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Virus Research 324 (2023) 199026

Contents lists available at ScienceDirect

Virus Research

journal homepage: www.elsevier.com/locate/virusres

A novel virus in the amily Marnaviridae as a potential pathogen o Penaeus


vannamei glass post-larvae disease
Ailan Xu b, 1, Shan Xu a, 1, Qihang Tu a, 1, Huanao Qiao a, 1, Wei Lin a, Jing Li a, Yugan He a,
Tie Xie a, Lingting Pan c, Qiang Pan d, Yunwei Zhao b, *, Xin Su a, *, Yigang Tong a, *
a
College o Lie Science and Technology, Beijing University o Chemical Technology, No. 15 Beisanhuan East Road, Chaoyang, Beijing 100089, China
b
The First Aliated Hospital o Jiamusi University, 348 Dexiang Street, Jiamusi, Heilongjiang 154003, China
c
Ningbo University, Ningbo 315211, China
d
Qingdao Nuoanbaite Biotechnology Co., China

A R T I C L E I N F O A B S T R A C T

Keywords: As an aquatic animal o great commercial relevance, Penaeus vannamei is currently the dominant species o
Marnaviridae cultured shrimp in China and many other countries worldwide. In recent years, the outbreak o glass post-larvae
P. vannamei disease (GPD), which accounts or more than 90% o the mortality o shrimp seedlings in serious cases, in many
Baishivirus
regions o China has caused signicant losses and threatened the sustainability o the aquaculture industry and
Genome analysis
Phylogenetic analysis
the economy. It is extremely urgent to determine the inectious agent o GPD in P. vannamei. In this work, we
perormed metagenomic sequencing o glass post-larvae collected rom diseased prawns in Tangshan Hebei,
where GPD broke out recently. An evolutionary tree was constructed by MEGA 7 to understand the evolutionary
history and relationship o the pathogen genome. A novel virus in the amily Marnaviridae was rst identied in
P. vannamei suering rom GPD, and we tentatively named this virus Baishivirus (GenBank: ON550424). The
identied pathogen was validated according to Koch’s rule with a pathogenic challenge assay and reverse
transcription-polymerase chain reaction. There was only 8% query coverage with 64.96% identity in the
Baishivirus genome when compared with its most closely related genome sequence o Wenzhou picorna-like virus
21 reported in 2016. Baishivirus genomic RNA is 9.895 kb in length and encodes three potential open reading
rames (ORFs). The identication o Baishivirus in P. vannamei enriches the amily Marnaviridae and potentially
provides a new candidate to study and prevent GPD in the aquaculture industry.

1. Introduction o production, which are mainly induced by viral and bacterial in-
ections. Strategies such as the application o antibacterial agents can be
P. vannamei arming is an important part o aquaculture, which used to resist bacterial inection (Ninawe and Selvin, 2009). Viral in-
greatly contributes to the development o the global economy. The ections usually cause immense losses to shrimp arming, which is
major producers include China, India, Ecuador, Indonesia and Vietnam drawing increasing attention rom researchers (Karunasagar and Aba-
(Fig. 1A) (https://www.ao.org/ishery/zh/culturedspecies/litopena bouch, 2012).Many DNA viruses have serious eects on shrimp, such as
eus_vannamei/en). In 2020, global P. vannamei production was esti- white spot syndrome virus (WSSV), monodon-type baculovirus (MBV),
mated at 5.82 million tons, and the annual growth rate declined by inectious hypodermal and hematopoietic necrosis virus (IHHNV),
2.15%. Disease in P. vannamei is one o the main reasons or the decline hepatopancreatic parvovirus (HPV), shrimp hemocyte iridescent virus

