First COVID-19 case in Zambia - Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries

Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study

Mutations have driven the evolution and development of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity and vaccine escape among others. Genome sequencing is a technique that allows scientists to read the genetic code of an organism and has become a powerful tool for studying emerging infectious diseases. Here, we conducted a cross-sectional study in selected districts of the Eastern Province of Zambia, from November 2021 to February 2022. We analyzed SARS-CoV-2 samples (n = 76) using high-throughput sequencing. A total of 4097 mutations were identified in 69 SARS-CoV-2 genomes with 47% (1925/4097) of the mutations occurring in the spike protein. We identified 83 unique amino acid mutations in the spike protein of the seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 and XT). Of these, 43.4% (36/83) were present in the receptor binding domain, while 14.5% (12/83) were in the receptor binding motif. While we identified a potential recombinant XT strain, the highly transmissible BA.2 sublineage was more predominant (40.8%). We observed the substitution of other variants with the Omicron strain in the Eastern Province. This work shows the importance of pandemic preparedness and the need to monitor disease in the general population.

Student's perspectives, satisfaction and experiences with online and classroom learning during the COVID-19 pandemic: Findings and implications on blended learning

Objectives

The coronavirus disease 2019 (COVID-19) pandemic disrupted classroom-based learning, necessitating the adoption of online learning in most universities. However, there has been a lack of information on university students' perspectives regarding online learning during the COVID-19 pandemic. This study assessed the perspectives, satisfaction and experiences with online and classroom learning among human health students at the University of Zambia.

Methods

This cross-sectional study was conducted among 737 students at the University of Zambia from October 2022 to April 2023. Data were analysed using Stata version 16.1.

Results

Of the 737 participants, 51.6% were female and 56.5% agreed that blended learning should continue even after the COVID-19 pandemic. However, 78.4% of the students believed that group discussions were more suitable in the classroom than online learning. Most students (67.1%) disagreed that they preferred online learning to classroom learning. Furthermore, 77.6% of the students disagreed that online learning gave more satisfaction than classroom learning.

Conclusions

This study found that most students recommended the continuation of blended learning after the pandemic. However, they believed that follow-up tutorials and assessments were better undertaken in physical classrooms than online learning. These findings are important in sensitising stakeholders in the education sector and governments to consider blended learning as a teaching strategy in the future. There is a need to develop and implement curricula that offer blended learning to students as well as ensure the students have the necessary facilities and equipment to support such learning.

COVID-19 vaccine uptake and associated factors among adolescents and youths: Findings and implications for future vaccination programmes

Adolescents and youths are a key part of the population that needs to be protected against the coronavirus disease 2019 (COVID-19). This is because they are more likely to spread the virus to vulnerable individuals. In view of these concerns, this study investigated the uptake of COVID-19 vaccines and associated factors among adolescents and youths attending secondary schools in Zambia. This cross-sectional study was conducted among 1500 school-going adolescents in Lusaka from September 2022 to November 2022. Overall, 1409 participants took part giving a response rate of 94%. Only 29.2% (n = 411) of the participants were vaccinated against COVID-19 at the time of the study. Compared to their unvaccinated counterparts, vaccinated adolescents and youths scored higher for knowledge (66.2% vs 57.8%) and attitudes (76.7% vs 39.4%) regarding COVID-19 vaccines. Healthcare workers, family/friends and social media were key sources of information regarding the vaccine. Factors associated with increased vaccine uptake were positive attitudes (AOR = 33.62, 95% CI: 19.92-56.73), indicating it was stressful to follow COVID-19 preventive measures (AOR = 1.47, 95% CI: 1.09-1.99), participants in Grade 12 (AOR = 3.39, 95% CI: 1.94-5.91), Grade 11 (AOR = 2.59, 95% CI: 1.94-5.91), Grade 10 (AOR = 3.48, 95% CI: 1.98-6.11) and Grade 9 (AOR = 3.04, 95% CI: 1.74-5.32) compared to Grade 8. This study found a relatively low uptake of COVID-19 vaccines among adolescents and youths in Zambia. There is a need to provide adequate strategies to address knowledge and attitude gaps regarding COVID-19 vaccines to improve uptake and reduce future morbidity and mortality.

