Epidemiological comparison of the first and second waves of the COVID-19 pandemic in Nigeria, February 2020-April 2021

Machine learning-driven development of a disease risk score for COVID-19 hospitalization and mortality: a Swedish and Norwegian register-based study

Aims

To develop a disease risk score for COVID-19-related hospitalization and mortality in Sweden and externally validate it in Norway.

Method

We employed linked data from the national health registries of Sweden and Norway to conduct our study. We focused on individuals in Sweden with confirmed SARS-CoV-2 infection through RT-PCR testing up to August 2022 as our study cohort. Within this group, we identified hospitalized cases as those who were admitted to the hospital within 14 days of testing positive for SARS-CoV-2 and matched them with five controls from the same cohort who were not hospitalized due to SARS-CoV-2. Additionally, we identified individuals who died within 30 days after being hospitalized for COVID-19. To develop our disease risk scores, we considered various factors, including demographics, infectious, somatic, and mental health conditions, recorded diagnoses, and pharmacological treatments. We also conducted age-specific analyses and assessed model performance through 5-fold cross-validation. Finally, we performed external validation using data from the Norwegian population with COVID-19 up to December 2021.

Results

During the study period, a total of 124,560 individuals in Sweden were hospitalized, and 15,877 individuals died within 30 days following COVID-19 hospitalization. Disease risk scores for both hospitalization and mortality demonstrated predictive capabilities with ROC-AUC values of 0.70 and 0.72, respectively, across the entire study period. Notably, these scores exhibited a positive correlation with the likelihood of hospitalization or death. In the external validation using data from the Norwegian COVID-19 population (consisting of 53,744 individuals), the disease risk score predicted hospitalization with an AUC of 0.47 and death with an AUC of 0.74.

Conclusion

The disease risk score showed moderately good performance to predict COVID-19-related mortality but performed poorly in predicting hospitalization when externally validated.

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

West Africa faced the COVID-19 pandemic in early March 2020 and, as of March 31, 2022, had more than 900,000 confirmed cases and more than 12,000 deaths. During this period, SARS-CoV-2 genomes evolved genetically, resulting in the emergence of distinct lineages. This review was conducted to provide the epidemiological profile of COVID-19, the mutational profile of SARS-CoV-2, and the dynamics of its lineages in the 16 west African countries by analyzing data from 33 studies and seven situation reports. For a more complete representation of the epidemiology and genetic diversity of SARS-CoV-2, we used reliable public data in addition to eligible studies. As of March 31, 2022, the 16 west African countries experienced four epidemic waves with variable intensities. Higher mortality was noted during the third wave with a case fatality rate (CFR) of 1.9%. After these four epidemic waves, Liberia recorded the highest CFR (4.0%), whereas Benin had the lowest CFR (0.6%). Through mutational analysis, a high genetic heterogeneity of the genomes was observed, with a predominance of mutations in the spike protein. From this high mutational rate, different lineages emerged. Our analysis of the evolutionary diversity allowed us to count 205 lineages circulating in west Africa. This study has provided a good representation of the mutational profile and the prevalence of SARS CoV-2 lineages beyond the knowledge of the global epidemiology of the 16 African countries.

Association between wealth, insurance coverage, urban residence, median age and COVID-19 deaths across states in Nigeria

This study measures associations between COVID-19 deaths and sociodemographic factors (wealth, insurance coverage, urban residence, age, state population) for states in Nigeria across two waves of the COVID-19 pandemic: February 27th 2020 to October 24th 2020 and October 25th 2020 to July 25th 2021. Data sources include 2018 Nigeria Demographic and Health Survey and Nigeria Centre for Disease Control (NCDC) COVID-19 daily reports. It uses negative binomial models to model deaths, and stratifies results by respondent gender. It finds that overall mortality rates were concentrated within three states: Lagos, Edo and Federal Capital Territory (FCT) Abuja. Urban residence and insurance coverage are positively associated with differences in deaths for the full sample. The former, however, is significant only during the early stages of the pandemic. Associative differences in gender-stratified models suggest that wealth was a stronger protective factor for men and insurance a stronger protective factor for women. Associative strength between sociodemographic measures and deaths varies by gender and pandemic wave, suggesting that the pandemic impacted men and women in unique ways, and that the effectiveness of interventions should be evaluated for specific waves or periods.

