Pasteur Institute Research Articles

Achievement of maximal SARS-CoV-2 collective immunity among the Tajik population by March 2022

Despite all efforts of the world community, the COVID-19 pandemic remains one of the main epidemiological challenges of our time. Even with its widespread distribution, the infection may have certain local features due to social, geographic, and climatic factors. Objective: to study collective immunity to SARS-CoV-2 in the population of the Republic of Tajikistan.A cross-sectional, randomized study of herd immunity was carried out according to a program developed by Rospotrebnadzor and the St. Petersburg Pasteur Institute, taking into account WHO recommendations. The ethics committees of the corresponding entities approved the study: Tajik Ministry of Health and Social Protection; and the St. Petersburg Pasteur Institute (Russia). Based on questionnaire results, 4,022 people were selected, representing 0.15% (95% CI: 0.14-0.15) of the total population randomized by age and region. In subsequent laboratory analysis, 3682 people took part. The distribution and quantitative content of antibodies (Abs) to viral nucleocapsid (N Ag) and receptor binding domain (RBD Ag) were determined by ELISA. When questioned, a history of SARS-CoV-2 vaccination was indicated by 69.7% (95% CI: 68.2-71.2) of the volunteer cohort. Vector vaccines were most frequently used (50.6%; 95% CI: 48.7-52.5), with whole-virion inactivated preparations in second place (23.0%: 95% CI: 21.4-26.6) and mRNA vaccines in third place (21.0%; 95% CI:19.4-22.6).The cohort (n = 3682) featured 27.5% men and 72.5% women. The overall seroprevalence was 98.5% (95% CI: 97.7-99.2) in men and 99.4% (95% CI: 99.0-99.6) in women (differences statistically insignificant). Overall seroprevalence in the cohort was 99.2% (95% CI: 98.8-99.4) and ranged from 97.2 to 100% in certain subgroups. Asymptomatic seropositivity in the whole cohort was 98.4% (95% CI: 97.6-99.1). As a result of a mandatory vaccination program introduced in Tajikistan under a COVID-19 Emergency Project, the level of herd immunity among vaccinated individuals reached 99.5% (95% CI: 99.1-99.7), which is similar to the level reached in the cohort as a whole.The epidemic situation that developed in Tajikistan by mid-March 2022 was characterized by an almost absolute level of herd immunity, as evidenced by an absence of detected overt COVID-19 cases since the end of February (2022).

Acceptability, feasibility, and accuracy of blood-based HIV self-testing: A cross-sectional study in Ho Chi Minh City, Vietnam.

HIV self-testing (HIVST) is an effective approach to increase testing uptake. While oral fluid-based HIVST has been rapidly scaled, use of blood-based HIVST remains limited. We evaluated the acceptability, feasibility, and accuracy of blood-based HIVST among lay users in Ho Chi Minh City (HCMC), Vietnam. We conducted a cross-sectional study among HIV testing clients at the HCMC Pasteur Institute from March 2019 to October 2020. Participants received one HIVST kit and performed the test in front of an observer. The observer used product-specific questionnaires to collect information on the HIVST process, test results, experiences. The participants' interpretations of HIVST results were compared to health staff's interpretations and gold standard laboratory EIA reference tests. Of 2,399 participants who accepted HIVST, 64.7% were men, 62.1% aged 25-49 years, 53.5% had a higher education level, 41.4% were employed, and 35.6% were first-time testers. The vast majority (94.4%) desired to use the test in the future, and 93.9% reported willingness to recommend the test. The majority (90.8%) of participants successfully completed the self-test. One factor associated with successful completion was higher education level (aOR = 1.85; 95% CI: 1.32-2.61); while participants self-testing with SURE CHECK (aOR = 0.21; 95% CI: 0.12-0.37), INSTI (aOR = 0.23; 95% CI: 0.13-0.39), and BioSURE (aOR = 0.29; 95% CI: 0.17-0.51) or being unemployed, retired, or doing housework (aOR = 0.45; 95% CI: 0.25-0.82) were less likely to perform the test successfully. Agreement of positive and negative HIVST results as interpreted by participants and health staff was high (98.1% and 99.9%, respectively). Sensitivity and specificity of the evaluated HIVST were 96.43% (95% CI: 93.62-99.23) and 99.9% (95% CI: 99.75-100), respectively. Our findings confirm that blood-based HIVST is highly acceptable, feasible, and accurate. This evidence informs scale-up of HIVST to increase uptake of essential HIV prevention and treatment services.