Characteristics of cases and deaths arising from SARS-CoV-2 infection in Zambia: March 2020 to April 2021

Introduction

since March 2020, Zambia has been experiencing a SARS-CoV-2 epidemic. Little data has been reported on cases and deaths arising from COVID-19 in Africa. We described the demographic characteristics of these cases and deaths in Zambia.

Methods

we analyzed data on all persons testing positive for SARS-CoV-2 from 18th March 2020 to 25th April 2021 in Zambia. COVID-19 cases were identified through port-of-entry surveillance, contact-tracing, health-care-worker testing, health-facility-based and community-based screening and community-death screening. All diagnoses were confirmed using real-time-polymerase-chain-reaction and rapid-antigen-test-kits of nasopharyngeal specimens. We analyzed age, sex, and date-of-reporting according to whether the cases or deaths occurred during the first wave (1st July to 15th September 2020) or the second wave (15th December 2020 to 10th April 2021). We computed Mann-Whitney-U-test to compare medians of continuous variables and chi-square tests to compare differences between proportions using R.

Results

a total 1,246 (1.36%) deaths were recorded among 91,378 confirmed cases during March 2020-April 2021 in Zambia. Persons who died were older than those who did not (median age 50 years versus 32.0 years, p< 0.001). Although only 4.7% of cases were among persons aged >60 years, most deaths (31.6%) occurred in this age group (p<0.001). More deaths (83.5%) occurred in the community than in health facilities (p<0.001).

Conclusion

during the SARS-CoV-2 epidemic in Zambia, most deaths occurred in the community, indicating potential gaps in public health messaging about COVID-19. Improving health-seeking behaviors for COVID-19 through public messaging campaigns and engaging key community stakeholders in Zambia might reduce avoidable mortality. As the group most impacted by COVID-19 mortality, older persons might need enhanced outreach and linkage to care.

Using mortuary and burial data to place COVID-19 in Lusaka, Zambia within a global context

Reported COVID-19 cases and associated mortality remain low in many sub-Saharan countries relative to global averages, but true impact is difficult to estimate given limitations around surveillance and mortality registration. In Lusaka, Zambia, burial registration and SARS-CoV-2 prevalence data during 2020 allow estimation of excess mortality and transmission. Relative to pre-pandemic patterns, we estimate age-dependent mortality increases, totalling 3212 excess deaths (95% CrI: 2104-4591), representing an 18.5% (95% CrI: 13.0-25.2%) increase relative to pre-pandemic levels. Using a dynamical model-based inferential framework, we find that these mortality patterns and SARS-CoV-2 prevalence data are in agreement with established COVID-19 severity estimates. Our results support hypotheses that COVID-19 impact in Lusaka during 2020 was consistent with COVID-19 epidemics elsewhere, without requiring exceptional explanations for low reported figures. For more equitable decision-making during future pandemics, barriers to ascertaining attributable mortality in low-income settings must be addressed and factored into discourse around reported impact differences.

Poor adherence to antiretroviral therapy among adult people living with HIV initiated during the COVID-19 epidemic waves – observations at the University Teaching Hospital in Lusaka, Zambia

Background

Coronavirus disease 2019 (COVID-19)-related disruptions in healthcare services and clinical outcomes have been predicted and documented. However, little is known about how antiretroviral therapy (ART) adherence disruptions caused by the COVID-19 pandemic have manifested amidst the ‘Undetectable = Untransmittable' campaign initiative. Using a patient's viral load as a proxy for medication adherence, our study aimed to determine the adherence to ART on first-line medications among adult people living with human immunodeficiency virus (PLWHIV) at the University Teaching Hospital in Lusaka, Zambia during the pandemic.

