Journal Article > ResearchFull Text
J Infect Dis. 16 December 2024; Volume 230 (Issue 6); e1235-e1244.; DOI:10.1093/infdis/jiae221
Cortes-Azuero O, Lefrancq N, Nikolay B, McKee C, Cappelle J, et al.
J Infect Dis. 16 December 2024; Volume 230 (Issue 6); e1235-e1244.; DOI:10.1093/infdis/jiae221
BACKGROUND
Nipah virus (NiV), a highly lethal virus in humans, circulates in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining viral genomes from bats means we have a poor understanding of NiV diversity.
METHODS
We develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N = 257, 175 from bats, 73 from humans) from 6 countries over 22 years (1999–2020). We divide the 4 major NiV sublineages into 15 genetic clusters. Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate the presence and the average size of genetic clusters per area.
RESULTS
We find that, within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1500–2000 km2. We estimate that each genetic cluster occupies an average area of 1.3 million km2 (95% confidence interval [CI], .6–2.3 million km2), with 14 clusters in an area of 100 000 km2 (95% CI, 6–24 km2). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most clusters have been identified, but only approximately 15% of overall NiV diversity has been uncovered.
CONCLUSIONS
Our findings are consistent with entrenched co-circulation of distinct lineages, even within roosts, coupled with slow migration over larger spatial scales.
Conference Material > Abstract
Langendorf C, Nikolay B
Epicentre Scientific Day 2024. 23 May 2024
BACKGROUND
While case confirmation is most of the time not necessary for case management decisions– the measles outbreak response relies on the timely biological confirmation of outbreaks to facilitate a vaccination response. Seroprevalence estimates, on the other hand, can help plan vaccination activities or evaluate them, by quantifying immunization levels in the population. In remote areas where transport of serum or plasma samples is challenging, we ideally would like to use dried blood spots (DBS) which are easy to collect, easy to transport, and theoretically stable in time and temperature. However, the practical use of DBS under field conditions is not as easy as we expect. Based on different examples of measles surveys in the DRC and Niger, we will describe the challenges we are facing regarding interpretation of serology results from DBS for both measles
biological confirmation and seroprevalence surveys.
RESULTS AND DISCUSSION
In the DRC, for biological confirmation , the sensitivity of DBS samples compared to plasma decreases with transport delays and is lower in remote settings. Measles seroprevalence based on DBS was lower than expected, raising questions about the use of the recommended seropositivity threshold and the correlation with seroprotection after vaccination. In Niger, we found that a good quality DBS can be obtain under field conditions, and an adjustment factor for DBS compared to serum is needed but may vary between settings.
CONCLUSION
Serology on DBS is the most acceptable procedure so far for biological confirmation of measles cases and seroprevalence. However, additional investigations are needed to better standardize, test, and interpret DBS samples to help making the most appropriate operational decisions.
While case confirmation is most of the time not necessary for case management decisions– the measles outbreak response relies on the timely biological confirmation of outbreaks to facilitate a vaccination response. Seroprevalence estimates, on the other hand, can help plan vaccination activities or evaluate them, by quantifying immunization levels in the population. In remote areas where transport of serum or plasma samples is challenging, we ideally would like to use dried blood spots (DBS) which are easy to collect, easy to transport, and theoretically stable in time and temperature. However, the practical use of DBS under field conditions is not as easy as we expect. Based on different examples of measles surveys in the DRC and Niger, we will describe the challenges we are facing regarding interpretation of serology results from DBS for both measles
biological confirmation and seroprevalence surveys.
RESULTS AND DISCUSSION
In the DRC, for biological confirmation , the sensitivity of DBS samples compared to plasma decreases with transport delays and is lower in remote settings. Measles seroprevalence based on DBS was lower than expected, raising questions about the use of the recommended seropositivity threshold and the correlation with seroprotection after vaccination. In Niger, we found that a good quality DBS can be obtain under field conditions, and an adjustment factor for DBS compared to serum is needed but may vary between settings.
CONCLUSION
Serology on DBS is the most acceptable procedure so far for biological confirmation of measles cases and seroprevalence. However, additional investigations are needed to better standardize, test, and interpret DBS samples to help making the most appropriate operational decisions.