Surveillance of antibiotic resistance in the northern zone of Senegal: Molecular characterization of beta-lactam resistance genes in Enterobacteriaceae (extended spectrum beta-lactamase, plasmid cephalosporinases, carbapenemases).

Introduction: With the increase in bacterial resistance to antibiotics, policies are being implemented on a national scale. These resistances are multiple, especially in enterobacteria, and represent a real public health problem due to the difficulty of their treatment. The objective of this work was to identify ESBL, cephalosporinase and carbapenemase producing enterobacteria in laboratories in the northern part of Senegal and to compare the mechanisms involved. Materials and methods: This is a retrospective study conducted at the Saint-Louis Regional Hospital and the Microbiology Unit of the Pasteur Institute of Dakar. Bacterial strains were collected between January and June 2021 in eight bacteriology laboratories in the regions of Saint-Louis, Louga and Matam. Bacterial identification was done by studying morphological, cultural and biochemical characteristics using an API® 20 E gallery and the MALDI-TOFF technique. The antibiogram was performed by the disc diffusion method according to the CA-SFM version 2021 procedure including the search for specific resistances (ESBL). The ESBL genes (CTX, TEM, OXA, and SHV) were identified by polymerase chain reaction (PCR) with specific primers and then analyzed by gel electrophoresis. Results: Forty-five strains of Enterobacteriaceae were ESBL producers and each had at least one beta-lactam resistance gene. The CTX-M gene was found in all strains, followed by the OXA (64.44%), TEM (53.33%) and SHV (20%) genes. A simultaneous presence of these 4 genes was noted in 6 isolates (13.33%). Apart from resistance to ertapenem, all strains were sensitive to imipenem. For quinolones, almost all strains (93%) were resistant. Conclusion: These results show the need to reinforce the surveillance of ESBL-producing Enterobacteriaceae in the Senegal area. These important data should help to orientate strategies for the reduction of MRBs and their dissemination in the community.

Co-circulation of dengue virus serotypes 1 and 3 in the Fatick region of senegal 2018

On 10th September 2018, the Syndromic Sentinel Surveillance network that monitors febrile illnesses in all 14 regions of Senegal detected a peak of fever in the Fatick region. On 13 September 2018, 10 samples were sent to the WHO Collaborating Centre for Arboviruses and Viral Haemorrhagic Fevers at the Institut Pasteur de Dakar (IPD). Laboratory investigations revealed an epidemic of dengue 1 genotype V and dengue 3 genotype III. Fatick neighbors the Holy City of Touba where 3.5 million people from all over the word gather every year for the Grand Magal pilgrimage. This article discusses the impact of mass gatherings and their role in the recent introduction of dengue serotypes in Senegal. Dengue is now endemic in Senegal and across many countries in Africa, highlighting the need for early detection, control measures and prevention of severe dengue cases in highly connected urban settings.

Bacterial Vaginosis: Prevalence and Risk Factors among Women in Dakar, Senegal

Introduction: Bacterial vaginosis (BV) is an imbalance of the vaginal flora that most commonly affects women of childbearing age. It is characterised by discomfort due to vaginal discharge and is associated with serious complications in women. We aimed to determine the prevalence of BV and its risk factors.
 Methodology: We conducted a prospective cross-sectional descriptive study in November 2020 at the Pasteur Institute of Dakar among women who were seen for vaginal sampling. We collected the following parameters: age, parity, history of infection, pregnancy and contraception. VB was diagnosed using the Amsel criteria and the Nugent score. Scoring is based on the presence of different bacterial morphotypes where a score ≥ 7 indicates the presence of BV, 4-6 indicates intermediate flora and 0- 3 normal flora. Analysis was performed using SPSS version 20.0.A statistically significant difference between the occurrence of bacterial vaginosis and a risk factor was retained for a p value < 0.05.
 Results: A total of 236 patients were included with a median age of 38 years. The prevalence of BV was 20.3%. It was more prevalent in women aged between [30-40 years] (28/101, 27.7%) followed by the age group [20-30 years] (13/51, 25.5%) with a statistically significant difference (p=0.0001).VB was more prevalent in nulliparous or primiparous women (28/118, 23.7%) and in those with no history of vaginal infections (20/83, 24.1%). Pregnant women and women without contraception were more affected with respectively (12/42, 28.6%) and (43/199, 21.6%). No relationship was found between BV and these previous potential risk factors.
 Conclusion: BV is a very common condition in women of childbearing age. Its complexity motivates numerous researches in order to elucidate its real implication in the occurrence of adverse gynecological conditions.