Abbreviations: GPD, glass post-larvae disease; WSSV, white spot syndrome virus; MBV, Monodon-type baculovirus; IHHNV, inectious hypodermal and he-
matopoietic necrosis virus; HPV, hepatopancreatic parvovirus; SHIV, shrimp hemocyte iridescent virus; WSSV-AU, Australian WSSV; IMNV, inectious myonecrosis
virus; PvNV, Penaeus vannamei nodavirus; MrNV, Macrobrachium rosenbergii nodavirus; CMNV, covert mortality nodavirus; LSNV, Laem-Singh virus; TSV, Taura
syndrome virus; mNGS, metagenomic next-generation sequencing; AHPND, acute hepatopancreatic necrosis disease; EHP, Enterocytozoon hepatopenaei; VP, viral
protein; UTRs, untranslated regions.
* Corresponding authors.
E-mail addresses: 1054237726@qq.com (Y. Zhao), xinsu@mail.buct.edu.cn (X. Su), tongyigang@mail.buct.edu.cn (Y. Tong).
1
These authors contributed equally to this work.

https://doi.org/10.1016/j.virusres.2022.199026
Received 4 August 2022; Received in revised orm 13 December 2022; Accepted 14 December 2022
Available online 15 December 2022
0168-1702/© 2022 Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
A. Xu et al. Virus Research 324 (2023) 199026

(SHIV), Taura syndrome virus, Spawner-isolated mortality virus (SMV), Once individual shrimp seedlings have GPD symptoms, almost all the
lymphoid parvo-like virus (LPV), Baculovirus penaei (BP) and baculovi- other shrimp seedlings in the same pond may develop GPD in approxi-
rus midgut gland necrosis virus (BMNV) (Santos et al., 2020; Zhu et al., mately 24 h (Zou et al., 2020). Recently, GPD has inected numerous
2019; Weerachatyanukul et al., 2021; Yan et al., 2016; Dhar et al., 2004; P. vannamei in Hebei Province, northern China, resulting in mass mor-
Phuthaworn et al., 2016; Qiu et al., 2017; Dhar et al., 2004; Owens et al., tality o shrimp and large economic losses. Zou et al. successully iso-
2003; Owens, 1991; Overstreet et al., 2010; Momoyama, 2009). lated a strain o Vibrio parahaemolyticus, which was shown to be highly
RNA viruses in shrimp aquaculture mainly include inectious myo- pathogenic and associated with GPD (Zou et al., 2020). However, the
necrosis virus (IMNV), Penaeus vannamei nodavirus (PvNV), Macro- V. parahaemolyticus identied in our work was not the cause o GPD.
brachium rosenbergii nodavirus (MrNV), covert mortality nodavirus Herein, we identied a novel virus in the amily Marnaviridae as a po-
(CMNV), Laem-Singh virus (LSNV), yellow head virus (YHV), gill asso- tential pathogen o GPD, and we named it Baishivirus. This work not only
ciated virus (GAV), and Taura syndrome virus (TSV) (Lightner, 2011; uncovers a novel member o the Marnaviridae amily but also provides
Naim et al., 2014; Ninawe and Selvin, 2009; Senapin et al., 2013; new insight into GPD research in the P. vannamei arming industry.
Wertheim et al., 2009). Both IMNV and PvNV can inect P. vannamei and
cause muscle necrosis (Flegel, 2012). CMNV, identied by Zhang’s 2. Materials and methods
team, is associated with a recessive atal disease in prawns and has
caused severe losses in China and some South Asian countries (Zhang 2.1. Sample collection and processing
et al., 2014). TSV was rst discovered in P. vannamei in 1992 and is
responsible or shrimp Taura syndrome and has impacted shrimp The shrimp seedlings (P7-P8 stages) used in the experiment were
aquaculture or decades (Cruz-Flores et al., 2021). The identication collected rom breeding arms (Fig. 1B) in Tangshan city, Hebei Prov-
and characterization o pathogens in the shrimp culture industry is ince, where 80% o the shrimp seedlings showed GPD symptoms. Ater
critical or reducing economic losses by preventing and controlling the samples were transported to the laboratory on dry ice, they were
shrimp disease. thawed and washed three times in 70% ethanol and then washed with
Glass post-larvae disease (GPD) is highly inectious and pathogenic. sterile deionized water to remove environmental contaminants.

