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1.
Preprint | medRxiv | ID: ppmedrxiv-21266967

ABSTRACT

Aim: The New Zealand government is transitioning from the Alert Level framework, which relies on government action and population level controls, to the COVID-19 Protection Framework, which relies on vaccination rates and allows for greater freedoms (for the vaccinated). As restrictions are eased, there is significant interest in understanding the relative risk of spreading COVID-19 posed by unvaccinated and vaccinated individuals. Methods: A stochastic branching process model is used to simulate the spread of COVID-19 for outbreaks seeded by unvaccinated or vaccinated individuals. The likelihood of infecting or getting infected with COVID-19 is calculated based on vaccination status. Results: A vaccinated traveler infected with COVID-19 is 9x less likely to seed an outbreak than an unvaccinated traveler infected with COVID-19. For a vaccination rate of 50%, unvaccinated individuals are responsible for 87% of all infections whereas 3% of infections are from vaccinated to vaccinated. When normalized by population, a vaccinated individual is 6.8x more likely to be infected by an unvaccinated individual than by a vaccinated individual. For a total population vaccination rate of 78.7%, which is equivalent to the 90% vaccination target for the eligible population (over 12 years old), this means that vaccinated individuals are 1.9x more likely to be infected by an unvaccinated individual than by a vaccinated, even though there are 3.7x more vaccinated individuals in the population. Conclusions: This work demonstrates that most new infections are caused by unvaccinated individuals. These simulations illustrate the importance of vaccination in stopping individuals from becoming infected with COVID-19 and in preventing onward transmission.

2.
Preprint in English | medRxiv | ID: ppmedrxiv-21266969

ABSTRACT

Like other congregate living settings, military basic training has been subject to outbreaks of COVID-19. We sought to identify improved strategies for preventing outbreaks in this setting using an agent-based model of a hypothetical cohort of trainees on a U.S. Army post. Our analysis revealed unique aspects of basic training that require customized approaches to outbreak prevention, which draws attention to the possibility that customized approaches may be necessary in other settings, too. In particular, we showed that introductions by trainers and support staff may be a major vulnerability, given that those individuals remain at risk of community exposure throughout the training period. We also found that increased testing of trainees upon arrival could actually increase the risk of outbreaks, given the potential for false-positive test results to lead to susceptible individuals becoming infected in group isolation and seeding outbreaks in training units upon release. Until an effective transmission-blocking vaccine is adopted at high coverage by individuals involved with basic training, need will persist for non-pharmaceutical interventions to prevent outbreaks in military basic training. Ongoing uncertainties about virus variants and breakthrough infections necessitate continued vigilance in this setting, even as vaccination coverage increases.

3.
Preprint in English | medRxiv | ID: ppmedrxiv-21266959

ABSTRACT

Purpose of this report: The aim of this rapid communication is a projection of the development of the fourth COVID-19 wave in the federal state of Bavaria in Germany, taking into account different lockdown scenarios especially for unvaccinated individuals. In particular, the number of infections and the occupancy of intensive care facilities are considered. Applied Methods: We use the agent-based epidemiological simulator Covasim for discussing various epidemiological scenarios. Firstly, we adapt and calibrate our model to reproduce the historical course of the COVID-19 pandemic in Bavaria. For this, we model and integrate numerous public health interventions imposed on the local population. As for some of the political actions rigorous quantification is currently not available, we fit those unknown (free) model parameters to published data on the measured epidemiological dynamics. Finally, we define and analyse scenarios of different lockdown scenarios with restrictions for unvaccinated individuals in different areas of life. Key message: The results of our simulations show that in all scenarios considered, the number of infections, but also the number of severe cases, exceed previous maximum values. Interventions, especially restrictions on contacts of unvaccinated persons, can still mitigate the impact of the fourth COVID-19 wave on populations substantially. Excluding unvaccinated students from attending classes has only a small impact on the public health burden. However, many severe cases can be prevented by reducing community and/or work related contacts of unvaccinated people, e.g, by achieving high home office rates.