Incidence and risk factors of SARS-CoV-2 infection among workers in a public health laboratory in Tunisia

The aim of this study was to measure the extent of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among workers at the Institut Pasteur de Tunis (IPT), a public health laboratory involved in the management of the COVID-19 pandemic in Tunisia, and to identify risk factors for infection in this occupational setting. A cross-sectional survey was conducted on IPT workers not vaccinated against coronavirus disease 2019 (COVID-19). Participants completed a questionnaire that included a history of reverse transcription-polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infection. Immunoglobulin G antibodies against the receptor-binding domain of the spike antigen (anti-S-RBD IgG) and the nucleocapsid protein (anti-N IgG) of the SARS-CoV-2 virus were detected by enzyme-linked immunoassay (ELISA). A multivariate analysis was used to identify factors significantly associated with SARS-CoV-2 infection. A total of 428 workers were enrolled in the study. The prevalence of anti-S-RBD and/or anti-N IgG antibodies was 32.9% [28.7-37.4]. The cumulative incidence of SARS-CoV-2 infection (positive serology and/or previous positive RT-PCR test) was 40.0% [35.5-44.9], while the proportion with asymptomatic infection was 32.9%. One-third of the participants with RT-PCR-confirmed infection tested seronegative more than 90 days postinfection. Participants aged over 40 and laborers were more susceptible to infection (adjusted OR [AOR] = 1.65 [1.08-2.51] and AOR = 2.67 [1.45-4.89], respectively), while tobacco smokers had a lower risk of infection (AOR = 0.54 [0.29-0.97]). The SARS-CoV-2 infection rate among IPT workers was not significantly different from that detected concurrently in the general population. Hence, the professional activities conducted in this public health laboratory did not generate additional risk to that incurred outside the institute in day-to-day activities.

A Six Years (2010–2016) Longitudinal Survey of the Four Serotypes of Dengue Viruses in Lao PDR

Dengue fever is the most prevalent arthropod-borne viral infection of humans in tropical and subtropical countries. Since 1979, dengue has been reported to be endemic in the Lao People's Democratic Republic (PDR), as in many countries in Southeast Asia, with a complex circulation of the four dengue viruses' serotypes (DENV-1 to DENV-4). By sequencing the complete envelope protein, we explored a panel of samples from five Lao Provinces (Vientiane capital, Luangprabang, Bolikhamxay, Saravane, Attapeu) to enrich knowledge about the co-circulation of DENVs in Lao PDR between 2010 and 2016. Phylogenetic analyses highlighted the specific circulation of DENV-1 genotype I, DENV-2 genotype Asian I, DENV-4 genotype I and the co-circulation of DENV-3 genotype II and III. The continuous co-circulation of the four serotypes was underlined, with genotype or cluster shifts among DENV-3 and DENV-1. These data suggested the emergence or re-emergence of DENV strains associated with epidemic events, potentially linked to the exchanges within the territory and with neighboring countries. Indeed, the increasing local or regional connections favored the dissemination of new isolates or new clusters around the country. Since 2012, the surveillance and alert system created in Vientiane capital by the Institut Pasteur du Laos appears to be a strategic tool for monitoring the circulation of the four serotypes, especially in this endemic country, and allows for improving dengue epidemiological knowledge to anticipate epidemic events better.

Evaluation of Safety and Immunogenicity of a Recombinant Receptor-Binding Domain (RBD)-Tetanus Toxoid (TT) Conjugated SARS-CoV-2 Vaccine (PastoCovac) in Recipients of Autologous Hematopoietic Stem Cell Transplantation Compared to the Healthy Controls; A Prospective, Open-Label Clinical Trial.

