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Estimation of the impact of vaccination and non-pharmaceutical interventions (NPIs) on COVID-19 incidence is complicated by several factors, including the successive emergence of SARS-CoV-2 variants of concern and changing population immunity resulting from vaccination and previous infection. We developed an age-structured multi-strain COVID-19 transmission model framework that could estimate the impact of vaccination and NPIs while accounting for these factors. We applied this framework to French Polynesia, which unlike many countries experienced multiple large COVID-19 waves from multiple variants over the course of the pandemic, interspersed with periods of elimination. We estimated that the vaccination programme averted 54.3% (95% CI 54.0-54.6%) of the 6840 hospitalisations and 60.2% (95% CI 59.9-60.5%) of the 1280 hospital deaths that would have occurred in a baseline scenario without any vaccination up to May 2022. Vaccination also averted an estimated 28.4% (95% CI 28.2-28.7%) of 193,000 symptomatic cases in the baseline scenario. We estimated the booster campaign contributed 3.4%, 2.9% and 3.3% to overall reductions in cases, hospitalisations and hospital deaths respectively. Our results suggested that removing, or altering the timings of, the lockdowns during the first two waves had non-linear effects on overall incidence owing to the resulting effect on accumulation of population immunity. Our estimates of vaccination and booster impact differ from those for other countries due to differences in age structure, previous exposure levels and timing of variant introduction relative to vaccination, emphasising the importance of detailed analysis that accounts for these factors.

Estimation of the impact of vaccination and non-pharmaceutical interventions (NPIs) on COVID-19 incidence is complicated by several factors, including the successive emergence of SARS-CoV-2 variants of concern and changing population immunity resulting from vaccination and previous infection. We developed an age-structured multi-strain COVID-19 transmission model framework that could estimate the impact of vaccination and NPIs while accounting for these factors. We applied this approach to French Polynesia, which unlike many countries experienced multiple large COVID-19 waves from multiple variants over the course of the pandemic, interspersed with periods of elimination. We estimated that the vaccination programme averted 54.3% (95% CI 54.0-54.6%) of the 6840 hospitalisations and 60.2% (95% CI 59.9–60.5%) of the 1280 hospital deaths that would have occurred in a baseline scenario without any vaccination up to May 2022. Vaccination also averted an estimated 28.4% (95% CI 28.2-28.7%) of 193,000 symptomatic cases in the baseline scenario. We estimated the booster campaign contributed 3.4%, 2.9% and 3.3% to overall reductions in cases, hospitalisations and hospital deaths respectively. Our results suggested that removing, or altering the timings of, the lockdowns during the first two waves had non-linear effects on overall incidence owing to the resulting effect on accumulation of population immunity. Our estimates of vaccination and booster impact differ from those for other countries due to differences in age structure, previous exposure levels and timing of variant introduction relative to vaccination, emphasising the importance of detailed analysis that accounts for these factors.

Background Several successive arbovirus outbreaks have affected French Polynesia (FP) in the recent past years due to different dengue serotypes (DENV) present for several decades, Zika (ZIKV) (2013–2014) and chikungunya (CHIKV) (2014–2015) viruses with a potential impact on blood safety and blood supply due to the geographical isolation of these islands. This study reports an assessment of the impact of these outbreaks on blood products supply and infectious safety in FP and discuss the effectiveness of implemented preventive measures. Methods To ensure the infectious safety of blood products during outbreaks, several measures have successively been introduced as the selection of donors suspected of infection, the nucleic acid testing (NAT) and the pathogen reduction of platelets and plasmas. Results The donor deferral rate increased by 6% between 2012 and 2014 without changes in the number of collected donations. NAT excluded five blood donations reactive for DENV RNA, 42 for ZIKV and 34 for CHIKV. As Zika screening could not been implemented before the third month of the outbreak, 36 blood products from ZIKV-infected donors were transfused to 26 recipients. However, no transfusion-transmitted arbovirus has been reported. Conclusion The last past arboviruses outbreaks did not have a significant impact on blood supply in FP. The measures introduced to prevent arbovirus transmission by transfusion were able to maintain infectious safety for all blood products without impairing self-sufficiency.

