Anthony Griffiths

Infections arising from a broadening variety of viruses are becoming increasingly widespread due to greater zoonotic transmission, with the COVID-19 pandemic exemplifying a global event that claimed the lives of millions worldwide. While targeted vaccines are being developed to thwart the spread of viral infections, they often become available to the public in response to an (expected) outbreak and must be repeatedly adjusted to account for mutations. An alternative to this strategy instead focuses on infection prevention by inactivating viruses prior to human exposure. In this study, we examine the inactivation kinetics of a broad range of infectious viruses on a self-cleaning polymer that functions by a surface pH-drop mechanism upon hydration. Photo-induced surface microscopy confirms that the sulfonic acid groups responsible for proton transport initially reside on the polymer surface, where protons lower the pH of the aqueous layer in contact with the polymer to below unity. This additive-free mechanism results in pH-driven inactivation of three coronaviruses (including SARS-CoV-2), human adenovirus, Tulane virus (a human norovirus surrogate), and four high-consequence viruses (Sudan virus, Marburg virus, Lassa virus, and Nipah virus), often reaching the limit of detection in 10 min or less.

The US Federal Select Agent program requires that inactivation procedures be validated before treated materials can be removed from biocontainment for downstream use. Although H5 avian influenza viruses are subject to temporary exemption from the Select Agent regulatory requirements, validated inactivation workflows remain critical for safe downstream handling of HPAIV-containing materials. Common treatments, including TRIzol, TRIzol LS, formalin, and ice-cold methanol, are frequently used to facilitate virus inactivation and downstream processing. However, facility-specific inactivation validation is required for Select Agent workflows and for safe handling of HPAIV-containing materials. In this study, HPAIV (H5N1)-infected samples were used to validate inactivation of material generated in cell culture, and low-pathogenicity (H1N1)-infected lung homogenates were used to validate inactivation of animal-derived tissues. Following inactivation, column-based buffer exchange was used to remove cytotoxic inactivants before viability testing. This step did not significantly reduce recovery of infectious virus, supporting the sensitivity of this approach. In inactivation tests, residual infectious virus was assessed by plaque assay and serial blind passages. No infectious virus was detected following any of the tested conditions. These data validate several procedures for inactivating influenza A virus-containing cell cultures, fluids, and tissue samples and provide a framework for facility-specific validation of similar workflows.

Biocontainment laboratories often have limited access to a range of instruments required for conducting standard assays on infected materials. Consequently, some of the protocols involving infected samples are conducted outside a biocontainment facility. To be compliant with regulatory requirements and minimize health and safety risks for scientific personnel, it is imperative to test procedures rigorously for safely removing infected samples from biocontainment areas. This study validated the chemical inactivation of Nipah virus (NiV), a representative member of the Henipavirus genus, in animal tissues and serum. Importantly, this work demonstrated successful NiV-spiking of non-human primate (NHP) tissues and their subsequent inactivation. This is important because NHP tissues contain unpredictable amounts of infectious virus. The primary objective was to establish standardized protocols that are compliant with regulations to permit safe retrieval of infected biological samples with high NiV infectious virus content from ABSL-4 laboratories for subsequent downstream processing under lower biocontainment conditions.

The emergence of SARS-CoV-2 variants has challenged the current spike protein–focused COVID-19 vaccine strategy due to neutralizing antibody escape and waning antibody-mediated immunity. In contrast, T cell–mediated immunity targeting conserved epitopes may offer broad and long-lasting protection. However, whether T cells alone can provide sufficient protection remains unclear. Here, we identified both Omicron BA.1–specific and ancestral (Wuhan)–conserved CD8 T cell epitopes in the SARS-CoV-2 spike protein and evaluated them as carrier-protein fusion vaccines in mouse models. Subcutaneous immunizations with two CD8 epitope peptides substantially lowered lung viral load and conferred protection against low-dose viral challenge, but not against high-dose challenge. Notably, intranasal boosting—with or without adjuvant—enhanced lung resident memory T cell responses and conferred potent, durable protection against high-dose infection. These findings emphasize the importance of mucosal vaccination to boost protective T cell immunity against SARS-CoV-2 and support the potential of T cell–based vaccines targeting conserved epitopes for broad immunity against SARS-CoV-2 and other respiratory viral threats.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily causes mild to moderate respiratory illness in humans, but infection can also lead to long-term complications, including chronic fatigue, respiratory and cardiac issues, or even death. In November 2021, the emergence of the highly transmissible Omicron variant marked a significant shift in the pandemic, with its subvariants rapidly spreading and continuing to evolve worldwide. The continuing introduction of Omicron subvariants underscores the need for the development of up-to-date vaccines, as well as for appropriate animal models in which they can be evaluated. Among these subvariants, XBB.1.5 stands out for its ability to evade the immune response from previous infection or vaccination. The objective of this study was to determine the disease course in African green monkeys (AGMs) following intranasal exposure to the XBB.1.5 subvariant. In four intranasally exposed AGMs, histopathological findings in the lungs consistent with SARS-CoV-2 infection included lymphohistiocytic and neutrophilic bronchiolitis with variable numbers of syncytial cells, to terminal bronchiole-centric, bronchointerstitial pneumonia with alveolar type II (AT2) pneumocyte hyperplasia, with evidence of acute alveolar injury, including alveolar septal necrosis and hyaline membrane formation. The two males showed more severe pneumonia compared to the two females. SARS-CoV-2 RNA was detected in the lungs or tracheobronchial lymph nodes in the males but not in the females, which correlated with higher cumulative lung pathology scores in the males. In the females, SARS-CoV-2 RNA was limited to the colon and nasal turbinates. Our results indicate that AGMs exhibit a disease course similar to most humans when exposed intranasally, making them a suitable model for studying mild to moderate SARS-CoV-2 infection. Therefore, further work is warranted to determine if this model could have utility for the evaluation of vaccine and therapeutic candidates against contemporary SARS-CoV-2 variants.