Background: The urgent need for prompt SARS-CoV-2 immunization of hematopoietic stem cell transplant (HSCT) recipients in an endemic area raises many challenges regarding selecting a vaccine platform appropriate for HSCT recipients being economical for widespread use in developing countries. Methods: The trial is a prospective, single-group, open-label study to investigate the safety and serologic response of two doses of the recombinant receptor-binding domain (RBD)-Tetanus Toxoid (TT) conjugated SARS-CoV-2 vaccine (PastoCovac) early after autologous (auto) HSCT. For this reason, a total of 38 patients who completed the two-dose SARS-CoV-2 RBD-based vaccine between three to nine months after auto-HSCT and had an available anti-spike serologic test at three predefined time points of baseline and after the first and second doses and 50 healthy control individuals were included in the analysis. The primary outcome was defined as an increase in IgG Immune status ratio (ISR) to the cut-off value for the positive result (≥1.1) in the semiquantitative test. Findings: The median time between auto-HSCT and vaccination was 127 days. No participant reported any significant adverse effects (Grade 3). Pain at the injection site was the most common adverse event. The ISR increased significantly (p < 0.001) during the three-time point sampling for both patients and healthy control groups. In patients, the mean ISR increased from 1.39 (95% CI: 1.13−1.65) at baseline to 2.48 (1.93−3.03) and 3.73 (3.13−4.38) following the first and second dosages, respectively. In multivariate analysis, the higher count of lymphocytes [OR: 8.57 (95% CI: 1.51−48.75); p = 0.02] and history of obtaining COVID-19 infection before transplantation [OR: 6.24 (95% CI: 1.17−33.15); p = 0.03] remained the predictors of the stronger immune response following two doses of the RBD-TT conjugated vaccine. Moreover, we found that the immunogenicity of the COVID-19 vaccine shortly after transplantation could be influenced by pre-transplant COVID-19 vaccination. Interpretation: The RBD-TT conjugated SARS-CoV-2 vaccine was safe, highly immunogenic, and affordable early after autologous transplants. Funding: This work was mainly financed by the Hematology-Oncology-Stem Cell Transplantation Research Center (HORCSCT) of Tehran University and the Pasteur Institute of Iran.

Hepatitis B Virus (HBV) Infection in Patients at Pasteur Institute of Dakar in Senegal from 2016 to 2020: Prevalence and Seroprotection Level

Hepatitis B virus (HBV) infection is highly endemic in Senegal. Vaccination of all children against HBV was introduced in 1999 and included in Expanded Programme on Immunisation in 2005. The aim of this study was to assess the prevalence and immune status against HBV in patients received at Pasteur Institut in Dakar, Senegal. Methods: Between January 2016 and December 2020, patients aged between 1 and 96 years received laboratory were included in the study. Serum samples were analysed for HBV serology (HBs antigen: HBsAg, HBs antibody: HBsAb and HBc antibody: HBcAb) using ARCHITECT? analyser. Patients with anti-HBs antibody levels (HBsAb ≥ 10 IU/l) were considered seroprotected against HBV. Results: A total of 5629 patients were analysed with a mean age of 39 years and extremes from 1 to 96 years. The most represented age group was 31 - 45 years with 38.4%. HBsAg was present in 520 patients (9.2%) and was signed by sex and age group. Anti-HBc antibodies were found in 52.7% of patients and 1603 (28.48%) had isolated anti-HBs antibodies reflecting proportion of people vaccinated at the time of the study. However, 2143 patients (41.9%) had no seroprotection (HBsAb 10 IU/L) and 640 (12.6%) had strong seroprotection defined as HBsAb > 1000 IU/L. Conclusion: Our results show a significant presence of virus in Senegalese population and low vaccination coverage, especially in adults. Evaluation of HBsAb levels and provision of HBV booster shots should be considered for children in Senegal.

Hélène Sparrow-Germa, a Polish-French biologist in the Resistance at the Pasteur Institute

Hélène Sparrow-Germa (1891–1970) was a renowned French-Polish microbiologist, specialist in infectious diseases. Professor at the University of Warsaw, then member of the Pasteur Institute of Tunis, she was particularly dedicated to the struggle against typhus, having tried to get an effective vaccine to overcome the plague still deadly in the first years of the twentieth century. Hélène Sparrow devised an ambitious strategy, developing a sanitary fender on the eastern border of Poland against the spread of epidemics from Russia. The story of this French-Polish doctor is also repeatedly characterised by the ordeal of war. Willingly confronted with extreme and highly dangerous situations, Hélène Sparrow devoted herself to treating and helping wounded and sick soldiers, offering them protection and assistance. Often risking her own life, she showed a remarkable temerity reflecting her highly charismatic personality.