International audience; Congenital Zika virus syndrome consists of a large spectrum of neurologic abnormalities seen in infants infected with Zika virus in utero. However, little is known about the effects of Zika virus intrauterine infection on the neurocognitive development of children born without birth defects. Using a case-control study design, we investigated the temporal association of a cluster of congenital defects with Zika virus infection. In a nested study, we also assessed the early childhood development of children recruited in the initial study as controls who were born without known birth defects,. We found evidence for an association of congenital defects with both maternal Zika virus seropositivity (time of infection unknown) and symptomatic Zika virus infection during pregnancy. Although the early childhood development assessment found no excess burden of developmental delay associated with maternal Zika virus infection, larger, longer-term studies are needed.

BACKGROUND AND OBJECTIVES French Polynesia, where dengue virus (DENV) has been present for a long time, experienced two successive outbreaks of Zika (ZIKV) and chikungunya viruses (CHIKV) between 2013 and 2015. To avoid the transmission of these viruses by transfusion, nucleic acid testing (NAT) has been in place for DENV since 2013 and for ZIKV and CHIKV during epidemics. The objective was to compare the estimated risk of viraemic blood donation with NAT results and to discuss the impact on the prevention of transfusion-related infectious risk. MATERIALS AND METHODS The average risks of viraemic blood donation were estimated per year for DENV, and during the epidemic periods for ZIKV and CHIKV, using the Biggerstaff and Petersen model based on the incidence rate, the mean length of viraemia and the frequency of asymptomatic infection. The estimated risks were compared with the number of viraemic blood donations detected by NAT. RESULTS According to the different assumptions, risks estimates ranged from 11·2 to 53·1/100 000 donations for DENV, 746 to 1924/100 000 for ZIKV and 1083 /100 000 for CHIKV. When compared to the number of donations collected during the study periods, these estimates match NAT results (5 blood donors reactive for DENV, 42 for ZIKV and 34 for CHIKV). CONCLUSION The risks of viraemic blood donation were related to the viral incidence in the general population and concordant with NAT results. These findings suggest that the screening may be optimized by a targeted NAT implementation based on incidence data.

Summary Background The emergence of Zika virus in the Americas has coincided with increased reports of babies born with microcephaly. On Feb 1, 2016, WHO declared the suspected link between Zika virus and microcephaly to be a Public Health Emergency of International Concern. This association, however, has not been precisely quantified. Methods We retrospectively analysed data from a Zika virus outbreak in French Polynesia, which was the largest documented outbreak before that in the Americas. We used serological and surveillance data to estimate the probability of infection with Zika virus for each week of the epidemic and searched medical records to identify all cases of microcephaly from September, 2013, to July, 2015. Simple models were used to assess periods of risk in pregnancy when Zika virus might increase the risk of microcephaly and estimate the associated risk. Findings The Zika virus outbreak began in October, 2013, and ended in April, 2014, and 66% (95% CI 62–70) of the general population were infected. Of the eight microcephaly cases identified during the 23-month study period, seven (88%) occurred in the 4-month period March 1 to July 10, 2014. The timing of these cases was best explained by a period of risk in the first trimester of pregnancy. In this model, the baseline prevalence of microcephaly was two cases (95% CI 0–8) per 10 000 neonates, and the risk of microcephaly associated with Zika virus infection was 95 cases (34–191) per 10 000 women infected in the first trimester. We could not rule out an increased risk of microcephaly from infection in other trimesters, but models that excluded the first trimester were not supported by the data. Interpretation Our findings provide a quantitative estimate of the risk of microcephaly in fetuses and neonates whose mothers are infected with Zika virus. Funding Labex-IBEID, NIH-MIDAS, AXA Research fund, EU-PREDEMICS.