Conference Material > Poster
Salou H, Nikolay B
Epicentre Scientific Day 2024. 23 May 2024
Français
Conference Material > Poster
Eyong J, Fai KN, Nikolay B, Gignoux EM, Nsaibirini R, et al.
Epicentre Scientific Day 2024. 23 May 2024
Français
Journal Article > ResearchFull Text
Sci Afr. 4 October 2023; Online ahead of print; e01925.; DOI:10.1016/j.sciaf.2023.e01925
Eyong J, Fai KN, Nikolay B, Gignoux EM, Nsaibirini R, et al.
Sci Afr. 4 October 2023; Online ahead of print; e01925.; DOI:10.1016/j.sciaf.2023.e01925
BACKGROUND
Although the first year of the COVID-19 pandemic in Africa did not produce the expected catastrophe, the true impact of COVID-19 in the Cameroonian population was unclear. We therefore assessed the seroprevalence of anti-SARS-CoV-2 antibodies and retrospective mortality in a representative sample of the general population in the 10 administrative regions of Cameroon more than one year after the first confirmed cases of COVID-19 in these regions. We aimed to assess the extent of SARS-COV-2 infection and to detect potential increases in the crude mortality rate (CMR) during the SARS-COV-2 pandemic phase.
METHODS
We assessed retrospective mortality and seroprevalence of anti-SARS-CoV-2 antibodies in the 10 capital cities of Cameroon using representative samples of the general population. The study included nested anti-SARS-CoV-2 antibody prevalence surveys and retrospective mortality surveys and was conducted between 27 July 2021 and 31 August 2021. To further analyse crude mortality rates by age group and COVID wave, pre-pandemic and pandemic periods were stratified. Both laboratory-based assays (ELFA) and rapid diagnostic tests (RDT) were used to measure anti-SARS-CoV-2 seroprevalence.
RESULTS
The crude mortality rate (CMR) increased from 0.06 deaths per 10 000 persons per day (pre-pandemic) to 0.17 deaths per 10 000 persons per day (pandemic). The increase in CMR was more pronounced in people aged 20-35 years (pre-pandemic 0.02 deaths per 10 000 persons per day; pandemic 0.06 deaths per 10 000 persons per day). The estimated seroprevalence among unvaccinated persons was 9.5% (RDT) and 15.4% (laboratory-based).
CONCLUSION
The seroprevalence results showed that cases were significantly underdetected by the national surveillance systems.
Although the first year of the COVID-19 pandemic in Africa did not produce the expected catastrophe, the true impact of COVID-19 in the Cameroonian population was unclear. We therefore assessed the seroprevalence of anti-SARS-CoV-2 antibodies and retrospective mortality in a representative sample of the general population in the 10 administrative regions of Cameroon more than one year after the first confirmed cases of COVID-19 in these regions. We aimed to assess the extent of SARS-COV-2 infection and to detect potential increases in the crude mortality rate (CMR) during the SARS-COV-2 pandemic phase.
METHODS
We assessed retrospective mortality and seroprevalence of anti-SARS-CoV-2 antibodies in the 10 capital cities of Cameroon using representative samples of the general population. The study included nested anti-SARS-CoV-2 antibody prevalence surveys and retrospective mortality surveys and was conducted between 27 July 2021 and 31 August 2021. To further analyse crude mortality rates by age group and COVID wave, pre-pandemic and pandemic periods were stratified. Both laboratory-based assays (ELFA) and rapid diagnostic tests (RDT) were used to measure anti-SARS-CoV-2 seroprevalence.
RESULTS
The crude mortality rate (CMR) increased from 0.06 deaths per 10 000 persons per day (pre-pandemic) to 0.17 deaths per 10 000 persons per day (pandemic). The increase in CMR was more pronounced in people aged 20-35 years (pre-pandemic 0.02 deaths per 10 000 persons per day; pandemic 0.06 deaths per 10 000 persons per day). The estimated seroprevalence among unvaccinated persons was 9.5% (RDT) and 15.4% (laboratory-based).
CONCLUSION
The seroprevalence results showed that cases were significantly underdetected by the national surveillance systems.