4.
Preprint in English | medRxiv | ID: ppmedrxiv-21264509

ABSTRACT

Against a backdrop of widespread global transmission, a number of countries have successfully brought large outbreaks of COVID-19 under control and maintained near-elimination status. A key element of epidemic response is the tracking of disease transmissibility in near real-time. During major outbreaks, the reproduction rate can be estimated from a time-series of case, hospitalisation or death counts. In low or zero incidence settings, knowing the potential for the virus to spread is a response priority. Absence of case data means that this potential cannot be estimated directly. We present a semi-mechanistic modelling framework that draws on time-series of both behavioural data and case data (when disease activity is present) to estimate the transmissibility of SARS-CoV-2 from periods of high to low -- or zero -- case incidence, with a coherent transition in interpretation across the changing epidemiological situations. Of note, during periods of epidemic activity, our analysis recovers the effective reproduction number, while during periods of low -- or zero -- case incidence, it provides an estimate of transmission risk. This enables tracking and planning of progress towards the control of large outbreaks, maintenance of virus suppression, and monitoring the risk posed by re-introduction of the virus. We demonstrate the value of our methods by reporting on their use throughout 2020 in Australia, where they have become a central component of the national COVID-19 response.

5.
Preprint in English | medRxiv | ID: ppmedrxiv-21266986

ABSTRACT

Since December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly from Wuhan (China) across the globe, affecting more than 200 countries by mid-2021, with over 190 M reported cases and around 4 M fatalities. During the first year of the pandemic, affected countries implemented a variety of non-pharmaceutical interventions to control virus transmission. In December 2020, countries started administering several authorised vaccines under a limited supply scenario. In this context, a SEIR-type continuous-time deterministic disease model was developed to explore the effect of vaccination in terms of vaccination rate and efficacy, together with varying non-pharmaceutical protection measures, on disease incidence in the initial phase of vaccination. For this, the model incorporates (i) a protection measure including low (self-protection), medium (mobility limitation), high (closure of indoor facilities) and very high (lockdown) protection levels, (ii) quarantine for confirmed cases, and (iii) vaccination rate and efficacy of four type of vaccines (Pfizer, Moderna, Astra Zeneca or Janssen). The model was veri[fi]ed and evaluated using the response timeline and vaccination strategies and rates in the Basque Country (N. Spain). Once the model performance was validated, different initial phase (when 30% of the population is vaccinated) vaccination scenarios were simulated, including (i) a realistic vaccine limited supply scenario, and (ii) four potential full vaccine supply scenarios where a unique vaccine type is administered. The Pfizer scenario resulted in the lowest prevalence of infection and cumulative mortality, particularly for low- and medium-level protection rates. However, regardless of the administered vaccine, a high-level protection scenario is the most effective to control the virus transmission and disease mortality in the studied initial phase of vaccination. The model here, which is based on this example, could be easily applied to other regions or countries, modifying the strategies implemented and initial conditions.

6.
Preprint in English | medRxiv | ID: ppmedrxiv-21266875

ABSTRACT

To guide evidence-based prevention of COVID-19 in children, we estimated risks of severe outcomes in 820,404 symptomatic paediatric cases reported by 10 EU Member States between August 2020 and October 2021. Case and hospitalisation rates rose as overall transmission increased but severe outcomes were rare: 9,611 (1.2%) were hospitalised, 640 (0.08%) required intensive care and 84 (0.01%) died. Despite increased individual risk (aOR; 95% CI for hospitalisation: 7.3; 3.3 - 16.2, ICU: 8.7; 6.2 - 12.3) in cases with comorbidities such as cancer, diabetes, cardiac or lung disease, most (83.7%) hospitalised children had no reported comorbidity.

7.
Preprint in English | medRxiv | ID: ppmedrxiv-21266976

ABSTRACT

Introduction: The COVID-19 pandemic and its collateral damage severely impact health systems globally and risk to worsen the malaria situation in endemic countries. Malaria is a leading cause of morbidity and mortality in Ghana. This study aims to analyze routine surveillance data to assess possible effects on the malaria burden in the first year of the COVID-19 pandemic in the Northern Region of Ghana. Methods: Monthly routine data from the District Health Information Management System II (DHIMS2) of the Northern Region of Ghana were analyzed. Overall outpatient department visits and malaria incidence rates from the years 2015 to 2019 were compared to the corresponding data of the year 2020. Results: Compared to the corresponding periods of the years 2015 to 2019, overall visits and malaria incidence in pediatric and adult outpatient departments in northern Ghana decreased in March and April 2020, when major movement and social restrictions were implemented in response to the pandemic. Incidence slightly rebounded afterwards in 2020 but stayed below the average of the previous years. Data from inpatient departments showed a similar but more pronounced trend when compared to outpatient departments. In pregnant women, however, malaria incidence in outpatient departments increased after the first COVID-19 wave. Discussion: The findings from this study show that the COVID-19 pandemic affects the malaria burden in health facilities of Ghana, with declines in in- and outpatient rates. Pregnant women may experience reduced access to intermittent preventive malaria treatment and insecticide treated nets, resulting in subsequent higher malaria morbidity. Further data from other African countries, particularly on community-based studies, are needed to fully determine the impact of the pandemic on the malaria situation.