Care seeking for under-five children and vaccine perceptions during the first two waves of the COVID-19 pandemic in Lagos State, Nigeria: a qualitative exploratory study

OBJECTIVE

To explore healthcare seeking practices for children and the context-specific direct and indirect effects of public health interventions during the first two waves of COVID-19 in Lagos State, Nigeria. We also explored decision-making around vaccine acceptance at the start of COVID-19 vaccine roll-out in Nigeria.

DESIGN, SETTING AND PARTICIPANTS

A qualitative explorative study involving 19 semistructured interviews with healthcare providers from public and private primary health facilities and 32 interviews with caregivers of under-five children in Lagos from December 2020 to March 2021. Participants were purposively selected from healthcare facilities to include community health workers, nurses and doctors, and interviews were conducted in quiet locations at facilities. A data-driven reflexive thematic analysis according to Braun and Clark was conducted.

FINDINGS

Two themes were developed: appropriating COVID-19 in belief systems, and ambiguity about COVID-19 preventive measures. The interpretation of COVID-19 ranged from fearful to considering it as a 'scam' or 'falsification from the government'. Underlying distrust in government fuelled COVID-19 misperceptions. Care seeking for children under five was affected, as facilities were seen as contagious places for COVID-19. Caregivers resorted to alternative care and self-management of childhood illnesses. COVID-19 vaccine hesitancy was a major concern among healthcare providers compared with community members at the time of vaccine roll-out in Lagos, Nigeria. Indirect impacts of COVID-19 lockdown included diminished household income, worsening food insecurity, mental health challenges for caregivers and reduced clinic visits for immunisation.

CONCLUSION

The first wave of the COVID-19 pandemic in Lagos was associated with reductions in care seeking for children, clinic attendance for childhood immunisations and household income. Strengthening health and social support systems with context-specific interventions and correcting misinformation is crucial to building adaptive capacity for response to future pandemics.

TRIAL REGISTRATION NUMBER

ACTRN12621001071819.

Clinical and Virological Features of SARS-CoV-2 Variants during the Four Waves of the Pandemic in the Mexican Southeast

We conducted a retrospective study using a population of patients who were hospitalized at Dr. Juan Graham Casasus Hospital in Villahermosa (Tabasco, Mexico) and had a positive RT-PCR test for SARS-CoV-2 between June 2020 and January 2022. We analyzed all medical records, including demographic data, SARS-CoV-2 exposure history, underlying comorbidities, symptoms, signs at admission, laboratory findings during the hospital stay, outcome, and whole-genome sequencing data. Finally, the data were analyzed in different sub-groups according to distribution during waves of the COVID-19 pandemic regarding Mexican reports from June 2020 to January 2022. Of the 200 patients who tested positive via PCR for SARS-CoV-2, only 197 had samples that could be sequenced. Of the samples, 58.9% (n = 116) were males and 41.1% (n = 81) females, with a median age of 61.7 ± 17.0 years. Comparisons between the waves of the pandemic revealed there were significant differences in the fourth wave: the age of patients was higher (p = 0.002); comorbidities such as obesity were lower (p = 0.000), while CKD was higher (p = 0.011); and hospital stays were shorter (p = 0.003). The SARS-CoV-2 sequences revealed the presence of 11 clades in the study population. Overall, we found that adult patients admitted to a third-level Mexican hospital had a wide range of clinical presentations. The current study provides evidence for the simultaneous circulation of SARS-CoV-2 variants during the four pandemic waves.

Clinical Characteristics and Outcomes of Patients with Acute Respiratory Failure Due to SARS-CoV-2 Interstitial Pneumonia Treated with CPAP in a Medical Intermediate Care Setting: A Retrospective Observational Study on Comparison of Four Waves

BACKGROUND

In COVID-19 patients non-invasive-positive-pressure-ventilation (NIPPV) has held a challenging role to reduce mortality and the need for invasive mechanical ventilation (IMV). The aim of this study was to compare the characteristics of patients admitted to a Medical Intermediate Care Unit for acute respiratory failure due to SARS-CoV-2 pneumonia throughout four pandemic waves.

METHODS

The clinical data of 300 COVID-19 patients treated with continuous positive airway pressure (CPAP) were retrospectively analysed, from March-2020 to April-2022.

RESULTS

Non-survivors were older and more comorbid, whereas patients transferred to ICU were younger and had fewer pathologies. Patients were older (from 65 (29-91) years in I wave to 77 (32-94) in IV, p < 0.001) and with more comorbidities (from Charlson's Comorbidity Index = 3 (0-12) in I to 6 (1-12) in IV, p < 0.001). No statistical difference was found for in-hospital mortality (33.0%, 35.8%, 29.6% and 45.9% in I, II, III and IV, p = 0.216), although ICU-transfers rate decreased from 22.0% to 1.4%.

