An Otorhinolaryngology Perspective Into a Hospital COVID-19 Cluster

In this commentary, we share our experience of a COVID-19 cluster which developed within a frontline healthcare facility designated for treating COVID-19 patients. We provide an Otorhinolaryngology perspective into the key challenges, analyses and responses. We discuss how we identified and isolated infected patients and staff, uncovered the responsible COVID-19 variant strain B1.617.2 and instituted various measures to overcome this cluster. The measures include ceasing non-essential services, limiting transfers of patients, a heightened stance of personal protective equipment, ring-fencing of staff and enhanced COVID-19 testing. With rapid hospital wide efforts, there were no new non-isolated cases from our hospital cluster 3 days after the wards were locked down. The cluster which developed on 28-April-2021 was closed on 6-Jun-2021, with 48 cases, ten of whom were healthcare workers. Some of these lessons may be useful for consideration should another healthcare institution face a similar crisis in the future.

Construction of a Quadruple Gene-deleted Vaccine Confers Complete Protective Immunity Against Emerging PRV Variant Challenge in Piglets

Background: Pseudorabies virus (PRV) causes Aujeszky’s disease or pseudorabies (PR) in pigs worldwide, which leads to heavy economic losses to the swine industry. Pigs are the natural host, meanwhile, animals such as dogs, cats, foxes, rabbits, cattle and sheep are susceptible to infection. In 2011, the emerging PRV variant led to the outbreak of PR in Bar-tha-K61-vaccinated pigs. The PR outbreaks demonstrated that the Bartha-K61 vaccine did not provide full protection against the emerging PRV variant. It is widely believed that PRV live-attenuated vaccines could control PRV infection. Methods: In this study, we developed a novel PRV live-attenuated vaccine by deleting its gI, gE, US9, and US2 genes through CRISPR/Cas9, which was named PRV GDFS-delgI/gE/US9/US2.Results: Safety experiments confirmed that PRV GDFS-delgI/gE/US9/US2 was safe for 5 to 7-day-old suckling piglets. Piglets immunized with the PRV GDFS-delgI/gE/US9/US2 vaccine did not produce PRV gE-specific antibodies but could generate PRV gB-specific antibodies and high neutralizing titers against the PRV GDFS strain (variant PRV strain) or PRV Ea strain (older PRV strain). After challenge with the emerging PRV GDFS variant, none of the piglets immunized with the PRV GDFS-delgI/gE/US9/US2 vaccine showed any clinical signs, and their rectal temperatures were normal. Moreover, the autopsy and histopathological analyses revealed that the piglets in the PRV GDFS-delgI/gE/US9/US2 vaccine group did not show apparent gross or pathological lesions. Furthermore, the piglets in the PRV GDFS-delgI/gE/US9/US2 vaccine groups did not present weight loss. According to the criteria of the OIE terrestrial manual, the results of the experiment confirmed that the PRV GDFS-delgI/gE/US9/US2 vaccine could provide full protection against the emerging PRV variant strain in piglets. Conclusions: The PRV GDFS-delgI/gE/US9/US2 strain is a potential new live-attenuated vaccine against emerging PRV variant strain infections in China.

TK/gI/gE/11K Genes Is Not Involved in the Virulence Enhancement of Highly Virulent Pseudorabies Virus

The large-scale outbreaks of Pseudorabies in china since 2011 in vaccine-immunized pig farms were caused by the highly virulent Pseudorabies virus (PRV). To investigate the factors involved in the virulence enhancement of the variant PRV, four recombinant viruses with the virulence gene’s replacement, gI/gE/11K and TK/gI/gE/11K, between the variant strain HN1201 and the classical strain Fa were constructed based on bacterial artificial chromosome infectious clones. Compared with their parental strain, the viral titers of the recombinant PRV strains are not strongly influenced by the replacement of TK/gI/gE/11K, while as previously reported, the strain HN1201 and its derived viruses showed the higher mortality, the severer clinical symptoms and tissues damage than that of strain Fa and its derived strains. In summary, the TK/gI/gE/11K genes of variant strain HN1201 showed no contribute to its virulence enhancement compares with the classical strain.

