Journal Article > ResearchFull Text
J Infect Dis. 2024 December 16; 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. 2024 December 16; 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.
Journal Article > ResearchFull Text
Sci Afr. 2021 July 1; Volume 12; e00802.; DOI:10.1016/j.sciaf.2021.e00802
Fai KN, Corine TM, Bebell LM, Mbroingong AB, Nguimbis EBPT, et al.
Sci Afr. 2021 July 1; 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 Paris 2022. 2022 June 21
Journal Article > ResearchFull Text
Lancet Public Health. 2021 April 1; Volume 6 (Issue 4); DOI:10.1016/s2468-2667(21)00001-3
Roederer T, Mollo B, Vincent C, Nikolay B, Llosa AE, et al.
Lancet Public Health. 2021 April 1; Volume 6 (Issue 4); DOI:10.1016/s2468-2667(21)00001-3
Between June 23 and July 2, 2020, 426 (52%) of 818 individuals recruited tested positive in 14 sites. Seroprevalence varied significantly by type of recruitment site (χ2 p<0·0001), being highest among those living in workers' residences (88·7%, 95% CI 81·8-93·2), followed by emergency shelters (50·5%, 46·3-54·7), and food distribution sites (27·8%, 20·8-35·7). More than two thirds of COVID-19 seropositive individuals (68%, 95% CI 64·2-72·2; 291 of 426) did not report any symptoms during the recall period. COVID-19 seropositivity was strongly associated with overcrowding (medium density: adjusted odds ratio [aOR] 2·7, 95% CI 1·5-5·1, p=0·0020; high density: aOR 3·4, 1·7-6·9, p<0·0001).
Conference Material > Abstract
Nikolay B
Epicentre Scientific Day Paris 2023. 2023 June 8
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 > Abstract
Langendorf C, Nikolay B
Epicentre Scientific Day 2024. 2024 May 23
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 > Video
Nikolay B
Epicentre Scientific Day Paris 2020. 2020 September 24
Conference Material > Poster
Salou H, Nikolay B
Epicentre Scientific Day 2024. 2024 May 23
Français
Conference Material > Poster
Eyong J, Fai KN, Nikolay B, Gignoux EM, Nsaibirini R, et al.
Epicentre Scientific Day 2024. 2024 May 23
Français
Conference Material > Video
Nikolay B
Epicentre Scientific Day Paris 2023. 2023 June 8
English
Français