The tidepool shrimp, Palaemon ritteri Holmes, constitutes a novel host to the white spot syndrome virus

Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa

White spot syndrome virus is a highly contagious pathogen affecting shrimp farming worldwide. The host range of this virus is primarily limited to crustaceans, such as shrimps, crabs, prawns, crayfish, and lobsters; however, several species of non-crustaceans, including aquatic insects, piscivorous birds, and molluscs may serve as the vectors for ecological dissemination. The present study was aimed at studying the faecal virome of domestic chickens (Gallus gallus domesticus) in Makhanda, Eastern Cape, South Africa. The cloacal swab specimens (n = 35) were collected from domestic chickens in December 2022. The cloacal swab specimens were pooled-each pool containing five cloacal swabs-for metagenomic analysis using a sequence-independent single-primer amplification protocol, followed by Nanopore MinION sequencing. While the metagenomic sequencing generated several contigs aligning with reference genomes of animal viruses, one striking observation was the presence of a White spot syndrome virus genome in one pool of cloacal swab specimens. The generated White spot syndrome virus genome was 273,795 bp in size with 88.5% genome coverage and shared 99.94% nucleotide sequence identity with a reference genome reported in China during 2018 (GenBank accession: NC_003225.3). The Neighbour-Joining tree grouped South African White spot syndrome virus genome with other White spot syndrome virus genomes reported from South East Asia. To our knowledge, this is the first report of a White spot syndrome virus genome generated from domestic chickens. The significance of White spot syndrome virus infection in domestic chickens is yet to be determined.

Vectors and reservoir hosts of covert mortality nodavirus (CMNV) in shrimp ponds

Covert mortality nodavirus (CMNV) is the pathogen that has been identified as the cause of viral covert mortality disease (VCMD) in marine and brackish water shrimp. Recent outbreaks of this disease have resulted, and continue to result, in substantial production and economic losses to shrimp aquaculture producers in China and elsewhere. To explore potential vectors and reservoir hosts of CMNV, we collected fifteen species of invertebrates from shrimp ponds affected by VCMD. Samples were tested through the use of: reverse transcription loop-mediated isothermal amplification (RT-LAMP), reverse transcription nested PCR (RT-nPCR) followed by gene sequencing, histopathology, and in situ RNA hybridization (ISH). The results of RT-LAMP and RT-nPCR assay indicated that CMNV positive samples were identified in eleven species including brine shrimp Artemia sinica, a barnacle Balanus sp., the rotifer Brachionus urceus, the amphipod Corophium sinense Zhang, the Pacific oyster Crassostrea gigas, a hermit crab Diogenes edwardsii, the common clam Meretrix lusoria, a ghost crab Ocypode cordimundus, the hyperiid amphipod Parathemisto gaudichaudi, a fiddler crab Tubuca arcuata, and an unidentified gammarid amphipod. The alignment of CMNV RNA-dependent RNA polymerase gene sequences from eight of the species demonstrated high identities (97-100% in nucleotide sequence) with that from the original CMNV isolates of Penaeus vannamei, which suggests that these species could either be infected with, or acting as mechanical vectors of, CMNV. The CMNV infection in C. sinense, D. edwardsii, O. cordimanus Zhang, P. gaudichalldi, and T. arcuata results, to varying degrees, in vacuolation and necrosis of targeted tissues, as was verified by ISH. The infection of CMNV in these five species suggests that they might act as reservoir hosts of CMNV. The results indicate that the common species of invertebrates inhabiting shrimp ponds may constitute biological risk factors for CMNV outbreaks.