Could a New COVID-19 Mutant Strain Undermine Vaccination Efforts? A Mathematical Modelling Approach for Estimating the Spread of B.1.1.7 Using Ontario, Canada, as a Case Study

Infections represent highly dynamic processes, characterized by evolutionary changes and events that involve both the pathogen and the host. Among infectious agents, viruses, such as Severe Acute Respiratory Syndrome-related Coronavirus type 2 (SARS-CoV-2), the infectious agent responsible for the currently ongoing Coronavirus disease 2019 (COVID-2019) pandemic, have a particularly high mutation rate. Taking into account the mutational landscape of an infectious agent, it is important to shed light on its evolution capability over time. As new, more infectious strains of COVID-19 emerge around the world, it is imperative to estimate when these new strains may overtake the wild-type strain in different populations. Therefore, we developed a general-purpose framework to estimate the time at which a mutant variant is able to take over a wild-type strain during an emerging infectious disease outbreak. In this study, we used COVID-19 as a case-study; however, the model is adaptable to any emerging pathogen. We devised a two-strain mathematical framework to model a wild- and a mutant-type viral population and fit cumulative case data to parameterize the model, using Ontario as a case study. We found that, in the context of under-reporting and the current case levels, a variant strain was unlikely to dominate until March/April 2021. The current non-pharmaceutical interventions in Ontario need to be kept in place longer even with vaccination in order to prevent another outbreak. The spread of a variant strain in Ontario will likely be observed by a widened peak of the daily reported cases. If vaccine efficacy is maintained across strains, then it is still possible to achieve high levels of immunity in the population by the end of 2021. Our findings have important practical implications in terms of public health as policy- and decision-makers are equipped with a mathematical tool that can enable the estimation of the take-over of a mutant strain of an emerging infectious disease.

Genetic Diversity of Recent Infectious Bursal Disease Viruses Isolated From Vaccinated Poultry Flocks in Malaysia

Vaccination is an essential component in controlling infectious bursal disease (IBD), however, there is a lack of information on the genetic characteristics of a recent infectious bursal disease virus (IBDV) that was isolated from IBD vaccinated commercial flocks in Malaysia. The present study investigated 11 IBDV isolates that were isolated from commercial poultry farms. The isolates were detected using reverse transcription-polymerase chain reaction (RT-PCR) targeting the hypervariable region (HVR) of VP2. Based on the HVR sequences, five isolates (IBS536/2017, IBS624/2017, UPM766/2018, UPM1056/2018, and UPM1432/2019) were selected for whole-genome sequencing using the MiSeq platform. The nucleotide and amino acid (aa) sequences were compared with the previously characterized IBDV strains. Deduced aa sequences of VP2HVR revealed seven isolates with 94–99% aa identity to very virulent strains (genogroup 3), two isolates with 97–100% aa identity to variant strains (genogroup 2), and two strains with 100% identity to the vaccine strain (genogroup 1) of IBDV. The phylogenetic analysis also showed that the isolates formed clusters with the respective genogroups. The characteristic motifs 222T, 249K, 286I, and 318D are typical of the variant strain and were observed for UPM1219/2019 and UPM1432/2019. In comparison, very virulent residues such as 222A, 249Q, 286T, and 318G were found for the vvIBDV, except for the UPM1056/2018 strain with a A222T substitution. In addition, the isolate has aa substitutions such as D213N, G254D, S315T, S317R, and A321E that are not commonly found in previously reported vvIBDV strains. Unlike the other vvIBDVs characterized in this study, UPM766/2018 lacks the MLSL aa residues in VP5. The aa tripeptides 145/146/147 (TDN) of VP1 were conserved for the vvIBDV, while a different motif, NED, was observed for the Malaysian variant strain. The phylogenetic tree showed that the IBDV variant clustered with the American and Chinese variant viruses and are highly comparable to the novel Chinese variants, with 99.9% identity. Based on the sequences and phylogenetic analyses, this is the first identification of an IBDV variant being reported in Malaysia. Further research is required to determine the pathogenicity of the IBDV variant and the protective efficacy of the current IBD vaccines being used against the virus.

Estimating SARS-CoV-2 variant strain infectiousness in Japan as of March 28, 2021

Background: A variant strain of SARS–CoV–2, VOC202012/01, emerged in the UK in September, 2020. Its infectiousness was estimated as higher than that of the original strain. Object: We estimated the infectiousness of the variant strain of SARS–CoV–2 in comparison to that of the original strain under conditions prevailing in Japan. Methods: We estimated infectiousness through a simple susceptible–infected–recovered (SIR) model by strain. The study period was March 1–28, 2020. The information used for the study was available as of April 3, 2020. Results: The estimated reproduction number of the SARS-CoV-2 variant strain was 1.799; its 95% CI was [1.642, 1.938]. The onset date of the first case in Japan was estimated as December 4 ([November 16, December 14]), 2020. However, infectiousness of the original strain was estimated as 1.123 ([1.093, 1.166]). Discussion and Conclusion: We demonstrated that infectiousness increased by 0.684 or 60%, increasing from the original to the variant. That finding might be comparable to that of a study conducted in the UK. However, the difference must be monitored continuously and carefully.