8.
Preprint in English | medRxiv | ID: ppmedrxiv-21266896

ABSTRACT

Studies report a strong impact of the COVID-19 pandemic and related stressors on the mental wellbeing of general population. In this paper, we investigated whether COVID-19 related concerns and social adversity affected schizotypal traits, anxiety and depression using structural equational modelling. In mediation analyses, we furthermore explored whether these associations were mediated by healthy (sleep and physical exercise) or unhealthy behaviours (drug and alcohol consumption, excessive media use). We assessed schizotypy, depression and anxiety as well as, healthy and unhealthy behaviours and a wide range of sociodemographic scores using online surveys from residents of Germany and the United Kingdom over one year during the COVID-19 pandemic. Four independent samples were collected (April/ May 2020: N=781, September/ October 2020: N=498, January/ February 2021: N=544, May 2021: N= 486). The results revealed that COVID-19 related life concerns were significantly associated with schizotypy in the autumn 2020 and spring 2021 surveys, and with anxiety and depressive symptoms in all surveys; and social adversity significantly affected the expression of schizotypal traits in all but the spring 2020 survey, and depressive and anxiety symptoms in all samples. Importantly, we found that excessive media consumption (>4h per day) fully mediated the relationship of COVID-19 related life concerns and schizotypal traits in the winter 2021 survey. Furthermore, several of the surveys showed that excessive media consumption was associated with increased depressive and anxiety-related symptoms in people burdened by COVID-19 related life. The ongoing uncertainties of the pandemic and the restrictions on social life have a strong impact on mental well-being and especially the expression of schizotypal traits. The negative impact is further boosted by excessive media consumption, which is especially critical for people with high schizotypal traits.

9.
Preprint in English | medRxiv | ID: ppmedrxiv-21266927

ABSTRACT

Introduction. As COVID-19 roared through the world, governments worldwide enforced containment measures that affected various treatment pathways, including those for hip fracture (HF). This study aimed to measure process and outcome indicators related to the quality of care provided to non-COVID-19 elderly patients affected by HF in Emilia-Romagna, a region of Italy severely hit by the pandemic. Methods. We collected the hospital discharge records of all patients admitted to the hospitals of Emilia-Romagna with a diagnosis of HF from January to May in the years 2019/2020. We analyzed surgery rate, surgery timeliness, length of hospital stay, timely rehabilitation, and 30-day mortality for each HF patient. We evaluated monthly data (2020 vs. 2019) with the chi-square and t-test, where appropriate. Logistic regression was used to investigate the differences in 30-day mortality. Results. Our study included 5379 patients with HF. In April and May 2020, there was a significant increase in the proportion of HF patients that did not undergo timely surgery. In March 2020, we found a significant increase in mortality (OR = 2.22). Female sex (OR = 0.52), age [≥]90 years (OR = 4.33), surgery after 48 hours (OR = 3.08) and not receiving surgery (OR = 6.19) were significantly associated with increased mortality. After adjusting for the aforementioned factors, patients hospitalized in March 2020 still suffered higher mortality (OR = 2.21). Conclusions. Our results show a reduction in the overall quality of care provided to non-COVID-19 elderly patients affected by HF. The mortality rate of patients with HF increased significantly in March 2020. Patients' characteristics and variations in processes of care partially explained this increase. Our analysis reveals the importance of including process and outcomes indicators, for both acute and post-acute care management issues, in emergency preparedness plans, to monitor healthcare systems' capacities and capabilities.