Conference Material > Abstract
Nikolay B
Epicentre Scientific Day 2023. 8 June 2023
BACKGROUND AND AIMS
To respond to measles epidemics more efficiently, MSF implemented a risk-targeted measles outbreak response project in the Katanga region in the Democratic Republic of the Congo. Here we capitalize on two of the epidemiological activities that took place before and during a large-scale epidemic in 2021/22: (i) the identification of high-risk health zones (HZ) for preventive activities and enhanced surveillance, and (ii) the prioritization of alerts for interventions.
METHODS
To evaluate the selection of high-risk HZ in 2021/22, as well as potential alternative selection approaches, we compared outbreak sizes by risk category based on national surveillance data and evaluated preventive vaccination activities in 9 selected high-risk HZ. We further evaluated the alert scoring algorithm by comparing outbreak sizes by alert score and assessed final operational decisions guided by the score.
RESULTS
Although, the initial selection of high-risk HZ in 2021 allowed the identification of HZ with large epidemics, choosing all HZ with coverage below 40% seems to be the most efficient approach. While a third (3/9) of HZ with preventive vaccination experienced a large epidemic, the proportion was 90% (9/10) among high-risk HZ without preventive/early vaccination. Regarding the evaluation of the alert scoring algorithm, the median size of epidemics and the risk of large epidemics increased with an increasing alert score. Median epidemic durations were shorter in HZ with MSF interventions than in HZ with non-MSF vaccination campaigns or HZ without any vaccination campaigns.
CONCLUSION
Selecting HZ with low vaccination coverage may be a simple efficient alternative to the current model-based strategy to identify high-risk HZ. The targeted implementing of preventive vaccination probably averted large epidemics in 6 of the 9 vaccinated HZ. The alert scoring algorithm allowed efficient operational decision making during the epidemic in 2021/22 resulting in shorter epidemics in HZ with MSF interventions.
KEY MESSAGE
A risk-targeted approach including preventive vaccination, enhanced surveillance, and reactive interventions allowed to limit the occurrence and scale of measles epidemics in several health zones in the Katanga region in 2021/22.
This abstract is not to be quoted for publication.
To respond to measles epidemics more efficiently, MSF implemented a risk-targeted measles outbreak response project in the Katanga region in the Democratic Republic of the Congo. Here we capitalize on two of the epidemiological activities that took place before and during a large-scale epidemic in 2021/22: (i) the identification of high-risk health zones (HZ) for preventive activities and enhanced surveillance, and (ii) the prioritization of alerts for interventions.
METHODS
To evaluate the selection of high-risk HZ in 2021/22, as well as potential alternative selection approaches, we compared outbreak sizes by risk category based on national surveillance data and evaluated preventive vaccination activities in 9 selected high-risk HZ. We further evaluated the alert scoring algorithm by comparing outbreak sizes by alert score and assessed final operational decisions guided by the score.
RESULTS
Although, the initial selection of high-risk HZ in 2021 allowed the identification of HZ with large epidemics, choosing all HZ with coverage below 40% seems to be the most efficient approach. While a third (3/9) of HZ with preventive vaccination experienced a large epidemic, the proportion was 90% (9/10) among high-risk HZ without preventive/early vaccination. Regarding the evaluation of the alert scoring algorithm, the median size of epidemics and the risk of large epidemics increased with an increasing alert score. Median epidemic durations were shorter in HZ with MSF interventions than in HZ with non-MSF vaccination campaigns or HZ without any vaccination campaigns.
CONCLUSION
Selecting HZ with low vaccination coverage may be a simple efficient alternative to the current model-based strategy to identify high-risk HZ. The targeted implementing of preventive vaccination probably averted large epidemics in 6 of the 9 vaccinated HZ. The alert scoring algorithm allowed efficient operational decision making during the epidemic in 2021/22 resulting in shorter epidemics in HZ with MSF interventions.
KEY MESSAGE
A risk-targeted approach including preventive vaccination, enhanced surveillance, and reactive interventions allowed to limit the occurrence and scale of measles epidemics in several health zones in the Katanga region in 2021/22.
This abstract is not to be quoted for publication.
Conference Material > Video
Nikolay B
Epicentre Scientific Day 2023. 8 June 2023
English
Français
Journal Article > ResearchFull Text
PLOS Glob Public Health. 8 June 2023; Volume 3 (Issue 6); e0001457.; DOI:10.1371/journal.pgph.0001457
Simons E, Nikolay B, Ouedraogo P, Pasquier E, Tiemeni C, et al.
