Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis

Ubiquitous influenza A virus in Chilean swine before the H1N1pdm09 introduction

Influenza A virus (IAV) was a neglected swine pathogen in South America before the 2009 H1N1 pandemic (A(H1N1)pdm2009). The A(H1N1)pdm2009 strain has widely spread among the Chilean swine population and co-circulates with endemic H1N2 and H3N2 viruses. The presence of IAV as a swine pathogen in Chilean swine before the 2009 pandemic is unknown. To understand the IAV in swine prior to 2009, aY retrospective study of samples from pigs affected with respiratory diseases was conducted. Ninety formalin-fixed and paraffin-embedded lung tissues belonging to 21 intensive pig production companies located in five different administrative regions of Chile, collected between 2005 and 2008, were evaluated. The tissues were tested by immunohistochemistry (IHC), identifying that 9 out of 21 farms (42.8%) and 31 out of 90 (34.4%) samples were IAV positive. Only three out of the 31 IHC-positive samples were positive upon RNA extraction and rtRT-PCR analysis. Partial nucleotide sequences were obtained from one sample and characterized as an H3N2 subtype closely related to a human seasonal H3N2 IAVs that circulated globally in the mid-90s. These results indicate that IAV was circulating in swine before 2009 and highlight the value of conducting retrospective studies through genomic strategies to analyse historical samples.

A simple and rapid approach for human herpesvirus type 8 subtype characterization using single base extension

Sequence analysis of the ORFK1 of human herpesvirus type 8 (HHV-8) allows the identification of six major subtypes (A-F), which are related to human migrations and the clinical progression of Kaposi's sarcoma. Sequencing and subsequent phylogenetic analysis of ORFK1 is considered to be the most reliable method for HHV-8 genotyping. However, it exhibits challenges and limitations. Herein, we designed and validated a single base extension (SBE) protocol for characterization of HHV-8 ORFK1 subtypes. A nested polymerase chain reaction (PCR) protocol was carried out to amplify a small 294-bp PCR product encompassing four single nucleotide polymorphisms at positions 360, 406, 465 and 527 of the HHV-8 genome. Finally, a multiplex SBE technique was developed and validated in 20 samples previously genotyped by phylogenetic analysis. The patterns obtained in this reaction could successfully discriminate between ORFK1 subtypes. The typing results obtained completely matched with those of the 'gold standard' method in all analysed samples. This method can reliably identify HHV-8 subtypes A, B and C, which are the most prevalent ones worldwide, and the remaining subtypes (D, E and F). SBE can be useful as an efficient, rapid and low-cost screening method for viral genotyping in a single tube, particularly samples with low-quality DNA, and with easy data interpretation.

SARS-CoV-2 detection in formalin-fixed paraffin-embedded tissue specimens from surgical resection of tongue squamous cell carcinoma

In the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, pathologists can be exposed to infection handling surgical specimens. Guidelines related to safety procedures in the laboratory have been released. However, there is a lack of studies performed on biopsy and surgical resection specimens. Here we report the detection of SARS-CoV-2 in formalin-fixed paraffin-embedded samples from surgical resection of tongue squamous cell carcinoma of a patient who developed COVID-19 postsurgery. RNA of SARS-CoV-2 strain was detected in the tumour and the normal submandibular gland samples using real-time PCR-based assay. No viral RNA was found in metastatic and reactive lymph nodes. We demonstrated that SARS-CoV-2 RNA can be detected in routine histopathological samples even before COVID-19 disease development. These findings may give important information on the possible sites of infection or virus reservoir, and highlight the necessity of proper handling and fixation before sample processing.

Retrospective phylogenetic analyses of formalin-fixed paraffin-embedded samples from the 2011 Rift Valley fever outbreak in South Africa, through sequencing of targeted regions

The last major Rift Valley fever outbreak in South Africa was between 2008 and 2011. Viruses isolated between 2008 and 2010 were phylogenetically assigned to Lineage C, Lineage K and the novel lineage H. The 2011 outbreaks occurred primarily in the Eastern, Western and Northern Cape provinces, with no sequence data or phylogenetic relationship published. Samples from these outbreaks were submitted to the Faculty of Veterinary Sciences, University of Pretoria, for immunohistochemical confirmation of Rift Valley fever phlebovirus presence. These samples were formalin-fixed and paraffin-embedded (FFPE) and stored at the Pathology section for several years. This study describes a modified extraction method used to obtain RNA from the FFPE samples, as well as the primer combinations used to phylogenetically classify them as belonging to the novel lineage H.

