Molecular Mechanisms of Poxvirus Evolution

Poxviruses are often thought to evolve relatively slowly because they are double-stranded DNA pathogens with proofreading polymerases. However, poxviruses have highly adaptable genomes and can undergo relatively rapid genotypic and phenotypic change, as illustrated by the recent increase in human-to-human transmission of monkeypox virus. Advances in deep sequencing technologies have demonstrated standing nucleotide variation in poxvirus populations, which has been underappreciated. There is also an emerging understanding of the role genomic architectural changes play in shaping poxvirus evolution. These mechanisms include homologous and nonhomologous recombination, gene duplications, gene loss, and the acquisition of new genes through horizontal gene transfer. In this review, we discuss these evolutionary mechanisms and their potential roles for adaption to novel host species and modulating virulence.

Stability of African swine fever virus in feed during environmental storage

African swine fever virus (ASFV) causes high case fatality in pigs and a trade-limiting disease resulting in significant economic losses to pork production. ASFV is resistant to environmental degradation and maintains infectivity in feed ingredients exposed to transoceanic shipment conditions. As ASFV is transmissible through consumption of contaminated feed, the objective of this study was to evaluate the stability of ASFV Georgia 2007 in three feed matrices (complete feed, soybean meal, ground corncobs) exposed to three environmental storage temperatures (40°F, 68°F, 95°F) for up to 365 days. ASFV DNA was highly stable and detectable by qPCR in almost all feed matrices through the conclusion of each study. Infectious ASFV was most stable in soybean meal, maintaining infectivity for at least 112 days at 40°F, at least 21 days at 68°F and at least 7 days at 95°F. These data help define risk of ASFV introduction and transmission through feed ingredients.

LINE-1 retrotransposons facilitate horizontal gene transfer into poxviruses

There is ample phylogenetic evidence that many critical virus functions, like immune evasion, evolved by the acquisition of genes from their hosts through horizontal gene transfer (HGT). However, the lack of an experimental system has prevented a mechanistic understanding of this process. We developed a model to elucidate the mechanisms of HGT into vaccinia virus, the prototypic poxvirus. All identified gene capture events showed signatures of long interspersed nuclear element-1 (LINE-1)-mediated retrotransposition, including spliced-out introns, polyadenylated tails, and target site duplications. In one case, the acquired gene integrated together with a polyadenylated host U2 small nuclear RNA. Integrations occurred across the genome, in some cases knocking out essential viral genes. These essential gene knockouts were rescued through a process of complementation by the parent virus followed by nonhomologous recombination during serial passaging to generate a single, replication-competent virus. This work links multiple evolutionary mechanisms into one adaptive cascade and identifies host retrotransposons as major drivers for virus evolution.

Mutations within scavenger receptor cysteine-rich (SRCR) protein domain 5 of porcine CD163 involved in infection with porcine reproductive and respiratory syndrome virus (PRRS)

CD163, a macrophage-specific membrane scavenger receptor, serves as a cellular entry receptor for porcine reproductive and respiratory syndrome virus (PRRSV). The removal of scavenger receptor cysteine-rich (SRCR) domain 5 (SRCR5) of CD163 is sufficient to make transfected cells or genetically modified pigs resistant to PRRSV-1 and PRRSV-2 genotypes, and substitution of SRCR5 with SRCR8 from human CD163-like protein (hCD163L1) confers resistance to PRRSV-1 but not PRRSV-2 isolates. However, the specific regions within the SRCR5 polypeptide involved in PRRSV infection remain largely unknown. In this report, we performed mutational studies in order to identify which regions or amino acid sequences in the SRCR5 domain are critical for PRRSV infection. The approach used in this study was to make proline-arginine (PR) insertions along the SRCR5 polypeptide. Constructs were transfected into HEK293T cells, and then evaluated for infection with PRRSV-2 or PRRSV-1. For PRRSV-2, four PR insertions located after amino acids 8 (PR-9), 47 (PR-48), 54 (PR-55), and 99 (PR-100) had the greatest impact on infection. For PRRSV-1, insertions after amino acids 57 (PR-58) and 99 (PR-100) were critical. Computer simulations based on the crystal structure of SRCR5 showed that the mutations that affected infection localized to a similar region on the surface of the 3-D structure. Specifically, we found two surface patches that are essential for PRRSV infection. PR-58 and PR-55, which were separated by only three amino acids, had reciprocal effects on PRRSV-1 and PRRSV-2. Substitution of Glu-58 with Lys-58 reduced PRRSV-1 infection without affecting PRRSV-2, which partially explains the resistance to PRRSV-1 caused by the SRCR5 replacement with the homolog human SRCR8 previously observed. Finally, resistance to infection was observed following the disruption of any of the four conserved disulfide bonds within SRCR5. In summary, the results confirm that there are distinct differences between PRRSV-1 and PRRSV-2 on recognition of CD163; however, all mutations that affect infection locate on a similar region on the same face of SRCR5.

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

RATIONALE

There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especially in a hospital setting, remains less clear.

OBJECTIVES

We aimed to analyze surface swabs for SARS-CoV-2 RNA and infectivity, and to determine their suitability for sequence analysis.

METHODS

Samples were collected during two waves of COVID-19 at the University of California, Davis Medical Center, in COVID-19 patient serving and staff congregation areas. qRT-PCR positive samples were investigated in Vero cell cultures for cytopathic effects and phylogenetically assessed by whole genome sequencing.