In April 2024, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was expanded by 1 new order, 1 new family, 6 new subfamilies, 34 new genera and 270 new species. One class, two orders and six species were renamed. Seven families and 12 genera were moved; ten species were renamed and moved; and nine species were abolished. This article presents the updated taxonomy of Negarnaviricota as currently accepted by the ICTV, providing an essential annual update on the classification of members of this phylum that deepen understandings of their evolution, and supports critical public health measures for virus identification and tracking.

Cellular nanoparticles (CNPs), which refer to nanoparticles coated with natural cell membranes, are promising for neutralizing pathological agents. Here, we use CNPs as a medical countermeasure against the infection of SARS-CoV-2 variants in an animal model. CNPs comprise polymeric cores coated with the plasma membranes of human macrophages. The resulting nanoparticles (MΦ-NPs) act as host cell decoys to intercept SARS-CoV-2 and block its cellular entry, thus inhibiting subsequent viral infection. Our findings indicate that MΦ-NPs bind to the spike proteins of SARS-CoV-2 variants in a dose-dependent manner and inhibit the infectivity of live viruses. In hamsters infected with SARS-CoV-2 variants, MΦ-NPs significantly reduce the viral burden in the lungs, demonstrating their effectiveness in inhibiting viral infectivity in vivo. Furthermore, MΦ-NPs are primarily taken up by alveolar macrophages without inducing noticeable adverse effects. Given the crucial role of macrophages in viral infections, MΦ-NPs present a promising approach to combating emerging viral threats.

Although next-generation sequencing (NGS) has been instrumental in determining the genomic sequences of emerging RNA viruses, de novo sequence determination often lacks sufficient coverage of the 5′ and 3′ ends of the viral genomes. Since the genome ends of RNA viruses contain the transcription and genome replication promoters that are essential for viral propagation, a lack of terminal sequence information hinders the efforts to study the replication and transcription mechanisms of emerging and re-emerging viruses. To circumvent this, we have developed a novel method termed ViBE-Seq (Viral Bona Fide End Sequencing) for the high-resolution sequencing of filoviral genome ends using a simple yet robust protocol with high fidelity. This technique allows for sequence determination of the 5′ end of viral RNA genomes and mRNAs with as little as 50 ng of total RNA. Using the Ebola virus and Marburg virus as prototypes for highly pathogenic, re-emerging viruses, we show that ViBE-Seq is a reliable technique for rapid and accurate 5′ end sequencing of filovirus RNA sourced from virions, infected cells, and tissue obtained from infected animals. We also show that ViBE-Seq can be used to determine whether distinct reverse transcriptases have terminal deoxynucleotidyl transferase activity. Overall, ViBE-Seq will facilitate the access to complete sequences of emerging viruses.

Filoviridae is a family of negative-sense RNA viruses with genomes of about 13.1–20.9 kb that infect fish, mammals and reptiles. The filovirid genome is a linear, non-segmented RNA with five canonical open reading frames (ORFs) that encode a nucleoprotein (NP), a polymerase cofactor (VP35), a glycoprotein (GP _1,2 ), a transcriptional activator (VP30) and a large protein (L) containing an RNA-directed RNA polymerase (RdRP) domain. All filovirid genomes encode additional proteins that vary among genera. Several filovirids (e.g., Ebola virus, Marburg virus) are pathogenic for humans and highly virulent. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Filoviridae , which is available at www.ictv.global/report/filoviridae .

The emergence of highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) that are resistant to the current COVID-19 vaccines highlights the need for continued development of broadly protective vaccines for the future. Here, we developed two messenger RNA (mRNA)-lipid nanoparticle (LNP) vaccines, TU88mCSA and ALCmCSA, using the ancestral SARS-CoV-2 spike sequence, optimized 5′ and 3′ untranslated regions (UTRs), and LNP combinations. Our data showed that these nanocomplexes effectively activate CD4 ⁺ and CD8 ⁺ T cell responses and humoral immune response and provide complete protection against WA1/2020, Omicron BA.1 and BQ.1 infection in hamsters. Critically, in Omicron BQ.1 challenge hamster models, TU88mCSA and ALCmCSA not only induced robust control of virus load in the lungs but also enhanced protective efficacy in the upper respiratory airways. Antigen-specific immune analysis in mice revealed that the observed cross-protection is associated with superior UTRs [Carboxylesterase 1d (Ces1d)/adaptor protein-3β (AP3B1)] and LNP formulations that elicit robust lung tissue-resident memory T cells. Strong protective effects of TU88mCSA or ALCmCSA against both WA1/2020 and VOCs suggest that this mRNA-LNP combination can be a broadly protective vaccine platform in which mRNA cargo uses the ancestral antigen sequence regardless of the antigenic drift. This approach could be rapidly adapted for clinical use and timely deployment of vaccines against emerging and reemerging VOCs.