OmniVira

Metagenomic Analysis of RNA Fraction Reveals the Diversity of Swine Oral Virome on South African Backyard Swine Farms in the uMgungundlovu District of KwaZulu-Natal Province.

Ravendra P Chauhan1 James E San2,3 Michelle L Gordon1
Affiliations 3 institutions
  1. School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
  2. KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
  3. Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa.
PMID36015047 DOI10.3390/pathogens11080927 Year2022 Journal Pathogens (Basel, Switzerland) Pathogens Languageeng Statusepublish

Abstract

Numerous RNA viruses have been reported in backyard swine populations in various countries. In the absence of active disease surveillance, a persistent knowledge gap exists on the diversity of RNA viruses in South African backyard swine populations. This is the first study investigating the diversity of oral RNA virome of the backyard swine in South Africa. We used three samples of backyard swine oral secretion (saliva) collected from three distantly located backyard swine farms (BSFs) in the uMgungundlovu District, KwaZulu-Natal, South Africa. Total viral RNA was extracted and used for the library preparation for deep sequencing using the Illumina HiSeq X instrument. The FASTQ files containing paired-end reads were analyzed using Genome Detective v 1.135. The assembled nucleotide sequences were analyzed using the PhyML phylogenetic tree. The genome sequence analysis identified a high diversity of swine enteric viruses in the saliva samples obtained from BSF2 and BSF3, while only a few viruses were identified in the saliva obtained from BSF1. The swine enteric viruses belonged to various animal virus families; however, two fungal viruses, four plant viruses, and five unclassified RNA viruses were also identified. Specifically, viruses of the family Astroviridae, according to the number of reads, were the most prevalent. Of note, the genome sequences of Rotavirus A (RVA) and Rotavirus C (RVC) at BSF2 and RVC and Hepatitis E virus (HEV) at BSF3 were also obtained. The occurrence of various swine enteric viruses in swine saliva suggests a high risk of diarrhoeic diseases in the backyard swine. Of note, zoonotic viruses in swine saliva, such as RVA, RVC, and HEV, indicate a risk of zoonotic spillover to the exposed human populations. We recommend the implementation of biosecurity to ensure sustainable backyard swine farming while safeguarding public health.

Supporting text Virus Host Location
backyard swine 1 deep sequencing 3 Illumina sequencing 2 phylogenetic analysis 66 RNA viruses 15 South African backyard farms 1 swine oral virome 1 swine viruses 1 zoonosis 116

Evidence records

7 total
Zoonotic Surveillance
7 records · 1 evidence types
Evidence type Viral Detection
7 records
OVE6275 Viral Detection
Key finding

Rotavirus A genome sequences were detected in saliva samples from backyard swine farms in the uMgungundlovu District, KwaZulu-Natal, South Africa.

Virus
Rotavirus A
Host
pig Sus scrofa Natural host
Location
South Africa
Supporting text

We used three samples of backyard swine oral secretion (saliva) collected from three distantly located backyard swine farms (BSFs) in the uMgungundlovu District, KwaZulu-Natal, South Africa. Of note, the genome sequences of Rotavirus A (RVA) and Rotavirus C (RVC) at BSF2 and RVC and Hepatitis E virus (HEV) at BSF3 were also obtained.

Method
deep sequencing | metagenomic analysis
Sample type
saliva
Geographic raw
uMgungundlovu District, KwaZulu-Natal, South Africa
Country inferred
ZAF
OVE6276 Viral Detection
Key finding

Rotavirus C genome sequences were detected in saliva samples from backyard swine farms in the uMgungundlovu District, KwaZulu-Natal, South Africa.

Virus
Rotavirus C
Host
pig Sus scrofa Natural host
Location
South Africa
Supporting text

We used three samples of backyard swine oral secretion (saliva) collected from three distantly located backyard swine farms (BSFs) in the uMgungundlovu District, KwaZulu-Natal, South Africa. Of note, the genome sequences of Rotavirus A (RVA) and Rotavirus C (RVC) at BSF2 and RVC and Hepatitis E virus (HEV) at BSF3 were also obtained.