Effect of Zebularine on Apoptotic Pathways in Hepatocellular Carcinoma Cell Lines

Background: The alteration of DNA cytosine methylation is one of the most common epigenetic changes that can play a significant role in human cancers. The enzymes involved in DNA methylation of promoter regions of the genes are DNA methyltransferases (DNMTs). The therapeutic activities and apoptotic effects of DNA methyltransferase inhibitors (DNMTIs) have been reported in various cancers. This study was assigned to assess the effect of zebularine on intrinsic and extrinsic pathways, DNAT 1, 3a, and 3b, p21, and p53, viability, and apoptosis in hepatocellular carcinoma (HCC) cell lines. Methods: Hepatocellular carcinoma cell lines (HCCLM3, MHCC97H, and MHCC97L) were purchased from the National Cell Bank of Iran, Pasteur Institute, treated with zebularine, and the MTT assay was performed. Then, flow cytometry assay and real-time RT-PCR analysis were performed with zebularine. Statistical comparisons between groups were made using GraphPad Prism software version 8.0. A significant difference was considered as P &lt; 0.05. Results: Zebularine up-regulated DR4, DR5, FAS, FAS-L, TRAIL, Bax, Bak, Bim, p21WAF/CIP1 (p21), and p53 and down-regulated DNMTs (DNAT 1, 3a, and 3b), Bcl-2, Bcl-xL, and Mcl-1, significantly resulting in apoptosis induction in HCC cell lines. Maximal and minimal apoptosis was seen in HCCLM3 and MHCC97L cell lines, respectively. Conclusions: Our findings indicated that DNMTI zebularine can induce apoptosis and inhibit cell growth through both pathways (extrinsic and intrinsic) in HCC cell lines HCCLM3, MHCC97H, and MHCC97L.

Evaluation of Glutathione Peroxidase Enzymatic Activity in Seminal Plasma of Patients Treated at the Institute Pasteur in Cote d’Ivoire

Evaluation of Glutathione Peroxidase Enzymatic Activity in Seminal Plasma of Patients Treated at the Institute Pasteur in Cote d’Ivoire

The Institut Pasteur of C&amp;#244;te D’Ivoire (Ivory Coast) in the Emergency Management of Air Travellers during the COVID-19 Pandemic: A Unique Experience in Supporting the Response Strategy in C&amp;#244;te D’Ivoire from 2021 to 2022

Since its outbreak in December 2019 in Wuhan Province (China), the Coronavirus (COVID-19) disease quickly spread around the world in such a way that most response plans were outdated. There was an urgent need to change and adapt response strategies as the virus globally spread. Entire firms and economies were brought to a standstill in order to reduce the virus’ capacity to spread and to limit some of the short-term impacts in order to save time and find out solutions to come back to a more or less normal way of life. Thus, most of the countries that closed their air, sea and land borders had to reopen them progressively, with travel restrictions submitted to rigid controls. In Côte d’Ivoire, as in all other countries, air travellers leaving the territory were required to provide a certificate for a negative COVID-19 test, valid for 24 to 72 hours depending on the country of destination. However, the national system implemented could not provide a result before 48 hours. The objective of this work was to develop an alternative strategy to the system for air travellers who were in a hurry and those who had a computer bug in obtaining their result. A total of 38,444 air travellers benefited from this strategy implemented by the Institut Pasteur de Côte d’Ivoire during these two years.

Selection of candidate strains for hand, foot and mouth disease vaccine against enterovirus 71

The study aimed to select candidate strains from Vietnam for the development of the hand, foot and mouth disease (HFMD) vaccine against enterovirus 71 (EV71). Annual EV71 virus surveillance data of Pasteur Institute in Ho Chi Minh city from 2003 to 2013 was used to predict evolutionary trends. One hundred VP1 sequences of Vietnam strains from the GenBank database were used to evaluate the identity of acid amin sequences and identify the consensus sequences at key epitopes. As a result, the subgenogroup B5 strain named B5-203P-2013 was selected. The strain was adapted on Vero cells by multiple passages and plaque isolated. The strain B5-203P-2013-P10.1 was selected as a candidate strain for the HFMD vaccine due to possessing genetic stability, hightiter of 108 TCID50/ml and cross-neutralising antibody responses against other subgenogroups B5, C4, C5.