Fig. 1. Distribution o major countries producing P. vannamei in the world and the sample-gathering locations in this study. (A) Major countries producing
P. vannamei in the world. The total global production o P. vannamei in 2020 was approximately 5.82 million tons. (The major producers o P. vannamei in 2020 rom
high to low are China, India, Ecuador, Indonesia and Vietnam). (B) Location where the P. vannamei samples were collected. (Guangdong and Hainan provinces are
marked in yellow, Hebei province is marked in purple, and Tangshan city is marked in red.)

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A. Xu et al. Virus Research 324 (2023) 199026

Approximately 1 g o shrimp larvae was ground in a rozen grinder at 70 10 sec and 40 cycles o 95◦ C or 5 sec, 60◦ C or 34 sec. Pathogens were
Hz or 60 s. The homogenate was centriuged at 12,000 × g or 10 min at urther veried using a highly specic and sensitive kit designed by our
4◦ C. The supernatant o each sample was ltered with a 0.45 μm Pellicon laboratory, which notably combines nucleic acid extraction and visual
II lter (Millipore, Billerica, MA, USA). The ltrate was stored at -80◦ C LAMP (loop-mediated isothermal amplication) (Tong, et al., 2021).
beore nucleic acid extraction and challenge testing.
3. Results
2.2. Nucleic acid extraction and library preparation
3.1. Clinical symptoms
Highly puried viral nucleic acids were extracted rom the ltered
supernatant by using a High Pure Viral Nucleic Acid Kit (Roche, In April 2021, GPD broke out suddenly in P. vannamei arms in
Switzerland) according to the instructions provided by the manuac- Tangshan, Hebei Province. The early clinical signs o GPD include not
turer. Ater quantication with a Qubit RNA Assay Kit (Thermo Fisher eating, poor motivation, sluggish action, slow response to external
Scientic, Inc.), extracted RNA was reverse transcribed into cDNA using stimulation, pale-yellow shrimp gills, and color change o liver pancre-
Hiair® II 1st Strand cDNA Synthesis SuperMix or qPCR (gDNA digester atic tissue rom ull brown to light brown. Approximately 24 h-48 h
plus) (Shanghai Yisheng Biotechnology Co., LTD.). A Qubit dsDNA HS later, shrimp developed more symptoms, such as empty jejunum and
Assay Kit (Thermo Fisher Scientic, Inc.) was used to determine the stomach, swollen and loose gill laments, a necrotic and pale hepato-
cDNA content on a Qubit 4.0 fuorescence photometer (Thermo Fisher pancreas outline, and a thin and turbid area rom the thymus to the
Scientic, Inc.). Libraries were prepared using the NEBNext® Ultra II abdomen. The body o dying shrimp becomes white and transparent,
Directional RNA Library Prep Kit or Illumina® (NEB # E7760S / L), and with muscle atrophy, gill tissue brittleness and erosion, hepatopancreas
the quality o the libraries was analyzed on an Agilent 2100 Bioanalyzer necrosis and paleness, glassy degeneration o the jejunum and an empty
(Agilent, Santa Clara, CA, USA) and LabChip Touch. The library was stomach (Fig. 2).
subjected to metagenomic next-generation sequencing (mNGS) on the
Illumina NovaSeq 6000 (Illumina, San Diego, CA, USA) platorm (150 3.2. Discovery o Baishivirus
bp paired-end).
Ater the shrimp with GPD were ground, the supernatant was
2.3. Bioinormatics analysis collected or metagenomic sequencing to identiy potential pathogens.
According to Blastx, 111 contigs related to Wenzhou Picorna-like virus
The low-quality reads were removed to obtain clean data. Clean data 21, which was the most abundant category, were obtained. Ater denovo
were compared to the nonredundant protein database (nr) and nonre- assembly, a novel picorna-like virus genomic sequence o 9859 bp was
dundant nucleotide database (nt) using the NCBI blastn and blastx obtained, which was validated by high coverage o the whole genome
programs. Clean data were de novo assembled using SPAdes v3.13.0 to sequence (Fig. S1). There was only 64.96% identity over 8% query cover
obtain whole genome sequences. The viral sequence was annotated compared to its closest Wenzhou picorna-like virus 21 (GenBank:
using the online RAST server (https://rast.nmpdr.org/rast.cgi), and the KX884351.1) reported in 2016 (Shi et al., 2016), and we named the
possible open reading rames (ORFs) were urther conrmed using newly identied pathogen Baishivirus. Three open reading rames
blastx (http://www.ncbi.nlm.nih.gov/BLAST/). The MOTIF Search tool (ORFs) were predicted in Baishivirus: ORF1, ORF2, and ORF3, encoding
(https://www.genome.jp/tools/moti/) was used to analyze the protein proteins with lengths o 76 aa, 1995 aa, and 877 aa, respectively. In
motis o the virus. To obtain genomic abundance, a map method was addition to Baishivirus, three other pathogens were discovered by met-
used in CLC Genomics Workbench 12.0.1 (Qiagen, Germany). The agenomic sequencing: pico1 (Wenzhou shrimp virus 8), VP (Vibrio par-
protein-based amino acid evolutionary tree were constructed using the ahaemolyticus) and VC (Vibrio campbellii). We separated primary GPD
MEGA 7 program (Kumar et al., 2016). Tree topology was assessed by samples into the supernatant (virus in theory) and precipitate (bacte-
bootstrap analysis using the neighbor-joining method with the deault rium in theory) and detected these pathogens by RT‒PCR. Pico1 existed
parameters o 1,000 replicates. in both the experimental group (diseased shrimp) and the control group
(healthy shrimp), indicating that pico1 was not the cause o the disease
2.4. Challenge test (Fig. 3).
Challenge experiments were perormed to satisy Koch’s postulates.
Healthy P. vannamei seedlings were purchased rom a shrimp arm in Ater we challenged healthy shrimp with the supernatant, prawns in the
Cangzhou, Hebei Province, and were cultured or 2 days beore being experimental group showed symptoms o GPD at 24-48 h, and all prawns
used in the challenge test. Sixty P. vannamei were divided into two died on the ourth day o the challenge experiment, while prawns in the
experimental groups and one control group, each with 20 prawns. control group were normal. The Ct values o Baishivirus in the two
Prawns in the experimental groups were immersed in a mixture o 3 mL original GPD samples S1’ and S2’ were 25.66 and 24.49, respectively,
ltered supernatant (20738 copies/μL Baishivirus in S1’and 46663 and the Ct value o Baishivirus in the control sample was undetectable
copies/μL Baishivirus in S2’) (S1′ , S2′ : primary GPD samples) and 27 mL (Fig. 3). Ater challenge with the GPD sample, the Ct values o Baishivirus
o PBS or 10 min. In the control group, 20 prawns were bathed in 30 mL in inected samples S1 and S2 (S1, S2: shrimp inected with the primary
PBS or 10 min. The soaked prawns and PBS were transerred into 1 L o supernatant) were 31.565 and 33.701, respectively, and the Ct value in
oxygenated water and ed normally or 5 days. Prawn mortality and the control group was undetectable. In contrast, neither VC nor VP were
morphological changes were recorded. Ater the dead prawns were detected in the inected shrimp sample by RT‒PCR with the challenge o
removed, they were individually sealed into bags marked with the group the precipitate, ruling out their roles in GPD (S3 and S4 in Fig. 3) (S3, S4:
name and time and stored at 2~8◦ C beore preparing samples or RT‒ shrimp inected with the primary precipitate). The results indicated that
PCR. To conrm the genome sequence o pathogens assembled by Baishivirus exists in GPD samples and is likely to inect normal
metagenomic sequencing, primers were designed by SnapGene, and the P. vannamei with GPD.
ragment size o the targeted ORF2 gene was 131 bp. The upstream
primer F: TGTGGAAGTCCAGCCATAAC, downstream primer R: 3.3. Phylogenetic analysis
AGCTGGGTTTCTCCTTCTTG, and probe: TGGGAGTGGCAAACGCCAT-
TACTT were used. The ragment was amplied using the One Step TB Construction o RNA libraries or S1’ and S2’ GPD samples generated
Green™ PrimeScript™ RT‒PCR Kit (TAKARA, Code No. RR066A). The a total o 4.7G and 8G data, respectively. Denovo assembly was per-
reaction conditions were as ollows: one cycle o 42◦ C or 5 min, 95◦ C or ormed through SPAdes v3.13.0 to obtain the complete Baishivirus