10.
Preprint in English | medRxiv | ID: ppmedrxiv-21266930

ABSTRACT

Background: In settings where the COVID-19 vaccine supply is constrained, extending the intervals between the first and second doses of the COVID-19 vaccine could let more people receive their first doses earlier. Our aim is to estimate the health impact of COVID-19 vaccination alongside benefit-risk assessment of different dosing intervals for low- and middle-income countries of Europe. Methods: We fitted a dynamic transmission model to country-level daily reported COVID-19 mortality in 13 low- and middle-income countries in the World Health Organization European Region (Albania, Armenia, Azerbaijan, Belarus, Bosnia and Herzegovina, Bulgaria, Georgia, Republic of Moldova, Russian Federation, Serbia, North Macedonia, Turkey, and Ukraine). A vaccine product with characteristics similar to the Oxford/AstraZeneca COVID-19 (AZD1222) vaccine was used in the base case scenario and was complemented by sensitivity analyses around efficacies related to other COVID-19 vaccines. Both fixed dosing intervals at 4, 8, 12, 16, and 20 weeks and dose-specific intervals that prioritise specific doses for certain age groups were tested. Optimal intervals minimise COVID-19 mortality between March 2021 and December 2022. We incorporated the emergence of variants of concern into the model, and also conducted a benefit-risk assessment to quantify the trade-off between health benefits versus adverse events following immunisation. Findings: In 12 of the 13 countries, optimal strategies are those that prioritise the first doses among older adults (60+ years) or adults (20-59 years). These strategies lead to dosing intervals longer than six months. In comparison, a four-week fixed dosing interval may incur 10.2% [range: 4.0% - 22.5%; n = 13 (countries)] more deaths. There is generally a negative association between dosing interval and COVID-19 mortality within the range we investigated. Assuming a shorter first dose waning duration of 120 days, as opposed to 360 days in the base case, led to shorter optimal dosing intervals of 8-12 weeks. Benefit-risk ratios were the highest for fixed dosing intervals of 8-12 weeks. Interpretation: We infer that longer dosing intervals of over six months, which are substantially longer than the current label recommendation for most vaccine products, could reduce COVID-19 mortality in low- and middle-income countries of WHO/Europe. Certain vaccine features, such as fast waning of first doses, significantly shorten the optimal dosing intervals.

11.
Preprint in English | medRxiv | ID: ppmedrxiv-21266899

ABSTRACT

Recent months have demonstrated that emerging variants may set back the global COVID-19 response. The ability to rapidly assess the threat of new variants in real-time is critical for timely optimisation of control strategies. We extend the EpiEstim R package, designed to estimate the time-varying reproduction number (Rt), to estimate in real-time the effective transmission advantage of a new variant compared to a reference variant. Our method can combine information across multiple locations and over time and was validated using an extensive simulation study, designed to mimic a variety of real-time epidemic contexts. We estimate that the SARS-CoV-2 Alpha variant is 1.46 (95% Credible Interval 1.44-1.47) and 1.29, (95% CrI 1.29-1.30) times more transmissible than the wild type, using data from England and France respectively. We further estimate that Beta and Gamma combined are 1.25 (95% CrI 1.24-1.27) times more transmissible than the wildtype (France data). All results are in line with previous estimates from literature, but could have been obtained earlier and more easily with our off-the-shelf open-source tool. Our tool can be used as an important first step towards quantifying the threat of new variants in real-time. Given the popularity of EpiEstim, this extension will likely be used widely to monitor the co-circulation and/or emergence of multiple variants of infectious pathogens.

12.
Preprint in English | medRxiv | ID: ppmedrxiv-21265946

ABSTRACT

We prepared severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) working standards and reference panels from a pool of swab fluid samples before and after inactivation by beta-propiolactone and quantified viral load in nucleic acid amplification technology (NAT) detectable RNA copies/mL using limiting dilution analysis. The following 50% lower limits of detection (LOD) were estimated by probit analysis as compared to detection limits of rapid antigen tests on 1.5 fold dilutions of the native material: Roche cobas PCR 1.8 (1.0-3.3), Hologic Aptima TMA 6.6 (4.4-9.9), DRW SAMBA 15 (7-30), Molgen LAMP 23 (13-42), Fluorecare antigen 50,000, Abbott Panbio antigen 75,000 and Roche antigen 100,000 copies/mL. One 50% Tissue Culture Infectious Dose (TCID50)/mL of culture fluid was estimated to be equivalent to approximately 1000 RNA copies/mL (2700- 4300 International Units) in our working standard. When assuming this level as start of contagiousness in a log-linear ramp up viremia model with 10-fold rise of viral load per day for the B.1 (Wuhan) type we estimated relative time points of first detectability of early infection by the different SARS-CoV-2 assays from the LODs mentioned above. The four NAT assays would be able to detect early viremia 40-66 hours earlier than the 1000 copies/mL infectivity threshold, whereas the three antigen tests would become positive 41-48 hours later. Our modeling of analytical sensitivity data was found to be compatible with clinical sensitivity data of rapid antigen tests and confirms that NAT assays are more reliable than antigen assays for identifying early infected asymptomatic individuals who are potentially infectious.