Minoarisoa Rajerison—fighting plague in Madagascar

Biochemist Minoarisoa Rajerison, Head of the Plague Unit, Institut Pasteur, Antananarivo, Madagascar, has lived a remarkable life. Born and raised in a village located in Ambohimanarina, Anta, Rajerison's household consisted of 10 siblings. “My mother passed away when I was in the final year of secondary school. She was my role model due to her perseverance”, reveals Rajerison. She divulges that the idea to enter the field of biomedicine was induced by a unique childhood experience. “When I was in primary school, I knew an elderly man who was suffering from a sore on his leg.

Design and Implementation of Nasopharyngeal Specimen Storage in Straws during the COVID19 Pandemic in Côte d'Ivoire

The Pasteur Institute of Côte d’Ivoire in its mission of surveillance and support to public health participates in the response to the COVID-19 pandemic in Côte d’Ivoire. It is involved in the diagnosis by RT-PCR of SARS-CoV-2. Through its biological resource center, which is the regional biobank of ECOWAS, the Pasteur Institute of Côte d’Ivoire keeps a priori or a posteriori nasopharyngeal samples of the COVID-19 pandemic and associated data. This study aimed to characterize the key issues driving the straw CBSTM storage of COVID-19 pandemic nasopharyngeal specimens in Côte d’Ivoire, the key determinants of the process and the final storage protocol. Planning was used to examine the technical, economic, logistical, and political aspects of the project. The study was designed to include 100,000 samples from Abidjan, the economic capital, and the interior of the country. In the interior of the country, the samples came from COVID-19 centers in the interior cities. The biobanking process of nasopharyngeal samples in straw CBS TM or high security straws from a primary tube was carried out using two techniques: manual and semi-automatic. These straws are properly sealed with a guaranteed airtightness using the System of Manual Sealing (SYMS) and the semi-automated instrument (PACE) of the company CryoBioSystem (Saint Ouen sur Iton, France). The average monthly performance of the straws obtained is 1,685 for the manual technique versus 2,820 for the semi-automatic technique. This performance is in line with the objective set during the design of the study. The acquisition of the semi-automated technique (PACE) has allowed the biobank to reinforce biosafety measures concerning the handling of samples. In the event of a large-scale epidemic, the collection in a biobank requires a complete automated chain for stratification to facilitate the provision of samples to applicants and to strengthen the heritage collection

Potential of RH5 Antisense on Plasmodium falciparum Proliferation Abatement.

Infections by Plasmodium falciparum, are becoming increasingly difficult to treat. Therefore, there is an urgent need for novel antimalarial agents' discovery against infection. In present study, we described a 2'-O-Methyl gapmer phosphorothioate oligonucleotide antisense targeting translation initiation region of 3D7 strain RH5 gene. The study was conducted in Pasteur Institute of Iran in 2020. ODNs effects were measured by microscopic examination and real time RT-PCR. For microscopy, microplates were charged with 2'-OMe ODNs at different dilutions. Unsynchronized parasites were added to a total of 0.4 ml (0.4% parasitemia, 5% red blood cells), and slides were prepared. Proportion of infected cells was measured by counting at least 500 red blood cells. RH5 genes start codon regions selected as conserved region besed on alignment results. Gap-RH5-As which was complementary to sequence surrounding AUG RH5 start codon significantly reduced parasite growth (>90% at 50 nM) compared to sense sequence control (Gap-RH5-Se) (17%), (P<0.001). RH5 transcripts were dramatically reduced after exposed to ODNs at a concentration of 5-500 nM for 48 h. Gemnosis delivery of a chimeric gapmer PS-ODN with 2'-OMe modifications at both sides had high antisense activity at low concentrations (10-100 nM) and shown a good efficiency to reach to target mRNA in human RBCs. Anti-parasite effect was correlated to reduction of target gene mRNA level. In addition, 2'-OMe ODNs free delivery is an effective way and does not need any carrier molecules or particles.