CONCLUSIONS

COVID-19 patients have become progressively older and with more comorbidities even in critical care area; from risk class analyses by age and comorbidity burden, in-hospital mortality rates remain high and are thus consistent over four waves while ICU-transfers have significantly reduced. Epidemiological changes need to be considered to improve the appropriateness of care.

Determinants of mortality among hospitalized patients with COVID-19 during first and second waves of the pandemic: A retrospective cohort study from an isolation center in Kano, Nigeria

BACKGROUND

Coronavirus disease 2019 (COVID-19) has emerged as an important cause of morbidity and mortality worldwide. The aim of this study is to identify the clinical predictors of mortality among patients with COVID-19 pneumonia during first and second waves in a treatment center in northwestern Nigeria.

METHODS

This was a retrospective cohort study of 195 patients hospitalized with COVID-19 between April 2020 to March 2021 at a designated COVID-19 isolation center in Kano State, Northwest Nigeria. Data were summarized using frequencies and percentages. Unadjusted odds ratios and 95% confidence intervals and p-values were obtained. To determine independent determinants of mortality, we performed a stepwise multivariate logistic regression model.

RESULTS

Of 195 patients studied, 21(10.77%) patients died. Males comprised 158 (81.03%) of the study population. In the adjusted stepwise logistic regression analysis, age>64 years (OR = 9.476, 95% CI: 2.181-41.165), second wave of the pandemic (OR = 49.340, 95% CI:6.222-391.247), cardiac complications (OR = 24.984, 95% CI: 3.618-172.508), hypertension (OR = 5.831, 95% CI:1.413-24.065) and lowest systolic blood pressure while on admission greater than or equal to 90mmHg were independent predictors of mortality (OR = 0.111, 95%CI: 0.021-0.581).

CONCLUSION

Strategies targeted to prioritize needed care to patients with identified factors that predict mortality might improve patient outcome.

SARS-CoV-2 variants-associated outbreaks of COVID-19 in a tertiary institution, North-Central Nigeria: Implications for epidemic control

The COVID-19 global pandemic is being driven by evolving SARS-CoV-2 variants with consequential implications on virus transmissibility, host immunity, and disease severity. Continuous molecular and genomic surveillance of the SARS-CoV-2 variants is therefore necessary for public health interventions toward the management of the pandemic. This study is a retrospective analysis of COVID-19 cases reported in a Nigerian tertiary institution from July to December 2021. In total, 705 suspected COVID-19 cases that comprised 547 students and 158 non-students were investigated by real time PCR (RT-PCR); of which 372 (~52.8%) tested positive for COVID-19. Using a set of selection criteria, 74 (~19.9%) COVID-19 positive samples were selected for next generation sequencing. Data showed that there were two outbreaks of COVID-19 within the university community over the study period, during which more females (56.8%) tested positive than males (47.8%) (p<0.05). Clinical data together with phylogenetic analysis suggested community transmission of SARS-CoV-2 through mostly asymptomatic and/or pre-symptomatic individuals. Confirmed COVID-19 cases were mostly mild, however, SARS-CoV-2 delta (77%) and omicron (4.1%) variants were implicated as major drivers of respective waves of infections during the study period. This study highlights the importance of integrated surveillance of communicable disease during outbreaks.

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health.

Evolving trend change during the COVID-19 pandemic

Coronavirus disease (COVID-19) has caused unimaginable damage to public health and socio-economic structures worldwide; thus, an epidemiological depiction of the global evolving trends of this disease is necessary. As of March 31, 2022, the number of cases increased gradually over the four waves of the COVID-19 pandemic, indicating the need for continuous countermeasures. The highest total cases per million and total deaths per million were observed in Europe (240,656.542) and South America (2,912.229), despite these developed countries having higher vaccination rates than other continents, such as Africa. In contrast, the lowest of the above two indices were found in undeveloped African countries, which had the lowest number of vaccinations. These data indicate that the COVID-19 pandemic is positively related to the socio-economic development level; meanwhile, the data suggest that the vaccine currently used in these continents cannot completely prevent the spread of COVID-19. Thus, rethinking the feasibility of a single vaccine to control the disease is needed. Although the number of cases in the fourth wave increased exponentially compared to those of the first wave, ~43.1% of deaths were observed during the first wave. This was not only closely linked to multiple factors, including the inadequate preparation for the initial response to the COVID-19 pandemic, the gradual reduction in the severity of additional variants, and the protection conferred by prior infection and/or vaccination, but this also indicated the change in the main driving dynamic in the fourth wave. Moreover, at least 12 variants were observed globally, showing a clear spatiotemporal profile, which provides the best explanation for the presence of the four waves of the pandemic. Furthermore, there was a clear shift in the trend from multiple variants driving the spread of disease in the early stage of the pandemic to a single Omicron lineage predominating in the fourth wave. These data suggest that the Omicron variant has an advantage in transmissibility over other contemporary co-circulating variants, demonstrating that monitoring new variants is key to reducing further spread. We recommend that public health measures, along with vaccination and testing, are continually implemented to stop the COVID-19 pandemic.