13.
Preprint in English | medRxiv | ID: ppmedrxiv-21266885

ABSTRACT

Objectives: The impact of the spread of COVID-19 on the mental health and its mitigating factors of high school athletes is not fully understood. The aims of this study were 1) to describe the psychological distress and stressors experienced by high school athletes during the COVID-19 pandemic and to elucidate the relationships between them and 2) to determine the relationship between psychological distress and social support. Methods: Participants of this cross-sectional study were recruited from public high schools in East Japan. We conducted either an online or paper-based questionnaire survey from July 12 to 31, 2020, and used data collected from 3017 high school student athletes (valid response rate: 88.7%) for the analyses. We evaluated psychological distress (K6 [≥]10), stressors to athletes during the COVID-19 pandemic (SAC-19), and perceived social support from others. Logistic regression analysis was used to calculate odds ratios (OR) and 95% confidence intervals (CI) for developing psychological distress. Results: Among the participants, 764 (25.3%) experienced psychological distress. Among the five factors extracted from the SAC-19, self-restraint requests (OR = 1.03, 95% CI: 1.01-1.04), pressure from the surrounding environment (OR = 1.15, 95% CI: 1.12-1.18), and difficulties in maintaining athletic activities (OR = 1.16, 95% CI: 1.12-1.21) increased the risk of psychological distress. On the other hand, participants who were satisfied with the support from family members (OR = 0.77, 95% CI: 0.67-0.90), teammates (the same grade) (OR = 0.81, 95% CI: 0.67-0.98), and coaches and instructors (OR = 0.77, 95% CI: 0.65-0.91) showed lower psychological distress. Conclusions: During the COVID-19 pandemic, high school athletes experienced more psychological distress than usual. Stressors such as self-restraint requests, pressure from the surrounding environment, and difficulties in maintaining athletic activities increased the risk. On the other hand, social support from family members, teammates (the same grade), and coaches and instructors can help alleviate these stressors.

14.
Preprint in English | medRxiv | ID: ppmedrxiv-21266786

ABSTRACT

Serological surveillance studies of infectious diseases provide population-level estimates of infection and antibody prevalence, generating crucial insight into population-level immunity, risk factors leading to infection, and effectiveness of public health measures. These studies traditionally rely on detection of pathogen-specific antibodies in samples derived from venipuncture, an expensive and logistically challenging aspect of serological surveillance. During the COVID-19 pandemic, guidelines implemented to prevent the spread of SARS-CoV-2 infection made collection of venous blood logistically difficult at a time when SARS-CoV-2 serosurveillance was urgently needed. Dried blood spots (DBS) have generated interest as an alternative to venous blood for SARS-CoV-2 serological applications due to their stability, low cost, and ease of collection; DBS samples can be self-generated via fingerprick by community members and mailed at ambient temperatures. Here, we detail the development of four DBS-based SARS-CoV-2 serological methods and demonstrate their implementation in a large serological survey of community members from 12 cities in the East Bay region of the San Francisco metropolitan area using at-home DBS collection. We find that DBS perform similarly to plasma/serum in enzyme-linked immunosorbent assays and commercial SARS-CoV-2 serological assays. In addition, we show that DBS samples can reliably detect antibody responses months post-infection and track antibody kinetics after vaccination. Implementation of DBS enabled collection of valuable serological data from our study population to investigate changes in seroprevalence over an eight-month period. Our work makes a strong argument for the implementation of DBS in serological studies, not just for SARS-CoV-2, but any situation where phlebotomy is inaccessible.

