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

Simulundu, Edgar; Mupeta, Francis; Chanda‐Kapata, Pascalina; Saasa, Ngonda; Changula, Katendi; Muleya, Walter; Chitanga, Simbarashe; Mwanza, Miniva; Simusika, Paul; Chambaro, Herman M.; Mubemba, Benjamin; Kajihara, Masahiro; Chanda, Duncan; Mulenga, Lloyd; Fwoloshi, Sombo; Shibemba, Aaron; Kapaya, Fred; Zulu, Paul Msanzya; Musonda, Kunda; Monze, Mwaka; Sinyange, Nyambe; Mazaba, Mazyanga L.; Kapina, Muzala; Chipimo, Peter J.; Hamoonga, Raymond; Simwaba, Davie; Ngosa, William; Morales, Albertina N.; Kayeyi, Nkomba; Tembo, John; Bates, Matthew; Orba, Yasuko; Sawa, Hirofumi; Takada, Ayato; Nalubamba, King S.; Malama, Kennedy; Mukonka, Victor; Zumla, Alimuddin; Kapata, Nathan

doi:10.1016/j.ijid.2020.09.1480

Cited by 33 publications

(32 citation statements)

References 24 publications

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“…All SARS-CoV-2 genomes carried the spike mutation D614 G which is associated with efficient replication ex vivo and transmission in vivo ( Hou et al, 2020 ). The B.1 and B.1.1 lineage, as observed in this study, is also widespread in other African regions ( Simulundu et al, 2021 ). Phylogenetic analysis revealed two distinct clusters, suggesting two separate introductions of the virus into the country, although the origin of the introduction remains unclear.…”

Section: Discussionsupporting

confidence: 81%

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

Ntoumi

Mapanguy

Tomazatos

et al. 2021

International Journal of Infectious Diseases

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Section: Discussionsupporting

confidence: 81%

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

Ntoumi

Mapanguy

Tomazatos

et al. 2021

International Journal of Infectious Diseases

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“…The World Health Organization currently estimates that there have been ~150 million COVID-19 cases and ~3 million COVID-19-related deaths globally [ 3 ]. The first cases of COVID-19 in Zambia were detected in March 2020 [ 4 ]. The COVID-19 surveillance and testing efforts in Zambia remain ongoing [ 5 ].…”

mentioning

confidence: 99%

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

Mudenda

Mumba

Pieciak

et al. 2021

Clinical Infectious Diseases

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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.

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“…On February 14, 2020, Egypt announced the rst cases of COVID-19 on the African continent [4]. Zambia recorded its rst two con rmed COVID-19 cases on 18th March 2020 [5]. The government moved quickly and enacted regulation aimed at limiting the spread of the virus within communities [6,7].…”

Section: Introductionmentioning

confidence: 99%

Simulation of the Third Wave of COVID 19 Infections in Zambia using the SIR Model

Mwale

Kanjere

Kanchele³

et al. 2022

Preprint

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Background Various mathematical modeling approaches are used to provide a robust framework for understanding the transmission dynamics of infectious diseases in human populations. In an epidemic, models can be used for the analysis of the spread of a disease, forecasting, identifying trends and making parameter estimates which can be used for planning and implementing intervention measures. Methods This study utilizes the classical Susceptible - Infected - Recovered (SIR) model to analyze the evolution of COVID-19 in Zambia during the third wave of infections. The model is fitted to actual COVID-19 data for Zambia for the third wave of the pandemic obtained from the Zambia National Public Health Institute (ZNPHI). The transmission and recovery rates are estimated by minimizing the error between the fitted curve and the real data using the least square approach. Results Model simulations indicate that the basic reproductive number (\({R}_{0}\)) for Zambia is 1.31 meaning that, on average, 1.31 persons are infected for each infected person. At the worst point of the epidemic, we expect that 591,743 people will contract the virus and 7,144 fatalities will be recorded. To prevent the spread of infection, the model estimates that at least 24 percent of the population will need to be vaccinated. With the country's projected population of about 18.91 million, this translates to roughly 4.5 million people. Conclusion The severity of COVID-19 infection, hospitalizations, and deaths in Zambia is substantially higher than national testing data suggests, according to model projections. More modeling work is needed to acquire accurate estimates of the disease burden in society, to inform resource allocation, and to aid mitigation planning, especially in countries that may lack adequate national surveillance systems.

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

Cited by 33 publications

References 24 publications

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

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

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

Simulation of the Third Wave of COVID 19 Infections in Zambia using the SIR Model

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