Epidemiological Comparison of Four COVID-19 Waves in the Democratic Republic of the Congo, March 2020-January 2022

PURPOSE

Nationwide analyses are required to optimise and tailor activities to control future COVID-19 waves of resurgence continent-wide. We compared epidemiological and clinical outcomes of the four COVID-19 waves in the Democratic Republic of Congo (DRC).

METHODS

This retrospective descriptive epidemiological analysis included data from the national line list of confirmed COVID-19 cases in all provinces for all waves between 9 March 2020 and 2 January 2022. Descriptive statistical measures (frequencies, percentages, case fatality rates [CFR], test positivity rates [TPR], and characteristics) were compared using chi-squared or the Fisher-Irwin test.

RESULTS

During the study period, 72,108/445,084 (16.2%) tests were positive, with 9,641/56,637 (17.0%), 16,643/66,560 (25.0%), 24,172/157,945 (15.3%), and 21,652/163,942 (13.2%) cases during the first, second, third, and fourth waves, respectively. TPR significantly decreased from 17.0% in the first wave to 13.2% in the fourth wave as did infection of frontline health workers (5.2% vs. 0.9%). CFR decreased from 5.1 to 0.9% from the first to fourth wave. No sex- or age-related differences in distributions across different waves were observed. The majority of cases were asymptomatic in the first (73.1%) and second (86.6%) waves, in contrast to that in the third (11.1%) and fourth (31.3%) waves.

CONCLUSION

Despite fewer reported cases, the primary waves (first and second) of the COVID-19 pandemic in the DRC were more severe than the third and fourth waves, with each wave being associated with a new SARS-CoV-2 variant. Tailored public health and social measures, and resurgence monitoring are needed to control future waves of COVID-19.

Epidemiological Trends of Coronavirus Disease 2019 in Sierra Leone From March 2020 to October 2021

Coronavirus disease 2019 (COVID-19), a serious public health challenge the world over, has led to significant health concerns in Sierra Leone. In the present study, epidemic indices, such as the number of cases, positivity rate, reproduction rate (R0), case fatality rate (CFR), age, and sex, were used to characterize the epidemiological trends of COVID-19. As of October 31, 2021, a total of 6,398 cases and 121 related deaths had been confirmed. The total number of COVID-19 reverse transcription polymerase chain reaction (RT-PCR) tests conducted to October 31, 2021, was 249,534, and the average positivity rate was 2.56%. Three waves of COVID-19 were recorded, occurring during weeks 15–46 in 2020 (2,369 cases), week 47 in 2020 to week 16 in 2021 (1,665 cases), and weeks 17–43 in 2021 (2,364 cases), respectively. Remarkably, there was no increase in the numbers of confirmed COVID-19 cases despite rising test numbers throughout the three waves. Moreover, three high R0 values were observed before each wave. The number of positive cases significantly correlated with positive numbers of international arrivals (P < 0.01), deaths (P < 0.01), and the positivity rate of tested samples (P < 0.01). Moreover, all of the deaths occurred during the peak of the three waves. Our results indicate that there was a low level of COVID-19 epidemic in Sierra Leone and that COVID-19's introduction led to local transmission. It is vital to fight against the spread of SARS-CoV-2 from the source of origin by strengthening testing and management of people entering the country. Our findings will provide important clues for expanding sample screening and will contribute to the reasonable allocation of medical resources.

A comparative analysis of experienced uncertainties in relation to risk communication during COVID19: a four-country study

Background

During outbreaks, uncertainties experienced by affected communities can influence their compliance to government guidance on public health. Communicators and authorities are, hence, encouraged to acknowledge and address such uncertainties. However, in the midst of public health crises, it can become difficult to define and identify uncertainties that are most relevant to address. We analyzed data on COVID-19-related uncertainties from four socio-economic contexts to explore how uncertainties can influence people’s perception of, and response to Risk Communication and Community Engagement (RCCE) strategies.

