Table 4.
Summary of the data extraction in the literature review for viral hazard identification
| Family | Characteristics | Viral hazard | Matrix | References |
|---|---|---|---|---|
| Adenoviridae | Non‐enveloped (linear) dsDNA | Porcine adenovirus (PAdV) | Spleen | Kadoi et al. (1997) |
| Swab slaughter line (bleeding) | Jones and Muehlhauser (2017a) | |||
| Faeces, liver, muscle, Sausages | Berto et al. (2012) | |||
| Faeces, liver, packaged meat, sausages | Di Bartolo et al. (2012) | |||
| Nasal/faecal swabs pools | Hause et al. (2016a) | |||
| Anelloviridae | Non‐enveloped (circular) ssDNA | Torque Teno virus (TTSuV) | Liver, serum, lung | de Arruda Leme et al. (2013) |
| Liver, pork | Leblanc et al. (2014) | |||
| Slaughterhouse collected fetuses | Martinez‐Guino et al. (2010) | |||
| Nasal/faecal swabs pools | Hause et al. (2016a) | |||
| Torque Teno virus 1 (TTSuV1) | Bile, fresh pork liver sausages | Monini et al. (2016) | ||
| Kidney | Ghosh et al. (2018) | |||
| Liver | Da Silva et al. (2020) | |||
| Blood | Luka et al. (2016) | |||
| Lymph nodes | Huang et al. (2013) | |||
| Torque Teno virus 2 (TTSuV2) | Liver | Da Silva et al. (2020) | ||
| Arteriviridae | Enveloped ssRNA+ | Porcine reproductive and respiratory syndrome virus (PRRS) | Serum | Almeida et al. (2018) |
| Meat sample from carcass, serum | Magar and Larochelle (2004) | |||
| Tonsils | O'Sullivan et al. (2011) | |||
| Lung | Hillen et al. (2014) | |||
| Cranioventral lobe, dorsocaudal lobe, heart, kidney, liver, lymph nodes, small intestine, spleen, testis, tonsils | Ho et al. (1999) | |||
| Nasal/faecal swabs pools | Hause et al. (2016a) | |||
| Spray‐dried porcine plasma | Blázquez et al. (2022) | |||
| Asfarviridae | Enveloped (linear) dsDNA | African Swine Fever (ASF) | Serum | Gallardo et al. (2011) |
| Tissue, blood | Cho et al. (2022) | |||
| Tissue | Abworo et al. (2017) | |||
| Blood | Thomas et al. (2016) | |||
| Tissue | Owolodun et al. (2010) | |||
| Blood | Adedeji et al. (2022) | |||
| Liver, lymph nodes, spleen | Owolodun et al. (2007) | |||
| Blood | Ebwanga et al. (2022) | |||
| Blood | Luka et al. (2016) | |||
| Not reported | Kong et al. (2021) | |||
| Astroviridae | Non‐enveloped ssRNA+ | Astrovirus (AstV) | Faeces | Machnowska et al. (2014) |
| Porcine astrovirus | Faeces | Luo et al. (2011) | ||
| Nasal/faecal swabs pools | Hause et al. (2016a) | |||
| Caliciviridae | Non‐enveloped ssRNA+ | Porcine enteric calicivirus (PEC) | Faeces | Halaihel et al. (2010) |
| Retail pork | Jones and Muehlhauser (2017b) | |||
| Calicivirus | Nasal/faecal swabs pools | Hause et al. (2016a) | ||
| European swine norovirus (NOV) | Faeces | Machnowska et al. (2014) | ||
| Norovirus | Faeces | Laconi et al. (2020) | ||
| Circoviridae | Non‐enveloped (circular) ssDNA | Porcine circovirus | Nasal/faecal swabs pools | Hause et al. (2016a) |
| Porcine circovirus Type 1 (PCV1) | Serum | Quintana et al. (2001) | ||
| Not reported | Csagola et al. (2008) | |||
| Kidney, lung, lymph nodes, spleen | Hu et al. (2022) | |||
| Liver | Da Silva et al. (2020) | |||
| Porcine circovirus Type 2 (PCV2) | Tonsils | Saekhow et al. (2015) | ||