Methods

This was a hospital-based cross-sectional study. Secondary data of PLWHIV registered to receive ART from the Adult Infectious Disease Centre was extracted from the SmartCare® electronic health record system to constitute a resultant data set that this study used. The data extraction form was used to extract values of dependent (ART adherence measured by viral load detectability) and independent variables and imported them into the statistical analysis tool, STATA version 16.1 MP. Descriptive statistics of individual characteristics, testing for associations using Pearson's chi-square test, and stratified and combined multivariable logistic regression were performed.

Results

Of the 7,281 adult PLWHIV included in this study, 9.0% (95% CI 8.3–9.6%) were virally detectable. Estimates of the odds ratios of detectable viral load remained significantly higher among adult PLWHIV who were initiated on ART after the U=U campaign was launched in Zambia and were on a monthly 2.51 (1.31–9.03) or 6-monthly 4.75 (3.52–6.41) dispensing of a dolutegravir-based regimen and those on 6-monthly dispensing of an efavirenz-based regimen 4.67 (2.16–10.08) compared to their counterparts. Overall estimates showed us the same picture 4.14 (3.22–5.31), having adjusted for all other predictor variables.

Conclusion

We found that a high proportion of people with detectable viral load in the study population, irrespective of medication refill interval and type of regimen, was concentrated among adult PLWHIV who started treatment during the COVID-19 epidemic waves, as compared to those who started treatment before the pandemic. This observed disparity suggests the inherent impact of the pandemic on the adherence to ART among adult PLWHIV in Lusaka, Zambia. This further illustrates how exposed program responses are to external shocks, especially in already weakened health systems, and the need to create program response buffers and resilient program-specific strategies to minimize the effect of external disruptions.

Different clinical features in Malawian outpatients presenting with COVID-19 prior to and during Omicron variant dominance: A prospective observational study

The SARS-CoV-2 Omicron variant has resulted in a high number of cases, but a relatively low incidence of severe disease and deaths, compared to the pre-Omicron variants. Therefore, we assessed the differences in symptom prevalence between Omicron and pre-Omicron infections in a sub-Saharan African population. We collected data from outpatients presenting at two primary healthcare facilities in Blantyre, Malawi, from November 2020 to March 2022. Eligible participants were aged >1month old, with signs suggestive of COVID-19, and those not suspected of COVID-19, from whom we collected nasopharyngeal swabs for SARS-CoV-2 PCR testing, and sequenced positive samples to identify infecting-variants. In addition, we calculated the risk of presenting with a given symptom in individuals testing SARS-CoV-2 PCR positive before and during the Omicron variant-dominated period. Among 5176 participants, 6.4% were under 5, and 77% were aged 18 to 50 years. SARS-CoV-2 infection prevalence peaked in January 2021 (Beta), July 2021 (Delta), and December 2021 (Omicron). We found that cough (risk ratio (RR), 1.50; 95% confidence interval (CI), 1.00 to 2.30), fatigue (RR 2.27; 95% CI, 1.29 to 3.86) and headache (RR 1.64; 95% CI, 1.15 to 2.34) were associated with a high risk of SARS-CoV-2 infection during the pre-Omicron period. In comparison, only headache (RR 1.41; 95% CI, 1.07 to 1.86) did associate with a high risk of SARS-CoV-2 infection during the Omicron-dominated period. In conclusion, clinical symptoms associated with Omicron infection differed from prior variants and were harder to identify clinically with current symptom guidelines. Our findings encourage regular review of case definitions and testing policies to ensure case ascertainment.

Factors influencing COVID-19 health protective behaviours in Zambian university students with symptoms of low mood

BACKGROUND

Health protective behaviours are crucial in the prevention of the spread of COVID-19, particularly in university students who typically live and study in large groups. Depression and anxiety are common in students and can impact young people's motivations to follow health advice. The study aims to assess the relationship between mental health and COVID-19 health-protective behaviours in Zambian university students with symptoms of low mood.

METHODS

The study was a cross-sectional, online survey of Zambian university students. Participants were also invited to take part in a semi-structured interview to explore views about COVID-19 vaccination. Invitation emails were sent explaining the study aims and directed students who self-identified as having low mood in the past two weeks to an online survey. Measures included COVID-19 preventive behaviours, COVID-19-related self-efficacy, and Hospital and Anxiety Depression scale.