French Polynesia and the French Territories of the Americas (FTAs) have experienced outbreaks of Zika virus (ZIKV) infection. These territories used similar sentinel syndromic surveillance to follow the epidemics. However, the surveillance system only takes into account consulting patients diagnosed with ZIKV disease, while non-consulting cases, as well as asymptomatic cases, are not taken into account. In the French territories under study, the ratio of consulting to non-consulting patients was found to likely be as low as 1/3 to 1/4, and rough estimates of the ZIKV asymptomatic infections indicated a lower rate than previously reported (i.e., not more than half). Keywords: Zika virus, Sentinel surveillance, Asymptomatic infections, Pacific islands, Caribbean region, Vector-borne infections

International audience; The Zika virus crisis exemplified the risk associated with emerging pathogens and was a reminder that preparedness for the worst-case scenario, although challenging, is needed. Herein, we review all data reported during the unexpected emergence of Zika virus in French Polynesia in late 2013. We focus on the new findings reported during this outbreak, especially the first description of severe neurological complications in adults and the retrospective description of CNS malformations in neonates, the isolation of Zika virus in semen, the potential for blood-transfusion transmission, mother-to-child transmission, and the development of new diagnostic assays. We describe the effect of this outbreak on health systems, the implementation of vector-borne control strategies, and the line of communication used to alert the international community of the new risk associated with Zika virus. This outbreak highlighted the need for careful monitoring of all unexpected events that occur during an emergence, to implement surveillance and research programmes in parallel to management of cases, and to be prepared to the worst-case scenario.

Between October, 2013, and April, 2014, French Polynesia experienced the largest Zika virus outbreak ever described at that time. During the same period, an increase in Guillain-Barré syndrome was reported, suggesting a possible association between Zika virus and Guillain-Barré syndrome. We aimed to assess the role of Zika virus and dengue virus infection in developing Guillain-Barré syndrome.In this case-control study, cases were patients with Guillain-Barré syndrome diagnosed at the Centre Hospitalier de Polynésie Française (Papeete, Tahiti, French Polynesia) during the outbreak period. Controls were age-matched, sex-matched, and residence-matched patients who presented at the hospital with a non-febrile illness (control group 1; n=98) and age-matched patients with acute Zika virus disease and no neurological symptoms (control group 2; n=70). Virological investigations included RT-PCR for Zika virus, and both microsphere immunofluorescent and seroneutralisation assays for Zika virus and dengue virus. Anti-glycolipid reactivity was studied in patients with Guillain-Barré syndrome using both ELISA and combinatorial microarrays.42 patients were diagnosed with Guillain-Barré syndrome during the study period. 41 (98%) patients with Guillain-Barré syndrome had anti-Zika virus IgM or IgG, and all (100%) had neutralising antibodies against Zika virus compared with 54 (56%) of 98 in control group 1 (p0.0001). 39 (93%) patients with Guillain-Barré syndrome had Zika virus IgM and 37 (88%) had experienced a transient illness in a median of 6 days (IQR 4-10) before the onset of neurological symptoms, suggesting recent Zika virus infection. Patients with Guillain-Barré syndrome had electrophysiological findings compatible with acute motor axonal neuropathy (AMAN) type, and had rapid evolution of disease (median duration of the installation and plateau phases was 6 [IQR 4-9] and 4 days [3-10], respectively). 12 (29%) patients required respiratory assistance. No patients died. Anti-glycolipid antibody activity was found in 13 (31%) patients, and notably against GA1 in eight (19%) patients, by ELISA and 19 (46%) of 41 by glycoarray at admission. The typical AMAN-associated anti-ganglioside antibodies were rarely present. Past dengue virus history did not differ significantly between patients with Guillain-Barré syndrome and those in the two control groups (95%, 89%, and 83%, respectively).This is the first study providing evidence for Zika virus infection causing Guillain-Barré syndrome. Because Zika virus is spreading rapidly across the Americas, at risk countries need to prepare for adequate intensive care beds capacity to manage patients with Guillain-Barré syndrome.Labex Integrative Biology of Emerging Infectious Diseases, EU 7th framework program PREDEMICS. and Wellcome Trust.