PLOS Glob Public Health. 8 June 2023; Volume 3 (Issue 6); e0001457.; DOI:10.1371/journal.pgph.0001457
Although seroprevalence studies have demonstrated the wide circulation of SARS-COV-2 in African countries, the impact on population health in these settings is still poorly understood. Using representative samples of the general population, we evaluated retrospective mortality and seroprevalence of anti-SARS-CoV-2 antibodies in Lubumbashi and Abidjan. The studies included retrospective mortality surveys and nested anti-SARS-CoV-2 antibody prevalence surveys. In Lubumbashi the study took place during April-May 2021 and in Abidjan the survey was implemented in two phases: July-August 2021 and October-November 2021. Crude mortality rates were stratified between pre-pandemic and pandemic periods and further investigated by age group and COVID waves. Anti-SARS-CoV-2 seroprevalence was quantified by rapid diagnostic testing (RDT) and laboratory-based testing (ELISA in Lubumbashi and ECLIA in Abidjan). In Lubumbashi, the crude mortality rate (CMR) increased from 0.08 deaths per 10 000 persons per day (pre-pandemic) to 0.20 deaths per 10 000 persons per day (pandemic period). Increases were particularly pronounced among <5 years old. In Abidjan, no overall increase was observed during the pandemic period (pre-pandemic: 0.05 deaths per 10 000 persons per day; pandemic: 0.07 deaths per 10 000 persons per day). However, an increase was observed during the third wave (0.11 deaths per 10 000 persons per day). The estimated seroprevalence in Lubumbashi was 15.7% (RDT) and 43.2% (laboratory-based). In Abidjan, the estimated seroprevalence was 17.4% (RDT) and 72.9% (laboratory-based) during the first phase of the survey and 38.8% (RDT) and 82.2% (laboratory-based) during the second phase of the survey. Although circulation of SARS-CoV-2 seems to have been extensive in both settings, the public health impact varied. The increases, particularly among the youngest age group, suggest indirect impacts of COVID and the pandemic on population health. The seroprevalence results confirmed substantial underdetection of cases through the national surveillance systems.
Journal Article > ResearchFull Text
Sci Afr. 1 July 2021; Volume 12; e00802.; DOI:10.1016/j.sciaf.2021.e00802
Fai KN, Corine TM, Bebell LM, Mbroingong AB, Nguimbis EBPT, et al.
Sci Afr. 1 July 2021; Volume 12; e00802.; DOI:10.1016/j.sciaf.2021.e00802
Official case counts suggest Africa has not seen the expected burden of COVID-19 as predicted by international health agencies, and the proportion of asymptomatic patients, disease severity, and mortality burden differ significantly in Africa from what has been observed elsewhere. Testing for SARS-CoV-2 was extremely limited early in the pandemic and likely led to under-reporting of cases leaving important gaps in our understanding of transmission and disease characteristics in the African context. SARS-CoV-2 antibody prevalence and serologic response data could help quantify the burden of COVID-19 disease in Africa to address this knowledge gap and guide future outbreak response, adapted to the local context. However, such data are widely lacking in Africa. We conducted a cross-sectional seroprevalence survey among 1,192 individuals seeking COVID-19 screening and testing in central Cameroon using the Innovita antibody-based rapid diagnostic. Overall immunoglobulin prevalence was 32%, IgM prevalence was 20%, and IgG prevalence was 24%. IgM positivity gradually increased, peaking around symptom day 20. IgG positivity was similar, gradually increasing over the first 10 days of symptoms, then increasing rapidly to 30 days and beyond. These findings highlight the importance of diagnostic testing and asymptomatic SARS-CoV-2 transmission in Cameroon, which likely resulted in artificially low case counts. Rapid antibody tests are a useful diagnostic modality for seroprevalence surveys and infection diagnosis starting 5-7 days after symptom onset. These results represent the first step towards better understanding the SARS-CoV-2 immunological response in African populations.
Conference Material > Video
Eisenhauer C, Nikolay B
Epicentre Scientific Day 2022. 21 June 2022