RESULTS

A total of 620 students (n=308 female, n=306 male) participated in the study, with a mean participant age of 22.47±3.29 years (range 18-51). Students reported a mean protective behaviour score of 74.09/105 and 74% scored above the threshold for possible anxiety disorder. Three-way ANOVA showed lower COVID-19 protective behaviours in students with possible anxiety disorder (p=.024) and those with low self-efficacy (p<0.001). Only 168 (27%) said they would accept vaccination against COVID-19, with male students being twice as likely to be willing to accept COVID-19 vaccination (p<0.001). Of 50 students interviewed. 30 (60%) expressed fears about the vaccination and 16 (32%) were concerned about a lack of information. Only 8 (16%) participants expressed doubts about effectiveness.

CONCLUSION

Students who self-identify as having symptoms of depression have high levels of anxiety. The results suggest that interventions to reduce anxiety and promote self-efficacy might enhance students' COVID-19 protective behaviours. Qualitative data provided insight into the high rates of vaccine hesitancy in this population.

A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study

BACKGROUND

Compared to the abundance of clinical and genomic information available on patients hospitalised with COVID-19 disease from high-income countries, there is a paucity of data from low-income countries. Our aim was to explore the relationship between viral lineage and patient outcome.

METHODS

We enrolled a prospective observational cohort of adult patients hospitalised with PCR-confirmed COVID-19 disease between July 2020 and March 2022 from Blantyre, Malawi, covering four waves of SARS-CoV-2 infections. Clinical and diagnostic data were collected using an adapted ISARIC clinical characterization protocol for COVID-19. SARS-CoV-2 isolates were sequenced using the MinION™ in Blantyre.

RESULTS

We enrolled 314 patients, good quality sequencing data was available for 55 patients. The sequencing data showed that 8 of 11 participants recruited in wave one had B.1 infections, 6/6 in wave two had Beta, 25/26 in wave three had Delta and 11/12 in wave four had Omicron. Patients infected during the Delta and Omicron waves reported fewer underlying chronic conditions and a shorter time to presentation. Significantly fewer patients required oxygen (22.7% [17/75] vs. 58.6% [140/239], p < 0.001) and steroids (38.7% [29/75] vs. 70.3% [167/239], p < 0.001) in the Omicron wave compared with the other waves. Multivariable logistic-regression demonstrated a trend toward increased mortality in the Delta wave (OR 4.99 [95% CI 1.0-25.0 p = 0.05) compared to the first wave of infection.

CONCLUSIONS

Our data show that each wave of patients hospitalised with SARS-CoV-2 was infected with a distinct viral variant. The clinical data suggests that patients with severe COVID-19 disease were more likely to die during the Delta wave.

Uptake of public health measures and vaccine acceptance during the COVID-19 pandemic in rural Zambia

Vaccines are effective tools to prevent COVID-19-related morbidity. However, coverage is low throughout sub-Saharan Africa. Uptake of public health measures, perceptions of COVID-19 illness and vaccines, and intention to vaccinate were evaluated in 2021-2022 in rural Zambia. Adherence to public health measures, perceptions of COVID-19 risk and severity, and vaccine acceptance increased significantly over time, particularly in December 2021, coinciding with the fourth pandemic wave and relaunch of the national vaccine campaign. Vaccine acceptance was associated with perceptions of vaccine safety and effectiveness, but not disease severity. These findings highlight the importance of strong pandemic response and public communication for increased uptake of mitigatory measures, including vaccine acceptance.