15.
Preprint in English | medRxiv | ID: ppmedrxiv-21266704

ABSTRACT

In immunocompetent subjects, the effectiveness of SARS-CoV-2 vaccines against the delta variant appears three-to five-fold lower than that observed against the alpha variant. Additionally, three doses of SARS-CoV-2 mRNA-based vaccines might be unable to elicit a sufficient immune response against any variant in immunocompromised kidney transplant recipients. This study describes the kinetics of the neutralizing antibody (NAbs) response against the delta strain before and after a fourth dose of a mRNA vaccine in 67 kidney transplant recipients who had experienced a weak antibody response after three doses. While only 16% of patients harbored NAbs against the delta strain prior to the fourth injection - this percentage raised to 66% afterwards. We also found that, after the fourth dose, the NAbs titer increased significantly (p=0.0001) from <7.5 (IQR : <7.5 -15.1) to 47.1 (IQR <7.5-284.2). Collectively, our data indicate that a fourth dose of the mRNA-1273 vaccine in kidney transplant recipients with a weak antibody response after three previous doses improves serum neutralization against the delta variant.

16.
Preprint in English | medRxiv | ID: ppmedrxiv-21266650

ABSTRACT

Shortly after the COVID-19 pandemic reached Aotearoa New Zealand, a stringent lockdown lasting seven weeks was introduced to manage community spread of the virus. This paper reports the findings of a qualitative study examining how lockdown policies impacted upon the lives of those caring for community-based patients. The study involved nationwide surveys and ethnographic interviews with 15 registered nurses (RN) employed in community settings, two community midwives, and five personal care assistants (PCAs). During the strict lockdown levels 4 and 3, RNs and PCAs in the community showed considerable courage in answering their 'call to duty' by taking on heightened care responsibilities and going 'the extra mile' to help others. They faced significant risks to personal and professional relationships when they were required to take on additional and complex responsibilities for community-based patients. Despite, and sometimes due to the hypervigilant monitoring of their personal protective equipment (PPE), the need to safeguard family and community members generated considerable stress and anxiety. Many also faced personal isolation and loneliness as a result of lockdown restrictions. Although 'care' and 'kindness' became social expectations throughout Aotearoa New Zealand during the lockdown, RNs and PCAs who were already doing care work in patient homes had to do more. This article makes five core service delivery and policy recommendations for supporting community-based nurses and PCAs in respiratory disease pandemics: acknowledging the crucial role played by community-based carers and the associated stress and anxiety endured, through championing respect and compassion; demystifying the 'heroism' or 'self-sacrifice' projected onto care workers to facilitate boundary setting; the timely provision of adequate protective equipment; improving remuneration with adequate provision for time off; and regular counselling, peer support groups, and education on work-life balance delivered by support workers in recognition of stressors arising from these complex and isolated working conditions.

17.
Preprint in English | medRxiv | ID: ppmedrxiv-21266251

ABSTRACT

The SARS-CoV-2 Variant of Concern (VOC) Delta was first detected in India in October 2020. The first imported cases of the Delta variant in Brazil were identified in April 2021 in the Southern region, followed by more cases in different country regions during the following months. By early September 2021, Delta was already the dominant variant in the Southeastern (87%), Southern (73%), and Northeastern (52%) Brazilian regions. This work aimed to understand the spatiotemporal dissemination dynamics of Delta in Brazil. To this end, we employed a combination of Maximum Likelihood (ML) and Bayesian methods to reconstruct the evolutionary relationship of 2,264 of VOC Delta complete genomes (482 from this study) recovered across 21 out of 27 Brazilian federal units. Our phylogeographic analyses identified three major transmission clusters of Delta in Brazil. The clade BR-I (n = 1,560) arose in Rio de Janeiro in late April 2021 and was the major cluster behind the dissemination of the VOC Delta in the Southeastern, Northeastern, Northern, and Central-Western regions. The clade BR-II (n = 207) arose in the Parana state in late April 2021 and aggregated the largest fraction of sampled genomes from the Southern region. Lastly, the clade BR-III emerged in the Sao Paulo state in early June 2021 and remained mostly restricted to this state. In the rapid turnover of viral variants characteristic of the SARS-CoV-2 pandemic, Brazilian regions seem to occupy different stages of an increasing prevalence of the VOC Delta in their epidemic profiles. This process demands continuous genomic and epidemiological surveillance toward identifying and mitigating new introductions, limiting their dissemination, and preventing the establishment of more significant outbreaks in a population already heavily affected by the COVID-19 pandemic.

