COVID-19: A comparative study of severity of patients hospitalized during the first and the second wave in South Africa (preprint)

Background South Africa has experienced two waves of COVID-19 infections, the second of which was inter alia attributed to the emergence of a novel SARS-CoV2 variant, 501Y.V2. This variant possibly has increased virulence and may be associated with increased mortality. The objective of this study was to determine if patients admitted in the second wave had more severe illness and higher mortality than those admitted in the first. Methods We analysed and compared the characteristics, biological severity markers, treatments, level of care and outcomes of patients hospitalised in a private hospital in the Eastern Cape Province, South Africa. Results Compared to the first wave, patients admitted in the second were older and less likely to have co-morbidities. In contrast, the D-dimer and interleukin-6 (IL-6) levels were significantly higher. Despite this, significantly less patients were admitted to ICU and/or were mechanically ventilated. The total length of hospital stay was identical in both groups. Whereas the overall mortality was not significantly higher during the second wave, the ICU mortality was. Those that died in the second wave were older than those in the first wave. Multivariable logistic regression showed that being admitted during the second wave was an independent risk factor for mortality. Conclusion This study appears to confirm previous reports that the 501Y.V2 variant is possibly more virulent as indicated by the higher levels of D-dimer and IL-6, the slight increase in mortality of hospitalised patients and the higher ICU mortality in the second wave.

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa (preprint)

Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.

Evaluating temperature and humidity gradients of COVID-19 infection rates in light of Non-Pharmaceutical Interventions (preprint)

We evaluate potential temperature and humidity impact on the infection rate of COVID-19 with a data up to June 10th 2020, which comprises a large geographical footprint. It is critical to analyse data from different countries or regions at similar stages of the pandemic in order to avoid picking up false gradients. The degree of severity of NPIs is found to be a good gauge of the stage of the pandemic for individual countries. Data points are classified according to the stringency index of the NPIs in order to ensure that comparisons between countries are made on equal footing. We find that temperature and relative humidity gradients do not significantly deviate from the zero-gradient hypothesis. Upper limits on the absolute value of the gradients are set. The procedure chosen here yields 6{middle dot}10^-3{degrees}C^-1 and 3.3{middle dot}10^-3(%)^-1 upper limits on the absolute values of the temperature and relative humidity gradients, respectively, with a 95% Confidence Level. These findings do not preclude existence of seasonal effects and are indicative that these are likely to be nuanced.

Risk Adjusted Non-Pharmaceutical Interventions for the Management of COVID-19 in South Africa (preprint)

A global analysis of the impact of non-pharmaceutical interventions (NPIs) on the dynamics of the spread of the COVID-19 indicates that these can be classified using the stringency index proposed by the Oxford COVID-19 Government Response Tracker(OxCGRT) team. The world average for the coefficient that linearises the level of transmission with respect to the OxCGRT stringency index is s= 0.01{+/-}0.0017 (95%C.I.). The corresponding South African coefficient is s= 0.0078{+/-}0.00036 (95%C.I.), compatible with the world average. Here, we implement the stringency index for the recently announced 5-tier regulatory alert system. Predictions are made for the spread of the virus for each alert level. Assuming constant rates of recovery and mortality, it is essential to increase s. For the system to remain sub-critical, the rate with which s increases should outpace that of the decrease of the stringency index. Monitoring of s becomes essential to controlling the post-lockdown phase. Data from the Gauteng province obtained in May 2020 has been used to re-calibrate the model, where s was found increase by 20% with respect to the period before lockdown. Predictions for the province are made in this light.

Worldwide Effectiveness of Various Non-Pharmaceutical Intervention Control Strategies on the Global COVID-19 Pandemic: A Linearised Control Model (preprint)

Background COVID-19 is a virus which has lead to a global pandemic. Worldwide, more than 130 countries have imposed severe restrictions, which form part of a set of non-pharmaceutical interventions (NPI)s. We aimed to quantify the country-specific effects of these NPIs and compare them using the Oxford COVID-19 Government Response Tracker (OxCGRT) stringency index, p, as a measure of NPI stringency. Methods We developed a dual latent/observable Susceptible Infected Recovered Deaths (SIRD) model and applied it on each of 22 countries and 25 states in the US using publicly available data. The observable model parameters were extracted using kernel functions. The regression of the transmission rate, {beta}, as a function of p in each locale was modeled through the intervention leverage, s, an initial transmission rate, {beta}0 and a typical adjustment time, br-1. Results The world average for the intervention leverage, s=0.01 (95% CI 0.0102 - 0.0112) had an ensemble standard deviation of 0.0017 (95% C.I. 0.0014 - 0.0021), strongly indicating a universal behavior. Discussion Our study indicates that removing NPIs too swiftly will result in the resurgence of the spread within one to two months, in alignment with the current WHO recommendations. Moreover, we have quantified and are able to predict the effect of various combinations of NPIs. There is a minimum NPI level, below which leads to resurgence of the outbreak (in the absence of pharmaceutical and clinical advances). For the epidemic to remain sub-critical, the rate with which the intervention leverage s increases should outpace that of the relaxation of NPIs.