Results

This qualitative study, which adopts an interpretative approach, is based on data from a documentary review, key informant interviews (KII), and focus group discussions (FGD) with members of the general public and people with barriers to information from Germany, Guinea, Nigeria, and Singapore. Transcripts from the KII and FGD were coded and analyzed thematically. We interviewed a total of 155 KIs and conducted 73 FGD. Our analysis uncovered a divergence between uncertainties deemed relevant by stakeholders involved in policy making and uncertainties that people reportedly had to navigate in their everyday lives and which they considered relevant during the pandemic. We identified four types of uncertainties that seemed to have influenced people’s assessment of the disease risk and their trust in the pandemic control strategies including RCCE efforts: epidemiological uncertainties (related to the nature and severity of the virus), information uncertainties (related to access to reliable information), social uncertainties (related to social behavior in times of heightened risk), and economic uncertainties (related to financial insecurities).

Conclusion

We suggest that in future outbreaks, communicators and policy makers could improve the way in which affected communities assess their risk, and increase the trust of these communities in response efforts by addressing non-epidemiological uncertainties in RCCE strategies.

Public risk perception and behaviours towards COVID-19 during the first and second waves in Nigeria: a secondary data analysis

OBJECTIVES

To describe changes in public risk perception and risky behaviours during the first wave (W1) and second wave (W2) of COVID-19 in Nigeria, associated factors and observed trend of the outbreak.

DESIGN

A secondary data analysis of cross-sectional telephone-based surveys conducted during the W1 and W2 of COVID-19 in Nigeria.

SETTING

Nigeria.

PARTICIPANTS

Data from participants randomly selected from all states in Nigeria.

PRIMARY OUTCOME

Risk perception for COVID-19 infection categorised as risk perceived and risk not perceived.

SECONDARY OUTCOME

Compliance to public health and social measures (PHSMs) categorised as compliant; non-compliant and indifferent.

ANALYSIS

Comparison of frequencies during both waves using χ² statistic to test for associations. Univariate and multivariate logistic regression analyses helped estimate the unadjusted and adjusted odds of risk perception of oneself contracting COVID-19. Level of statistical significance was set at p<0.05.

RESULTS

Triangulated datasets had a total of 6401 respondents, majority (49.5%) aged 25-35 years. Overall, 55.4% and 56.1% perceived themselves to be at risk of COVID-19 infection during the W1 and W2, respectively. A higher proportion of males than females perceived themselves to be at risk during the W1 (60.3% vs 50.3%, p<0.001) and the W2 (58.3% vs 52.6%, p<0.05). Residing in the south-west was associated with not perceiving oneself at risk of COVID-19 infection (W1-AOdds Ratio (AOR) 0.28; 95% CI 0.20 to 0.40; W2-AOR 0.71; 95% CI 0.52 to 0.97). There was significant increase in non-compliance to PHSMs in the W2 compared with W1. Non-compliance rate was higher among individuals who perceived themselves not to be at risk of getting infected (p<0.001).

CONCLUSION

Risk communication and community engagement geared towards increasing risk perception of COVID-19 should be implemented, particularly among the identified population groups. This could increase adherence to PHSMs and potentially reduce the burden of COVID-19 in Nigeria.

The mechanism of governments' and individuals' influence on protective behaviours during the second wave of COVID-19: a multiple mediation model

Background: The SARS-CoV-2 virus continues to spread and resurge globally with signs of a second wave, despite actions by governments to curb the COVID-19 pandemic. However, evidence-based strategies to combat COVID-19 recurrence are poorly documented. Objective: To reveal how governments and individuals should act to effectively cope with future waves, this study proposed a preventive model of COVID-19 resurgence. Method: A questionnaire survey was conducted among 1,137 residents of Beijing, where the epidemic reoccurred. Structural equation model was used to explore the mechanism among government intervention, perceived efficacy, positive emotions, posttraumatic growth (PTG) and protective behaviours. Results: Data analysis revealed that during COVID-19 resurgence, government intervention could directly and indirectly influence protective behaviours through individual factors (i.e. perceived efficacy, positive emotions), and PTG could mediate the indirect pathway to protective behaviours. Conclusions: These findings implied that government intervention needs to be integrated with individual factors to effectively control repeated COVID-19 outbreaks.