18.
Preprint in English | medRxiv | ID: ppmedrxiv-21266918

ABSTRACT

Massive testing is a cornerstone in efforts to effectively track infections and stop COVID-19 transmission, including places where good vaccination coverage has been achieved. However, SARS-CoV-2 testing by RT-qPCR requires specialized personnel, protection equipment, commercial kits, and dedicated facilities, which represent significant challenges for massive testing implementation in resource-limited settings. It is therefore important to develop testing protocols that facilitate implementation and are inexpensive, fast, and sufficiently sensitive. In this work, we optimized the composition of a buffer (PKTP) containing a protease, a detergent, and an RNase inhibitor, that is compatible with the RT-qPCR chemistry, allowing for direct testing of SARS-CoV-2 from saliva in an RNA extraction-independent manner. This buffer is compatible with heat-inactivation reducing the biohazard risk of handling the samples. We assessed the PKTP buffer performance in comparison to the RNA-extraction-based protocol of the US Centers for Disease Control and Prevention in saliva samples from 70 COVID-19 patients finding a good sensitivity (82.2% for the N1 and 84.4% for the N2 target, respectively) and correlations (R=0.77, p<0.001 for N1, and R=0.78, p<0.001 for N2). We also propose an auto-collection protocol for saliva samples and a multiplex reaction to reduce the number of PCR reactions per patient and further reduce overall costs while maintaining diagnostic standards in favor of massive testing.

19.
Preprint in English | medRxiv | ID: ppmedrxiv-21266298

ABSTRACT

Outbreaks of COVID at university campuses can spread rapidly and threaten the broader community. We describe the management of an outbreak at a Malawian university in April 2021 during Malawi's second wave. Classes were suspended following detection of infections by routine testing and campus-wide PCR mass testing was conducted. Fifty seven cases were recorded, 55 among students, two among staff. Classes resumed 28 days after suspension following two weeks without cases. Just 6.3% of full-time staff and 87.4% of outsourced staff tested while 65% of students at the main campus and 74% at the extension campus were tested. Final year students had significantly higher positivity and lower testing coverage compared to freshmen. All viruses sequenced were beta variant and at least four separate virus introductions onto campus were observed. These findings are useful for development of campus outbreak responses and indicate the need to emphasize staff, males and senior students in testing.

20.
Preprint in English | medRxiv | ID: ppmedrxiv-21266916

ABSTRACT

Objectives: Multisystem inflammatory syndrome of children (MISC) carries a high attributable morbidity. We describe children aged <16 years hospitalised with COVID-19 and/or MISC, April 2020 to June 2021. Methods: All were tested for SARS-CoV-2, infectious disease consultations performed, modified CDC criteria for MISC applied, charts reviewed and data analyzed. Results: Among 79 consecutive children with SARS-CoV-2, 41(52%) were hospitalised; with median age 10.5 years; Afro-Caribbean ethnicity 40(98%); males 21(51%); SARS-CoV-2 RT-PCR positivity 26 (63%), IgG/IgM positivity 7(17%), community exposures 8 (20%). MISC-cases 18 (44%) vs. non-MISC 23(56%) had fever (94% vs. 30%; p<0.01), fatigue/lethargy (41% vs. 4%; p=0.004), rhinorrhoea (28% vs. 4%; p=0.035), elevated neutrophils (100% vs. 87%; p=0.024) and [≥]4 abnormal inflammatory biomarkers 13 (72%). MISC-cases had >2 organ/systems (100% vs. 35%; p<0.01), including gastrointestinal (72% vs. 17%; p<0.01), haematological/coagulopathic (67% vs. 4%; p<0.01); dermatologic (56% vs. 0%; p<0.01), cardiac (17% vs. 0%; p=0.042) with Kawasaki Syndrome (44% vs. 0%; p<0.01) and pleural effusions (17% vs. 0%; p=0.042). MISC-cases were treated with intravenous immune gammaglobulin (14, 78%), aspirin (12, 68%), steroids (9, 50%) and intensive care with non-invasive ventilation (2, 11%). One (6%) with pre-morbid illness died, the remainder recovered. Conclusion: MISC was treated successfully with intravenous gammaglobulin, steroids and/or aspirin in 94% before cardiopulmonary decompensation, or need for inotropes, vasopressors, or invasive ventilation.

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