Retrospective Multi-Locus Sequence Analysis of African Swine Fever Viruses by "PACT" Confirms Co-Circulation of Multiple Outbreak Strains in Uganda

African swine fever (ASF) is a haemorrhagic fever of swine that severely constrains pig production, globally. In Uganda, at least 388 outbreaks of ASF were documented from 2001 to 2012. We undertook a retrospective serological and molecular survey of ASF virus (ASFV) using banked samples collected from seven districts (Pallisa, Lira, Abim, Nebbi, Kabarole, Kibaale, and Mukono) of Uganda. Six assays (ELISA for antibody detection, diagnostic p72 gene PCR and genomic amplification, and sequencing of four gene regions (p72 [P], p54 [A], CVR of the 9RL-ORF [C], and TK [T]), hereinafter referred to as P-A-C-T (PACT)) were evaluated. Antibodies to ASFV were detected in the Abim district (6/25; 24.0%), and the remainder of the serum samples were negative (187/193; 96.9%). For the tissue samples, ASFV detection by assay was 8.47% for P, 6.78% for A, 8.47% for C, and 16.95% for T. The diagnostic PCR (p72 gene) detected seven positive animals from four districts, whereas the TK assay detected ten positives from all seven districts. In addition to the superior detection capability of TK, two virus variants were discernible, whereas CVR recovered three variants, and p72 and p54 sequencing each identified a single variant belonging to genotype IX. Our results indicate that dependence on serology alone underestimates ASF positivity in any infected region, that multi-locus sequence analysis provides better estimates of outbreak strain diversity, and that the TK assay is superior to the WOAH-prescribed conventional p72 diagnostic PCR, and warrants further investigation.

A Rapid Nucleic Acid Visualization Assay for Infectious Bovine Rhinotracheitis Virus That Targets the TK Gene

Infectious bovine rhinotracheitis virus (IBRV) can cause various degrees of symptoms in the respiratory system, reproductive system, and whole body of cattle. It also can lead to persistent and latent infection in cattle, posing a challenge to timely control of infectious bovine rhinotracheitis (IBR) in farms and causing large financial losses in the global cattle industry. Therefore, the goal of this study was to establish a rapid, simple, and accurate method that can detect IBRV in order to facilitate the control and eradication of IBR in cattle. We combined recombinant polymerase amplification (RPA) with a closed vertical flow visualization strip (VF) and established an RPA-VF assay that targets the thymidine kinase (TK) gene to rapidly detect IBRV. This method (reaction at 42°C for 25 min) was able to detect a minimum of 3.8 × 101 copies/μL of positive plasmid and 1.09 × 101 50% tissue culture infective dose (TCID50) of the IBRV. This assay has high specificity for IBRV and does not cross-react with other respiratory pathogens in cattle. The concordance between the RPA-VF assay and the gold standard was 100%. In addition, this assay was also suitable for the detection of DNA from clinical samples extracted by a simple method (heating at 95°C for 5 min), which can achieve the rapid detection of clinical samples in the field. Overall, the present sensitivity, specificity, and clinical applicability assessments indicated that the RPA-VF assay we developed can be utilized as a quick and accurate on-site test for IBRV detection in farms. IMPORTANCE IBRV causes different degrees of clinical symptoms in cattle and poses a great threat to the cattle industry. The infection is persistent and latent, and the elimination of IBRV in infected herds is difficult. A rapid, simple, and accurate method to detect IBRV is therefore vital to control and eradicate IBR. Combining RPA with an VF, we established an RPA-VF assay for the rapid detection of IBRV, which can complete the test of clinical samples in 35 min. The assay shows good sensitivity, specificity, and clinical applicability and can be used as an on-site test for IBRV in farms.

Detection of Carp pox virus (CyHV-1) from koi (Cyprinus carpio L.) in Iran; clinico-pathological and molecular characterization

Cyprinid herpesvirus 1 (CyHV-1) is the causative agent of carp pox characterized by epidermal papillomas in common carp and other cyprinids. In this study, we identified CyHV-1 in koi (Cyprinus carpio) from Iran in 2017 and 2019, showing clinical signs of the carp pox disease. Histopathology showed severe epidermal hyperplasia and the absence of club and goblet cells. Degenerative changes, including spongiosis and single-cell necrosis, were also observed. Keratinocyte dysplasia and a moderate lymphocytic infiltration were observed within the epidermis. PCR of the extracted DNA from skin lesions of affected koi from both outbreaks showed CyHV-1 specific TK amplicons, with high sequence identity (above 99%) among themselves and with other CyHV-1 isolates belong to Cluster I, as well as show 97% similarity to Cluster II isolates. To the best of our knowledge, this is the first report of Carp pox disease (CyHV-1) of koi in Iran and the Middle East.

Research Note: Rapid detection of avian infectious laryngotracheitis virus with real-time fluorescence-based recombinase-aided amplification

In this study, specific primers and fluorescent probes were designed to target the thymidine kinase (TK) gene sequence of avian infectious laryngotracheitis virus (ILTV). Through specificity and sensitivity tests, a real-time fluorescence-based recombinase-aided amplification (RF-RAA) method for detecting ILTV was established. The results showed that the method was specific and could be used to accurately detect ILTV, and there was no cross-reaction with Newcastle disease virus (NDV), avian influenza virus (AIV), or infectious bronchitis virus (IBV). Real-time fluorescence-based recombinase-aided amplification had high sensitivity, and the lowest detectable limit (LDL) for ILTV could reach 10 copies/μL, 1,000 times more sensitive than conventional PCR (10⁴ copies/μL), to rival that of real-time fluorescence-based quantitative PCR (RFQ-PCR) (10 copies/μL). This method and RFQ-PCR were used to detect 96 samples of chicken throat swabs with ILT initially diagnosed in clinic from the north of China, and the coincidence rate of the 2 methods was 100%. The RF-RAA reaction required only 20-30 minutes to completing, and its sensitivity was much higher than that of conventional PCR. Real-time fluorescence-based recombinase-aided amplification is similar to RFQ-PCR and has the advantages of specificity, sensitivity, and high efficiency, so it is suitable for early clinical detection and epidemiological investigation of ILTV.

First detection of koi herpesvirus from koi, Cyprinus carpio L. experiencing mass mortalities in Iran: clinical, histopathological and molecular study

Koi herpesvirus (KHV) is the aetiological agent of an emerging disease (KHVD) associated with mass mortalities in koi and common carp and reported from at least 30 countries. We report the first detection of KHV from koi in Iran using clinical, histopathological and molecular studies. KHV-infected fish showed reduced swimming activity, sunken eyes and increased mucus production on skin and fins. On post-mortem examination, gill necrosis was observed in the majority of fish. Histopathologically, the gill showed diffuse necrosis of the branchial epithelial cells. Margination of chromatin was detected in gills, kidney, heart, spleen, intestine and brain. In addition, sequence analyses of the TK gene, ORF 136 and marker I and II, demonstrates that Iranian KHV isolates were identical and classified as variant A1 of TUSMT1 (J strain) and displayed the I(++) II(+) allele of this Asian genotype.