Biology subjects

Kroeger, A.

Publications and source records attributed to Kroeger, A..

3 recordsLinked to original sources

bioRxiv2021

Validation of the Early Warning and Response System (EWARS) for dengue outbreaks: Evidence from the national vector control program in Mexico

BackgroundDuring 2017, twenty health districts (locations) in Mexico implemented a dengue outbreak early warning and response system (EWARS) that uses epidemiological, meteorological and entomological variables (alarm indicators) to predict dengue outbreaks and triggers early response activities. Eleven of these districts were analyzed as they presented reliable information. Nine districts presented outbreak alarms but without subsequent outbreaks ("non-outbreak districts") and two presented after the alarms dengue outbreaks ("outbreak districts"). This study is concerned with i) if the alarms without outbreaks were false alarms or if the control services had established effective response activities averting an outbreak and ii) if vector control activities can mitigate or even avert dengue outbreaks. MethodsFive components of dengue outbreak response (larval control, entomological studies with water container interventions, focal spraying, indoor residual spraying, space spraying) were quantitatively analyzed across two groups ("outbreak districts" and "non-outbreak districts"). ResultsThe average coverage of vector control and responses were higher in non-outbreak districts and across all five components. In the "outbreak districts" the response activities started late and were of much lower intensity compared to "non-outbreak districts". District vector control teams demonstrated diverse compliance with local guidlines for initial, early and late responses to outbreak alarms which could explain the different outcomes observed following the outbreak alarms. Conclusionfindings from this study plausibly demonstrates important operational scenarios when succeeding or failing alarms signals generated by EWARS at national level. This study presents evidence warranting for further investigation into the effectiveness and cost-effectiveness of EWARS using gold-standard designs.

scientific communication and education↗

bioRxiv2020

SARS-CoV-2 Quasispecies Mediate Rapid Virus Evolution and Adaptation

Since the pandemic spread of SARS-CoV-2, the virus has exhibited remarkable genome stability, but recent emergence of novel variants show virus evolution potential. Here we show that SARS-CoV-2 rapidly adapts to Vero E6 cells that leads to loss of furin cleavage motif in spike protein. The adaptation is achieved by asymptotic expansion of minor virus subpopulations to dominant genotype, but wildtype sequence is maintained at low percentage in the virus swarm, and mediate reverse adaptation once the virus is passaged on human lung cells. The Vero E6-adapted virus show defected cell entry in human lung cells and the mutated spike variants cannot be processed by furin or TMPRSS2. However, the mutated S1/S2 site is cleaved by cathepsins with higher efficiency. Our data show that SARS-CoV-2 can rapidly adapt spike protein to available proteases and advocate for deep sequence surveillance to identify virus adaptation potential and novel variant emergence. Significance StatementRecently emerging SARS-CoV-2 variants B1.1.1.7 (UK), B.1.351 (South Africa) and B.1.1.248 (Brazil) harbor spike mutation and have been linked to increased virus pathogenesis. The emergence of these novel variants highlight coronavirus adaptation and evolution potential, despite the stable consensus genotype of clinical isolates. We show that subdominant variants maintained in the virus population enable the virus to rapidly adapt upon selection pressure. Although these adaptations lead to genotype change, the change is not absolute and genome with original genotype are maintained in virus swarm. Thus, our results imply that the relative stability of SARS-CoV-2 in numerous independent clinical isolates belies its potential for rapid adaptation to new conditions.

microbiology↗

bioRxiv2020

SARS-CoV-2 neutralizing human recombinant antibodies selected from pre-pandemic healthy donors binding at RBD-ACE2 interface

COVID-19 is a severe acute respiratory disease caused by SARS-CoV-2, a novel betacoronavirus discovered in December 2019 and closely related to the SARS coronavirus (CoV). Both viruses use the human ACE2 receptor for cell entry, recognizing it with the Receptor Binding Domain (RBD) of the S1 subunit of the viral spike (S) protein. The S2 domain mediates viral fusion with the host cell membrane. Experience with SARS and MERS coronaviruses has shown that potent monoclonal neutralizing antibodies against the RBD can inhibit the interaction with the virus cellular receptor (ACE2 for SARS) and block the virus cell entry. Assuming that a similar strategy would be successful against SARS-CoV-2, we used phage display to select from the human naive universal antibody gene libraries HAL9/10 anti-SARS-CoV-2 spike antibodies capable of inhibiting interaction with ACE2. 309 unique fully human antibodies against S1 were identified. 17 showed more than 75% inhibition of spike binding to cells expressing ACE2 in the scFv-Fc format, assessed by flow cytometry and several antibodies showed even an 50% inhibition at a molar ratio of the antibody to spike protein or RBD of 1:1. All 17 scFv-Fc were able to bind the isolated RBD, four of them with sub-nanomolar EC50. Furthermore, these scFv-Fc neutralized active SARS-CoV-2 virus infection of VeroE6 cells. In a final step, the antibodies neutralizing best as scFv-Fc were converted into the IgG format. The antibody STE73-2E9 showed neutralization of active SARS-CoV-2 with an IC50 0.43 nM and is binding to the ACE2-RBD interface. Universal libraries from healthy human donors offer the advantage that antibodies can be generated quickly and independent from the availability of material from recovered patients in a pandemic situation.

biochemistry↗