We detected an unusual increase in congenital cerebral malformations and dysfunction in fetuses and newborns in French Polynesia, following an epidemic of Zika virus (ZIKV), from October 2013 to March 2014. A retrospective review identified 19 cases, including eight with major brain lesions and severe microcephaly, six with severe cerebral lesions without microcephaly and five with brainstem dysfunction without visible malformations. Imaging revealed profound neurological lesions (septal and callosal disruption, ventriculomegaly, abnormal neuronal migration, cerebellar hypoplasia, occipital pseudocysts, brain calcifications). Amniotic fluid was drawn from seven cases at gestation weeks 20 to 29. ZIKV RNA was detected by RT-PCR and infectious ZIKV isolates were obtained in four of five microcephalic, but not in two non-microcephalic cases with severe brain lesions. Medical termination of pregnancy was performed in eleven cases; two cases with brainstem dysfunction died in the first months of life; six cases are alive, with severe neurological impairment. The results show that four of seven tested fetuses with major neurological injuries were infected with ZIKV in utero. For other non-microcephalic, congenital abnormalities we were not able to prove or exclude ZIKV infection retrospectively. The unusual occurrence of brain malformations or dysfunction without microcephaly following a ZIKV outbreak needs further studies.

International audience; Outbreaks of Salmonella enterica serotype Enteritidis infections associated with eggs occurred in French Polynesia during 2008-2013. Molecular analysis of isolates by using clustered regularly interspaced short palindromic repeat polymorphisms and multilocus variable-number tandem-repeat analysis was performed. This subtyping made defining the epidemic strain, finding the source, and decontaminating affected poultry flocks possible.

Background Few data are available on prescriber adherence to tuberculosis (TB) treatment guidelines. In particular, excessively long treatment carries a risk of avoidable adverse effects and represents a waste of healthcare resources. We examined factors potentially associated with excessively long treatment. Methods We reviewed the medical records of patients diagnosed with TB in 2004 in the eastern Paris region. Sociodemographic and clinical factors associated with excessively long treatment were identified by logistic regression analyses. Based on contemporary guidelines, excessively long treatment was defined as more than 6 months of a four-drug regimen for thoracic TB with full sensitive strains, and more than 12 months for patients with extrathoracic TB. Results Analyses concerned 478 patients with a median age of 36.0 ± 13.5 years, of whom 48% were living in precarious conditions (i.e. poor living conditions and/or no health insurance), 80% were born abroad, and 17% were HIV-seropositive. TB was restricted to the chest in 279 patients (isolated pulmonary, pleuropulmonary, and isolated pleural TB in 245, 13, and 21 patients, respectively), exclusively extrathoracic in 115 patients, and mixed in the remaining 84 patients. Treatment was prescribed by a chest specialist in 211 cases (44.1%) and 295 patients (61.7%) were managed in a single institution. The treatment duration complied with contemporary guidelines in 316 cases (66.1%) and was excessively long in 162 cases (33.9%). The median duration of excessively long treatment was 313 days (IQR: 272-412). In multivariate analysis, isolated thoracic TB, previous TB, HIV infection, a prescriber other than a chest specialist, and management in more than one healthcare center during treatment were independently associated with excessively lengthy treatment. Conclusion One-third of TB patients received excessively long treatment, reflecting inadequate awareness of management guidelines or unwillingness to implement them.

Zika fever, considered as an emerging disease of arboviral origin, because of its expanding geographic area, is known as a benign infection usually presenting as an influenza-like illness with cutaneous rash. So far, Zika virus infection has never led to hospitalisation. We describe the first case of Guillain-Barré syndrome (GBS) occurring immediately after a Zika virus infection, during the current Zika and type 1 and 3 dengue fever co-epidemics in French Polynesia.