance of four rapid antigen detection tests for SARS-CoV-2 in respiratory samples. Immunochromatographic SARS-CoV-2 assays from RapiGEN, Liming bio, Savant, and Bioeasy were evaluated using universal transport medium containing naso-oropharyngeal swabs from suspected Covid-19 cases. The diagnostic accuracy was determined in comparison to SARS-CoV-2 RT-PCR. A total of 111 samples were included; 80 were RT-PCR positive. Median patients age was 40 years, 55% were female, and 88% presented within the first week after symptom onset. The evaluation of the Liming bio assay was discontinued due to insufficient performance. The overall sensitivity values of RapiGEN, Liming bio, and Bioeasy tests were 62.0% (CI95% 51.0-71.9), 16.7% (CI95% 10.0-26.5), and 85.0% (CI95% 75.6-91.2), respectively, with specificities of 100%. Sensitivity was significantly higher in samples with high viral loads (RapiGEN, 84.9%; Bioeasy, 100%). The study highlighted the significant heterogeneity of test performance among evaluated assays, which might have been influenced by the use of a non-validated sample material. The high sensitivity of some tests demonstrated that rapid antigen detection has the potential to serve as an alternative diagnostic method, especially in patients presenting with high viral loads in early phases of infection. This is particularly important in situations with limited access to RT-PCR or prolonged turnaround time. Further comparative evaluations are necessary to select products with high performance among the growing market of diagnostic tests for SARS-CoV-2.