Analysis of a Dengue Virus Outbreak in Rosso, Senegal 2021.

Senegal is hyperendemic for dengue. Since 2017, outbreaks have been noticed annually in many regions around the country, marked by the co-circulation of DENV1-3. On 8 October 2021, a Dengue virus outbreak in the Rosso health post (sentinel site of the syndromic surveillance network) located in the north of the country was notified to the WHO Collaborating Center for arboviruses and hemorrhagic fever viruses at Institut Pasteur de Dakar. A multidisciplinary team was then sent for epidemiological and virologic investigations. This study describes the results from investigations during an outbreak in Senegal using a rapid diagnostic test (RDT) for the combined detection of dengue virus non-structural protein 1 (NS1) and IgM/IgG. For confirmation, samples were also tested by real-time RT-PCR and IgM ELISA at the reference lab in Dakar. qRT-PCR positive samples were subjected to whole genome sequencing using nanopore technology. Virologic analysis scored 102 positives cases (RT-PCR, NS1 antigen detection and/or IgM) out of 173 enrolled patients; interestingly, virus serotyping showed that the outbreak was caused by the DENV-1, a serotype different from DENV-2 involved during the outbreak in Rosso three years earlier, indicating a serotype replacement. Nearly all field-tested NS1 positives samples were confirmed by qRT-PCR with a concordance of 92.3%. Whole genome sequencing and phylogenetic analysis of strains suggested a re-introduction in Rosso of a DENV-1 strain different to the one responsible for the outbreak in the Louga area five years before. Findings call for improved dengue virus surveillance in Senegal, with a wide deployment of DENV antigenic tests, which allow easy on-site diagnosis of suspected cases and early detection of outbreaks. This work highlights the need for continuous monitoring of circulating serotypes which is crucial for a better understanding of viral epidemiology around the country.

Re-Introduction of West Nile Virus Lineage 1 in Senegal from Europe and Subsequent Circulation in Human and Mosquito Populations between 2012 and 2021.

West Nile virus (WNV) is a virus of the Japanese encephalitis antigenic complex and belongs to the family Flaviviridae of the genus flavivirus. The virus can cause infection in humans which in most cases is asymptomatic, however symptomatic cases exist and the disease can be severe causing encephalitis and meningoencephalitis. The virus is maintained in an enzootic cycle involving mosquitoes and birds, humans and other mammals such as horses can be accidental hosts. A mosquito-based arbovirus surveillance system and the sentinel syndromic surveillance network (4S) have been in place since 1988 and 2015 respectively, to better understand the transmission dynamics of arboviruses including WNV in Senegal. Arthropod and human samples have been collected from the field and analysed at Institut Pasteur de Dakar using different methods including RT-PCR, ELISA, plaque reduction neutralization test and viral isolation. RT-PCR positive samples have been analysed by Next Generation Sequencing. From 2012 to 2021, 7912 samples have been analysed and WNV positive cases have been detected, 20 human cases (19 IgM and 1 RT-PCR positive cases) and 41 mosquito pools. Phylogenetic analyzes of the sequences of complete genomes obtained showed the circulation of lineage 1a, with all these recent strains from Senegal identical to each other and very close to strains isolated from horse in France in 2015, Italy and Spain. Our data showed lineage 1a endemicity in Senegal as previously described, with circulation of WNV in humans and mosquitoes. Phylogenetic analyzes carried out with the genome sequences obtained also revealed exchanges of WNV strains between Europe and Senegal which could be possible via migratory birds. The surveillance systems that have enabled the detection of WNV in humans and arthropods should be extended to animals in a one-health approach to better prepare for global health threats.

Science knows no country: fulfilling Louis Pasteur's legacy

2022 marks the bicentenary of Louis Pasteur's birth. Pasteur's discoveries helped lay the foundation of modern public health, microbiology, and medicine. His legacy echoes in the many streets, schools, and hospitals that bear his name, and in the widespread use of pasteurised food worldwide. After his pioneering work on veterinary vaccines, Pasteur developed the rabies vaccine for humans in 1885, the success of which led to the foundation of a dedicated institute in Paris, France.1 The Institut Pasteur was registered in 1887 as a private foundation of public utility, and its statutes state that the institute's dual purposes were “the treatment of rabies according to the method developed by M.