Knowledge, Attitudes, and Acceptance of COVID-19 Vaccines among Secondary School Pupils in Zambia: Implications for Future Educational and Sensitisation Programmes

The coronavirus disease 2019 (COVID-19) pandemic resulted in the closure of schools to slow the spread of the virus across populations, and the administration of vaccines to protect people from severe disease, including school children and adolescents. In Zambia, there is currently little information on the acceptance of COVID-19 vaccines among school-going children and adolescents despite their inclusion in the vaccination programme. This study assessed the knowledge, attitudes, and acceptance of COVID-19 vaccines among secondary school pupils in Lusaka, Zambia. A cross-sectional study was conducted from August 2022 to October 2022. Of the 998 participants, 646 (64.7%) were female, and 127 (12.7%) would accept to be vaccinated. Those who were willing to be vaccinated had better knowledge (68.5% vs. 56.3%) and a positive attitude (79.1% vs. 33.7%) compared to those who were hesitant. Overall, the odds of vaccine acceptance were higher among pupils who had higher knowledge scores (AOR = 11.75, 95% CI: 6.51-21.2), positive attitude scores (AOR = 9.85, 95% CI: 4.35-22.2), and those who knew a friend or relative who had died from COVID-19 (AOR = 3.27, 95% CI: 2.14-5.09). The low vaccine acceptance among pupils is of public health concern, emphasising the need for heightened sensitisation programmes that promote vaccine acceptance among pupils in Zambia.

What is the prevalence of COVID-19 detection by PCR among deceased individuals in Lusaka, Zambia? A postmortem surveillance study

OBJECTIVES

To determine the prevalence of COVID-19 postmortem setting in Lusaka, Zambia.

DESIGN

A systematic, postmortem prevalence study.

SETTING

A busy, inner-city morgue in Lusaka.

PARTICIPANTS

We sampled a random subset of all decedents who transited the University Teaching Hospital morgue. We sampled the posterior nasopharynx of decedents using quantitative PCR. Prevalence was weighted to account for age-specific enrolment strategies.

INTERVENTIONS

Not applicable-this was an observational study.

PRIMARY OUTCOMES

Prevalence of COVID-19 detections by PCR. Results were stratified by setting (facility vs community deaths), age, demographics and geography and time.

SECONDARY OUTCOMES

Shifts in viral variants; causal inferences based on cycle threshold values and other features; antemortem testing rates.

RESULTS

From 1118 decedents enrolled between January and June 2021, COVID-19 was detected among 32.0% (358/1116). Roughly four COVID-19+ community deaths occurred for every facility death. Antemortem testing occurred for 52.6% (302/574) of facility deaths but only 1.8% (10/544) of community deaths and overall, only ~10% of COVID-19+ deaths were identified in life. During peak transmission periods, COVID-19 was detected in ~90% of all deaths. We observed three waves of transmission that peaked in July 2020, January 2021 and ~June 2021: the AE.1 lineage and the Beta and Delta variants, respectively. PCR signals were strongest among those whose deaths were deemed 'probably due to COVID-19', and weakest among children, with an age-dependent increase in PCR signal intensity.

CONCLUSIONS

COVID-19 was common among deceased individuals in Lusaka. Antemortem testing was rarely done, and almost never for community deaths. Suspicion that COVID-19 was the cause of deaths was highest for those with a respiratory syndrome and lowest for individuals <19 years.

HIV care experiences and health priorities during the first wave of COVID-19: clients' perspectives - a qualitative study in Lusaka, Zambia

BACKGROUND

The novel COVID-19 pandemic threatened to disrupt access to human immunodeficiency (HIV) treatment for persons living with HIV (PLHIV), two-thirds of whom live in sub-Saharan Africa. To inform a health system response supportive of continuity of care, we sought to understand clients' HIV care experiences and health priorities during the first wave of COVID-19 outbreak in Lusaka, Zambia.

METHODS

Leveraging a study cohort of those who completed periodic SMS surveys on HIV care, we purposefully sampled 25 PLHIV after first confirmed COVID-19 case was reported in Zambia on 18^th March 2020. We phone-interviewed participants, iteratively refining interview guide to capture emergent themes on COVID-19 awareness, health facility interactions, and social circumstances, which we analyzed using matrix analysis.

