Low-dose bivalent mRNA vaccine is highly effective against different SARS-CoV-2 variants in a transgenic mouse model (preprint)

Combining optimized spike (S) protein-encoding mRNA vaccines to target multiple SARS CoV-2 variants could improve COVID-19 control. We compared monovalent and bivalent mRNA vaccines encoding B.1.351 (Beta) and/or B.1.617.2 (Delta) SARS-CoV-2 S protein, primarily in a transgenic mouse model and a Wistar rat model. The low-dose bivalent mRNA vaccine contained half the mRNA of each respective monovalent vaccine, but induced comparable neutralizing antibody titres, enrichment of lung-resident memory CD8+ T cells, specific CD4+ and CD8+ responses, and fully protected transgenic mice from SARS-CoV-2 lethality. The bivalent mRNA vaccine significantly reduced viral replication in both Beta- and Delta-challenged mice. Sera from bivalent mRNA vaccine immunized Wistar rats also contained neutralizing antibodies against the B.1.1.529 (Omicron BA.1) variant. These data suggest that low-dose and fit-for-purpose multivalent mRNA vaccines encoding distinct S-proteins is a feasible approach for increasing the potency of vaccines against emerging and co-circulating SARS-CoV-2 variants.

Virus capture facilitates a sensitive viral diagnosis for pathogens including SARS-CoV-2 (preprint)

When new viruses emerge, early detection is critical, but the detection of pathogens in clinical and environmental samples using high-throughput sequencing is often hampered by large amounts of background material. Enormous sequencing depth can be necessary to gain sufficient information to identify a certain pathogen. Now, a study demonstrates a new method to improve the sensitivity of viral diagnosis. Combining high-throughput sequencing with in-solution virus capture, researchers compiled a virus genome dataset for the design of a RNA-baits panel. The panel, called VirBaits, consists of about 178,000 RNA-baits based on over 18,000 complete viral genomes, targeting 35 epizootic and zoonotic viruses, including SARS-CoV-2. In a test of complex samples, viruses with both DNA and RNA genomes were enriched by anywhere from 10-fold to 10,000-fold, with enriched viruses having at least 72% overall identity shared with the viruses in the bait set. Although the cost and risk of cross-contamination remain concerns for this method, the VirBaits approach represents a promising technique for improving the sensitivity of viral diagnosis in complex samples, enabling the rapid detection of emerging pathogens.

Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2 (preprint)

BackgroundThe detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples. MethodsA virus panel based on the principle of biotinylated RNA-baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2 positive samples. Libraries generated from complex samples were sequenced via generic HTS and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted. ResultsThe VirBaits set consists of 177,471 RNA-baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also point to the risk of carryover between samples. ConclusionsThe VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector or research question. The risk of carryover needs to be taken into consideration. The application of the RNA-baits principle turned out to be user-friendly, and even non-experts (without sophisticated bioinformatics skills) can easily use the VirBait workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible without any problems as shown for SARS-CoV-2.

Experimental Transmission Studies of SARS-CoV-2 in Fruit Bats, Ferrets, Pigs and Chickens (preprint)

Background: A novel zoonotic SARS-related coronavirus emerged in China at the end of 2019. The novel SARS-CoV-2 became pandemic within weeks and the number of human infections and severe cases is increasing. The role of potential animal hosts is still understudied.Methods: We intranasally inoculated fruit bats (Rousettus aegyptiacus; n=9), ferrets (n=9), pigs (n=9) and chickens (n=17) with 105 TCID50 of a SARS-CoV-2 isolate per animal. Animals were monitored clinically and for virus shedding. Direct contact animals (n=3) were included. Animals were humanely sacrificed for virological and immune-pathohistological analysis at different time points.Findings: Under these settings, pigs and chickens were not susceptible to SARS-CoV-2. All swabs as well as organ samples and contact animals remained negative for viral RNA, and none of the animals seroconverted. Rousettus aegyptiacus fruit bats experienced a transient infection, with virus detectable by RT-qPCR, immunohistochemistry (IHC) and in situ hybridization (ISH) in the nasal cavity, associated with rhinitis. Viral RNA was also identified in the trachea, lung and lung associated lymphatic tissue. One of three contact bats became infected. More efficient virus replication but no clinical signs were observed in ferrets with transmission to all direct contact animals. Prominent viral RNA loads of up to 104 viral genome copies/ml were detected in the upper respiratory tract. Mild rhinitis was associated with viral antigen detection in the respiratory and olfactory epithelium. Both fruit bats and ferrets developed SARS-CoV-2 reactive antibodies reaching neutralizing titers of up to 1:1024.Interpretation: Pigs and chickens could not be infected intranasally by SARS-CoV-2, whereas fruit bats showed characteristics of a reservoir host. Virus replication in ferrets resembled a subclinical human infection with efficient spread. These animals might serve as a useful model for further studies e.g. testing vaccines or antivirals.Funding Statement: Intramural funding of the German Federal Ministry of Food and Agriculture provided to the Friedrich-Loeffler-Institut.Declaration of Interests: All authors declare no competing interest.Ethics Approval Statement: The animal experiments were evaluated and approved by the ethics committee of the State Office of Agriculture, Food safety, and Fishery in Mecklenburg – Western Pomerania (LALLF M-V: LVL MV/TSD/7221.3-2-010/18-12). All procedures were carried out in approved biosafety level 3 (BSL3) facilities.