Method
deep sequencing | metagenomic analysis
Sample type
saliva
Geographic raw
uMgungundlovu District, KwaZulu-Natal, South Africa
Country inferred
ZAF
OVE6277 Viral Detection
Key finding

Hepatitis E virus genome sequences were detected in saliva samples from backyard swine farms in the uMgungundlovu District, KwaZulu-Natal, South Africa.

Virus
hepatitis E virus
Host
pig Sus scrofa Natural host
Location
South Africa
Supporting text

We used three samples of backyard swine oral secretion (saliva) collected from three distantly located backyard swine farms (BSFs) in the uMgungundlovu District, KwaZulu-Natal, South Africa. Of note, the genome sequences of Rotavirus A (RVA) and Rotavirus C (RVC) at BSF2 and RVC and Hepatitis E virus (HEV) at BSF3 were also obtained.

Method
deep sequencing | metagenomic analysis
Sample type
saliva
Geographic raw
uMgungundlovu District, KwaZulu-Natal, South Africa
Country inferred
ZAF
OVE6278 Viral Detection
Key finding

A high diversity of swine enteric viruses, including Astroviridae, was detected in saliva samples from backyard swine farms in the uMgungundlovu District, KwaZulu-Natal, South Africa.

Virus
swine enteric viruses Astroviridae
Host
pig Sus scrofa Natural host
Location
South Africa
Supporting text

We used three samples of backyard swine oral secretion (saliva) collected from three distantly located backyard swine farms (BSFs) in the uMgungundlovu District, KwaZulu-Natal, South Africa. The genome sequence analysis identified a high diversity of swine enteric viruses in the saliva samples obtained from BSF2 and BSF3, while only a few viruses were identified in the saliva obtained from BSF1. Specifically, viruses of the family Astroviridae, according to the number of reads, were the most prevalent.

Method
deep sequencing | metagenomic analysis
Sample type
saliva
Geographic raw
uMgungundlovu District, KwaZulu-Natal, South Africa
Country inferred
ZAF
OVE6279 Viral Detection
Key finding

Detection of Rotavirus A in swine saliva indicates a potential animal-to-human spillover risk to exposed human populations.

Virus
Rotavirus A
Host
pig Sus scrofa Natural host human Homo sapiens Natural host
Location
South Africa
Supporting text

Of note, zoonotic viruses in swine saliva, such as RVA, RVC, and HEV, indicate a risk of zoonotic spillover to the exposed human populations.

Method
metagenomic sequencing | Illumina HiSeq X | Genome Detective analysis | phylogenetic tree (PhyML)
Geographic raw
South Africa | uMgungundlovu District | KwaZulu-Natal Province
OVE6280 Viral Detection
Key finding

Detection of Rotavirus C in swine saliva indicates a potential animal-to-human spillover risk to exposed human populations.

Virus
Rotavirus C
Host
pig Sus scrofa Natural host human Homo sapiens Natural host
Location
South Africa
Supporting text

Of note, zoonotic viruses in swine saliva, such as RVA, RVC, and HEV, indicate a risk of zoonotic spillover to the exposed human populations.

Method
metagenomic sequencing | Illumina HiSeq X | Genome Detective analysis | phylogenetic tree (PhyML)
Geographic raw
South Africa | uMgungundlovu District | KwaZulu-Natal Province
OVE6281 Viral Detection
Key finding

Detection of Hepatitis E virus in swine saliva indicates a potential animal-to-human spillover risk to exposed human populations.

Virus
hepatitis E virus
Host
pig Sus scrofa Natural host human Homo sapiens Natural host
Location
South Africa
Supporting text

Of note, zoonotic viruses in swine saliva, such as RVA, RVC, and HEV, indicate a risk of zoonotic spillover to the exposed human populations.

Method
metagenomic sequencing | Illumina HiSeq X | Genome Detective analysis | phylogenetic tree (PhyML)
Geographic raw
South Africa | uMgungundlovu District | KwaZulu-Natal Province