Optimization of RNA extraction protocol for long-term archived formalin-fixed paraffin-embedded tissues of horses

A suitable RNA extraction protocol was established to gain high quality RNA from formalin-fixed paraffin-embedded tissues to perform reliable molecular assays either applicable for using FFPE tissue archives or tissues with harsh formalin-fixation. Eighteen FFPE samples from the central nervous system of horses, stored up to 11 years, were used as archive cases. To test the influence of the fixation period, brain, liver, kidney, and skeletal muscle tissue fragments from another horse, were treated either with water or tris-acetate-EDTA buffer after fixation under different timepoints with 10% unbuffered formalin. Two deparaffinization methods and three proteinase K-based lysis step were tested and translated into three protocols. After detailed statistical analysis it was determined that a longer period and increase in volume of proteinase K incubation provide higher yields and purity of RNA (P < 0.01) of archived samples. Alongside, amplification of equid-housekeeping gene up to 298 bp was successful with the protocol adaptations. For different formalin-fixation timepoints, it was demonstrated that the right choice for treatment and formalin-fixation period is organ-related (P ≤ 0.05). Essentially, little alterations to pre-existing extraction protocols unwound the RNA of up to 11-year-old samples, enabling the use of FFPE tissue archives or e.g. harshly fixed material needed in infection research under high biosafety levels for a variety of molecular analysis.

Enhanced phylogenetic resolution of Newcastle disease outbreaks using complete viral genome sequences from formalin-fixed paraffin-embedded tissue samples

Highly virulent Newcastle disease virus (NDV) causes Newcastle disease (ND), which is a threat to poultry production worldwide. Effective disease management requires approaches to accurately determine sources of infection, which involves tracking of closely related viruses. Next-generation sequencing (NGS) has emerged as a research tool for thorough genetic characterization of infectious organisms. Previously formalin-fixed paraffin-embedded (FFPE) tissues have been used to conduct retrospective epidemiological studies of related but genetically distinct viruses. However, this study extends the applicability of NGS for complete genome analysis of viruses from FFPE tissues to track the evolution of closely related viruses. Total RNA was obtained from FFPE spleens, lungs, brains, and small intestines of chickens in 11 poultry flocks during disease outbreaks in Pakistan. The RNA was randomly sequenced on an Illumina MiSeq instrument and the raw data were analyzed using a custom data analysis pipeline that includes de novo assembly. Genomes of virulent NDV were detected in 10/11 birds: eight nearly complete (> 95% coverage of concatenated coding sequence) and two partial genomes. Phylogeny of the NDV complete genome coding sequences was compared to current methods of analysis based on the full and partial fusion genes and determined that the approach provided a better phylogenetic resolution. Two distinct lineages of sub-genotype VIIi NDV were identified to be simultaneously circulating in Pakistani poultry. Non-targeted NGS of total RNA from FFPE tissues coupled with de novo assembly provided a reliable, safe, and affordable method to conduct epidemiological and evolutionary studies to facilitate management of ND in Pakistan.

Isolation of Viral-Infected Brain Regions for miRNA Profiling from Formalin-Fixed Paraffin-Embedded Tissues by Laser Capture Microdissection

Brain is a highly heterogeneous organ with numerous layers of specialized cells. Viral infection further adds complexity to downstream analysis because only a subpopulation of the brain is infected. In these instances, molecular changes that occur within infected cells are not truly reflected when whole tissue is used for downstream analysis. Laser capture microdissection (LCM) is a tool that allows for the selection and isolation of cells or regions of interest as determined by microscopic observation. It provides a platform for visually selecting the tissue that truly represents the material one wishes to study, such as viral infected cells. Formalin-fixed paraffin-embedded viral-infected tissue allows for safe handling and processing by LCM. Here, we describe a method whereby viral-infected regions of the brain were specifically isolated by LCM from the rest of the FFPE tissue. The isolated regions were then used to extract RNA for microRNA profiling. This approach can be applied to study microRNA changes from any viral infection in any given tissue.