MEASUREMENTS AND MAIN RESULTS

Improved cleaning and patient management practices between April and August 2020 were associated with a substantial reduction of SARS-CoV-2 qRT-PCR positivity (from 11% to 2%) in hospital surface samples. Even though we recovered near-complete genome sequences in some, none of the positive samples (11 of 224 total) caused cytopathic effects in cultured cells suggesting this nucleic acid was either not associated with intact virions, or they were present in insufficient numbers for infectivity. Phylogenetic analysis suggested that the SARS-CoV-2 genomes of the positive samples were derived from hospitalized patients. Genomic sequences isolated from qRT-PCR negative samples indicate a superior sensitivity of viral detection by sequencing.

CONCLUSIONS

This study confirms the low likelihood that SARS-CoV-2 contamination on hospital surfaces contains infectious virus, disputing the importance of fomites in COVID-19 transmission. Ours is the first report on recovering near-complete SARS-CoV-2 genome sequences directly from environmental surface swabs.

Mitigating the risk of African swine fever virus in feed with anti-viral chemical additives

African swine fever (ASF) is currently considered the most significant global threat to pork production worldwide. Disease caused by the ASF virus (ASFV) results in high case fatality of pigs. Importantly, ASF is a trade-limiting disease with substantial implications on both global pork and agricultural feed commodities. ASFV is transmissible through natural consumption of contaminated swine feed and is broadly stable across a wide range of commonly imported feed ingredients and conditions. The objective of the current study was to investigate the efficacy of medium-chain fatty acid and formaldehyde-based feed additives in inactivating ASFV. Feed additives were tested in cell culture and in feed ingredients under a transoceanic shipment model. Both chemical additives reduced ASFV infectivity in a dose-dependent manner. This study provides evidence that chemical feed additives may potentially serve as mitigants for reducing the risk of ASFV introduction and transmission through feed.

Stability of classical swine fever virus and pseudorabies virus in animal feed ingredients exposed to transpacific shipping conditions

Classical swine fever virus (CSFV) and pseudorabies virus (PRV) are two of the most significant trade-limiting pathogens affecting swine worldwide. Both viruses are endemic to China where millions of kilograms of feed ingredients are manufactured and subsequently imported into the United States. Although stability and oral transmission of both viruses through contaminated pork products has been demonstrated as a risk factor for transboundary spread, stability in animal feed ingredients had yet to be investigated. The objective of this study was to determine the survival of CSFV and variant PRV in 12 animal feeds and ingredients exposed to environmental conditions simulating a 37-day transpacific shipment. Virus was detected by PCR, virus isolation and nursery pig bioassay. CSFV and PRV nucleic acids were stable throughout the 37-day period in all feed matrices. Infectious CSFV was detected in two ingredients (conventional soybean meal and pork sausage casings) at 37 days post-contamination, whereas infectious PRV was detected in nine ingredients (conventional and organic soybean meal, lysine, choline, vitamin D, moist cat and dog food, dry dog food and pork sausage casings). This study demonstrates the relative stability of CSFV and PRV in different feed ingredients under shipment conditions and provides evidence that feed ingredients may represent important risk factors for the transboundary spread of these viruses.

Half-Life of African Swine Fever Virus in Shipped Feed

African swine fever virus is transmissible through animal consumption of contaminated feed. To determine virus survival during transoceanic shipping, we calculated the half-life of the virus in 9 feed ingredients exposed to 30-day shipment conditions. Half-lives ranged from 9.6 to 14.2 days, indicating that the feed matrix environment promotes virus stability.

Infectious Dose of African Swine Fever Virus When Consumed Naturally in Liquid or Feed

African swine fever virus (ASFV) is a contagious, rapidly spreading, transboundary animal disease and a major threat to pork production globally. Although plant-based feed has been identified as a potential route for virus introduction onto swine farms, little is known about the risks for ASFV transmission in feed. We aimed to determine the minimum and median infectious doses of the Georgia 2007 strain of ASFV through oral exposure during natural drinking and feeding behaviors. The minimum infectious dose of ASFV in liquid was 10⁰ 50% tissue culture infectious dose (TCID₅₀), compared with 10⁴ TCID₅₀ in feed. The median infectious dose was 10^1.0 TCID₅₀ for liquid and 10^6.8 TCID₅₀ for feed. Our findings demonstrate that ASFV Georgia 2007 can easily be transmitted orally, although higher doses are required for infection in plant-based feed. These data provide important information that can be incorporated into risk models for ASFV transmission.

Challenges for Porcine Reproductive and Respiratory Syndrome (PRRS) Vaccine Design: Reviewing Virus Glycoprotein Interactions with CD163 and Targets of Virus Neutralization

One of the main participants associated with the onset and maintenance of the porcine respiratory disease complex (PRDC) syndrome is porcine reproductive and respiratory syndrome virus (PRRSV), an RNA virus that has plagued the swine industry for 30 years. The development of effective PRRS vaccines, which deviate from live virus designs, would be an important step towards the control of PRRS. Potential vaccine antigens are found in the five surface proteins of the virus, which form covalent and multiple noncovalent interactions and possess hypervariable epitopes. Consequences of this complex surface structure include antigenic variability and escape from immunity, thus presenting challenges in the development of new vaccines capable of generating broadly sterilizing immunity. One potential vaccine target is the induction of antibody that disrupts the interaction between the macrophage CD163 receptor and the GP2, GP3, and GP4 heterotrimer that protrudes from the surface of the virion. Studies to understand this interaction by mapping mutations that appear following the escape of virus from neutralizing antibody identify the ectodomain regions of GP5 and M as important immune sites. As a target for antibody, GP5 possesses a conserved epitope flanked by N-glycosylation sites and hypervariable regions, a pattern of conserved epitopes shared by other viruses. Resolving this apparent conundrum is needed to advance PRRS vaccine development.

Correction: Survival of viral pathogens in animal feed ingredients under transboundary shipping models

[This corrects the article DOI: 10.1371/journal.pone.0194509.].