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A. Xu et al. Virus Research 324 (2023) 199026

Fig. 2. Clinical symptoms o P. vannamei inected with glass post-larvae disease (GPD) compared with normal prawns. As shown in the lower let corner o the
picture, the black arrow indicates normal prawns, and the red arrow indicates diseased prawns.

Fig. 3. Ct values o RT‒PCR in the challenge experiment. S0: control sample, S1′ , S2′ : primary GPD samples, S1, S2: shrimp inected with the primary supernatant,
S3, S4: shrimp inected with the primary precipitate. Pico1: Wenzhou shrimp virus 8, pico2: Baishivirus, VP: Vibrio parahaemolyticus, VC: Vibrio campbellii. UD:
undetectable.

genome sequence. Protein motis o Baishivirus ORFs were analyzed by picorna-like virus 21 (GenBank KX884351.1) identied in 2016 (upda-
the MOTIF Search tool, and multiple protein motis were predicted as ted in 2018). Both Baishivirus and Wenzhou picorna-like virus 21
indicated (Fig. 4A and 4B). The amino acid sequence phylogenetic tree (KX884351.1) were closest to members o the Marnaviridae amily,
o Baishivirus was rst constructed based on capsids (Fig. 4C). Members indicating they probably belong to the Marnaviridae amily.
o eight amilies within the order Picornavirales, namely, Caliciviridae, The Marnaviridae amily can be dierentiated rom other amilies
Dicistroviridae, Ifaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, within the Picornavirales order by the RdRP sequence (Lang et al., 2021).
Secoviridae, and Solinviviridae, were selected to construct the evolu- Thereore, a phylogenetic tree was constructed based on the Baishivirus
tionary tree. In the evolutionary tree, Baishivirus is closest to Wenzhou RdRP sequence to urther investigate the evolutionary relationships o

4
A. Xu et al. Virus Research 324 (2023) 199026

Fig. 4. Phylogenetic tree o Baishivirus based on amino acids encoded by the capsid. (A) Schematic diagram o the Baishivirus genome structure. (B) Protein motis o
Baishivirus ORF2 and ORF3 analyzed by MOTIF Search. (C) Homology analysis o the amino acid sequence encoded by the capsid (the red dot and ont represent
Baishivirus).