RESULTS

All participants were aware of COVID-19, and HIV care experiences and health priorities of clients were affected by associated changes at health system, household, and individual level. The health system instituted early clinic visits to provide 6-months of antiretroviral therapy (ART) for stable patients and 3-months for unstable patients to reduce clinic visits and wait times. Most patients welcomed this long-desired extended appointment spacing. Some reported feeling respected and engaged when health care workers telephoned requesting their early clinic visit. However, others felt discouraged by an absence of physical distancing during their clinic visit due to 'severe acute respiratory syndrome coronavirus 2' (SARS-CoV-2) infection concerns. Several expressed a lack of clarity regarding next viral load monitoring date and means for receiving results. Patients suggested regular patient-facility communication by telephone and SMS. Patients emphasized that COVID-19 restrictions led to loss of employment and household income, exacerbating poverty and difficulties in taking ART. At individual level, most participants felt motivated to stay healthy during COVID-19 by ART adherence and regular laboratory monitoring.

CONCLUSIONS

Clients' HIV care and health priorities during the first wave of COVID-19 in Lusaka province were varied with a combination of positive and negative experiences that occurred especially at health system and individual levels, while at household level, the experiences were all negative. More research is needed to understand how patients practice resiliency in the widespread context of socio-economic instability. Governments and patients must work together to find local, health systems solutions to support ART adherence and monitoring. Additionally, the health system should consider how to build on changes for long-term HIV management and service delivery.

Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares international borders with Botswana, Namibia, and Zimbabwe and is a major tourist destination. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116), and multiple Omicron subvariants with the BA.1 subvariant being predominant. Whereas Beta, Delta, and Omicron variants were associated with the second, third, and fourth pandemic waves, respectively, the Alpha variant was not associated with any wave in the country. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Zambia from different European and African countries. Across the 40 genomes analysed, a total of 292 mutations were observed, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. This study stresses the need for the continued monitoring of SARS-CoV-2 circulation in Zambia, particularly in strategically positioned regions such as the Southern Province which could be at increased risk of introduction of novel VOCs.

A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study

Background

Compared to the abundance of clinical and genomic information available on patients hospitalised with COVID-19 disease from high-income countries, there is a paucity of data from low-income countries. Our aim was to explore the relationship between viral lineage and patient outcome.

Methods

We enrolled a prospective observational cohort of adult patients hospitalised with PCR-confirmed COVID-19 disease between July 2020 and March 2022 from Blantyre, Malawi, covering four waves of SARS-CoV-2 infections. Clinical and diagnostic data were collected using an adapted ISARIC clinical characterization protocol for COVID-19. SARS-CoV-2 isolates were sequenced using the MinIONâ"¢ in Blantyre.

Results

We enrolled 314 patients, good quality sequencing data was available for 55 patients. The sequencing data showed that 8 of 11 participants recruited in wave one had B.1 infections, 6/6 in wave two had Beta, 25/26 in wave three had Delta and 11/12 in wave four had Omicron. Patients infected during the Delta and Omicron waves reported fewer underlying chronic conditions and a shorter time to presentation. Significantly fewer patients required oxygen (22.7% [17/75] vs. 58.6% [140/239], p<0.001) and steroids (38.7% [29/75] vs. 70.3% [167/239], p<0.001) in the Omicron wave compared with the other waves. Multivariable logistic-regression demonstrated a trend toward increased mortality in the Delta wave (OR 4.99 [95% CI 1.0-25.0 p=0.05) compared to the first wave of infection.

Conclusions

Our data show that each wave of patients hospitalised with SARS-CoV-2 was infected with a distinct viral variant. The clinical data suggests that patients with severe COVID-19 disease were more likely to die during the Delta wave.

Summary

We used genome sequencing to identify the variants of SARS-CoV-2 causing disease in Malawi, and found that each of the four waves was caused by a distinct variant. Clinical investigation suggested that the Delta wave had the highest mortality.

COVID-19 Diagnosis: A Comprehensive Review of the RT-qPCR Method for Detection of SARS-CoV-2

The world is grappling with the coronavirus disease 2019 (COVID-19) pandemic, the causative agent of which is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 symptoms are similar to the common cold, including fever, sore throat, cough, muscle and chest pain, brain fog, dyspnoea, anosmia, ageusia, and headache. The manifestation of the disease can vary from being asymptomatic to severe life-threatening conditions warranting hospitalization and ventilation support. Furthermore, the emergence of mutecated variants of concern (VOCs) is paramount to the devastating effect of the pandemic. This highly contagious virus and its emergent variants challenge the available advanced viral diagnostic methods for high-accuracy testing with faster result yields. This review is to shed light on the natural history, pathology, molecular biology, and efficient diagnostic methods of COVID-19, detecting SARS-CoV-2 in collected samples. We reviewed the gold standard RT-qPCR method for COVID-19 diagnosis to confer a better understanding and application to combat the COVID-19 pandemic. This comprehensive review may further develop awareness about the management of the COVID-19 pandemic.

Histopathological Evaluation of Deceased Persons in Lusaka, Zambia With or Without Coronavirus Disease 2019 (COVID-19) Infection: Results Obtained From Minimally Invasive Tissue Sampling

Background

Although much has been learned about the pathophysiology of coronavirus disease 2019 (COVID-19) infections, pathology data from patients who have died of COVID-19 in low- and middle-income country settings remain sparse. We integrated minimally invasive tissue sampling (MITS) into an ongoing postmortem surveillance study of COVID-19 in deceased individuals of all ages in Lusaka, Zambia.

Methods

We enrolled deceased subjects from the University Teaching Hospital Morgue in Lusaka, Zambia within 48 hours of death. We collected clinical and demographic information, a nasopharyngeal swab, and core tissue biopsies from the lung, liver, and kidneys for pathologic analysis. Individuals were considered eligible for MITS if they had a respiratory syndrome prior to death or a COVID-19+ polymerase chain reaction (PCR) nasopharyngeal swab specimen. Samples were retested using quantitative reverse transcriptase PCR.

Results

From June to September 2020 we performed MITS on 29 deceased individuals. PCR results were available for 28/29 (96.5%) cases. Three had a COVID-19+ diagnosis antemortem, and 5 more were identified postmortem using the recommended cycle threshold cut-point <40. When expanding the PCR threshold to 40 ≤ cycle threshold (Ct) ≤ 45, we identified 1 additional case. Most cases were male and occurred in the community The median age at death was 47 years (range 40–64). Human immunodeficiency virus (HIV)/AIDS, tuberculosis, and diabetes were more common among the COVID-19+ cases. Diffuse alveolar damage and interstitial pneumonitis were common among COVID-19+ cases; nonspecific findings of hepatic steatosis and acute kidney injury were also prevalent in the COVID-19+ group. Vascular thrombi were rarely detected.

Conclusions

Lung abnormalities typical of viral pneumonias were common among deceased COVID-19+ individuals, as were nonspecific findings in the liver and kidneys. Pulmonary vascular thrombi were rarely detected, which could be a limitation of the MITS technique. Nonetheless, MITS offers a valuable alternative to open autopsy for understanding pathological changes due to COVID-19.

Genomic surveillance of SARS-CoV-2 in the Republic of Congo

Objective

The aim of this study was to carry out whole-genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using samples collected from Congolese individuals between April and July 2020.

Methods

Ninety-six samples were screened for SARS-CoV-2 using RT-PCR, and 19 samples with Ct values <30 were sequenced using Illumina Next-Generation Sequencing (NGS). The genomes were annotated and screened for mutations using the web tool ‘coronapp’. Subsequently, different SARS-CoV-2 lineages were assigned using PANGOLIN and Nextclade.

Results

Eleven SARS-CoV-2 genomes were successfully sequenced and submitted to the GSAID database. All genomes carried the spike mutation D614G and were classified as part of the GH clade. The Congolese SARS-CoV-2 sequences were shown to belong to lineage B1 and Nextclade 20A and 20C, which split them into distinct clusters, indicating two separate introductions of the virus into the Republic of Congo.

Conclusion

This first study provides valuable information on SARS CoV-2 transmission in the central African region, contributing to SARS CoV-2 surveillance on a temporal and spatial scale.