Baishivirus (Fig. 5). As shown in the phylogenetic tree, Baishivirus was worldwide, as it not only enhances the economic development o
closest to members o the Marnaviridae and Dicistroviridae amilies. China’s aquaculture industry but also promotes the globalization o the
Consequently, a phylogenetic tree based on the RdRP sequence was aquaculture industry. In recent years, viral diseases and bacterial dis-
urther constructed by including all members o Marnaviridae and eases have continuously emerged in aquaculture, which may involve
Dicistroviridae (Fig. S2). We selected members o Secoviridae as out- multiple drivers, such as regional geographic actors, viral inection,
groups o the tree to better understand the evolutionary relationships. bacterial inection, and anthropogenic actors (Kibenge, 2019). The
Baishivirus and Wenzhou picorna-like virus 21 (KX884351.1) constituted epidemic in P. vannamei aquaculture has brought about continuous
a new branch o Marnaviridae. The evolutionary tree based on RdRP also shrimp seedling death and a huge crisis to the shrimp arming industry.
conrms that Baishivirus is a novel virus in the amily Marnaviridae Determination o the critical pathogen in shrimp aquaculture is bene-
within the order Picornavirales. In addition, Baishivirus and Wenzhou cial or the individualized treatment o shrimp disease. For instance, to
virus 21 probably orm a novel genus o the Marnaviridae amily, which prevent white spot syndrome caused by WSSV, 30 ppm chlorine is rec-
we tentatively named Baishivirus. ommended to kill inected shrimp and carriers, and water exchange
should be minimized to prevent virus carriers rom entering the pond.
4. Discussion The epidemic o Enterocytozoon hepatopenaei (EHP) appeared in several
countries and is caused by ungal microsporidians. In this situation,
As an important export product, P. vannamei is very popular accumulated organic matter in the pond bottoms is suggested to be

5
A. Xu et al. Virus Research 324 (2023) 199026

Fig. 5. Phylogenetic tree o Baishivirus based on amino acids encoded by RdRP (the red dot and ont represent Baishivirus).

removed physically, and biosecurity should be ensured in the hatchery. and the structural proteins are encoded at the 3’ terminal ends. Because
For acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio the gene character in this amily is similar to some Picornaviridae
parahaemolyticus, the eeding rate is strictly controlled, and an appro- members, phylogenetic analysis o Marnaviridae RdRP amino acid se-
priate stocking density is proposed to prevent symptoms. Although the quences is suggested to distinguish it rom other amilies. Currently, a
gross clinical signs o GPD are similar to those o AHPND syndrome to total o 7 genera belong to Marnaviridae: Bacillarnavirus, Kusarnavirus,
some degree, GPD is a novel disease with dierent inectious agents Labyrnavirus, Locarnavirus, Marnavirus, Salisharnavirus and Sogarnavirus.
(Kumar et al., 2021). The novel Baishivirus in the amily Marnaviridae The viral gene is replicated in the cytosol, and the latent periods range
reported in this work provides new insight into studying GPD in the rom 8 to 48 h. Isolation o puried virus particles will urther clariy the
P. vannamei aquaculture industry. Histopathology and electron micro- characteristics o the Baishivirus structure and replication mechanism.
scopy should be perormed in urther studies to prove the dominant role GPD-inected P. vannamei samples were analyzed by metagenomic
o Baishivirus in GPD occurrence. sequencing to reveal a new pathogen in GPD, named Baishivirus. A
Positive-strand RNA viruses o eukaryotes can be divided into three comparison o the protein sequences o dierent picorna-like viral su-
superamilies: the picorna-like, alpha-like and favi-like amilies (Koo- peramily members revealed that Baishivirus is most likely to be a
nin et al., 2008). Members belonging to the picorna-like superamily are member o Marnaviridae. Because o the relatively low similarity with
characterized by RdRP, a chymotrypsin-like protease, a superamily 3 the known members o Marnaviridae, we suggest that Baishivirus is a
helicase (S3H) and viral proteins (VPs). In general, these viruses have novel virus within Marnaviridae. Baishivirus and Wenzhou picorna-like
icosahedral virions composed o capsid proteins. As members o the 21 possibly represent a new genus in the Marnaviridae amily, which
picorna-like superamily, the virus taxonomy o Marnaviridae was sub- we tentatively named Baishivirus. However, we cannot completely rule
mitted to ICTV in 2021 (Lang et al., 2021). Marnaviridae is a non- out the possibility that both Baishivirus and Wenzhou picorna-like 21
enveloped, 22-35 nm virion with our structural proteins (VP1-4) on the virus are unclassied in the Picornavirales order, which may constitute a
surace. The nonstructural proteins are encoded at the 5’ terminal ends, new amily. Overall, the discovery o Baishivirus enriches the marine

6
A. Xu et al. Virus Research 324 (2023) 199026

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