| Not reported | Csagola et al. (2008) | |||
| Lymph nodes | Ojok et al. (2013) | |||
| Tissue | Jia et al. (2022) | |||
| Lymph nodes | Laisse et al. (2018) | |||
| Kidney, lung, lymph nodes, spleen | Hu et al. (2022) | |||
| Kidney | Ghosh et al. (2018) | |||
| Faeces, kidney | Kleymann et al. (2020) | |||
| Liver | Da Silva et al. (2020) | |||
| Tonsils | O'Sullivan et al. (2011) | |||
| Lung | Hillen et al. (2014) | |||
| Lung | Yue et al. (2022) | |||
| Plasma | Blazquez et al. (2019) | |||
| Spray‐dried porcine plasma | Blázquez et al. (2022) | |||
| Porcine circovirus Type 2a (PCV2a) | Plasma | Shen et al. (2011) | ||
| Porcine circovirus Type 2b (PCV2b) | Plasma | Shen et al. (2011) | ||
| Porcine circovirus Type 3 (PCV3) | Tissue | Jia et al. (2022) | ||
| Kidney, lymph nodes | Hu et al. (2022) | |||
| Lung | Wen et al. (2018) | |||
| Lymph nodes | Liu et al. (2019) | |||
| Lung | Yue et al. (2022) | |||
| Porcine circovirus Type 4 (PCV4) | Lung | Yue et al. (2022) | ||
| Coronaviridae | Enveloped ssRNA+ | Porcine epidemic diarrhoea virus (PEDV) | Swabs from lower floor of truck after animal unloading at slaughterhouse | Boniotti et al. (2018) |
| Nasal/faecal swabs pools | Hause et al. (2016a) | |||
| Spray‐dried porcine plasma | Blázquez et al. (2022) | |||
| Porcine hemagglutinating encephalomyelitis virus | Nasal/faecal swabs pools | Hause et al. (2016a) | ||
| Porcine deltacoronavirus (PDCoV) | Nasal/faecal swabs pools | Hause et al. (2016a) | ||
| Flaviviridae | Enveloped ssRNA+ | Classical swine fever (CSF) | Tissue | Sarma and Meshram (2008) |
| Spleen | Rout and Saikumar (2016) | |||
| Tissue | Rout et al. (2015) | |||
| Tissue | Sarma et al. (2008) | |||
| Intestine, kidney, lymph nodes, spleen, tonsils | Sarma et al. (2007) | |||
| Atypical porcine pestivirus | Nasal/faecal swabs pools | Hause et al. (2016a) | ||
| Hepadnaviridae | Enveloped partially‐dsDNA | Hepatitis B virus (HBV) | Bile, liver | Vieira et al. (2014) |
| Hepeviridae | Quasi‐enveloped* (non‐enveloped) ssRNA+ | Hepatitis E virus (HEV) | Liver | Jori et al. (2016) |
| Faeces | Jones and Johns (2012) | |||
| Liver | Muller et al. (2017) | |||
| Liver | Bouquet et al. (2011) | |||
| Swab slaughter line | Lainšček et al. (2017) | |||
| Faeces | Machnowska et al. (2014) | |||
| Liver | Gutierrez‐Vergara et al. (2015) | |||
| Faeces | Lainšček et al. (2017) | |||
| Blood, kidney, liver | Geng et al. (2019) | |||
| Faeces | Di Martino et al. (2010) | |||
| Faeces | Cappai et al. (2018) | |||
| Bile | Wang et al. (2015) | |||
| Liver | Vonlanthen‐Specker et al. (2021) | |||
| Pork liver surface | Dzierzon et al. (2022) | |||
| Liver | Traore et al. (2015) | |||
| Liver | de Paula et al. (2013) | |||
| Bile, liver | Gardinali et al. (2012) | |||
| Blood | Sooryanarain et al. (2020) | |||
| Bile, faeces, liver pork, meat | Intharasongkroh et al. (2017) | |||
| Faeces liver sausages | Berto et al. (2012) | |||
| Faeces, liver, packaged meat, sausages | Di Bartolo et al. (2012) | |||
| Bile | dos Santos et al. (2011) | |||
| Bile | Mughini‐Gras et al. (2017) | |||
| Faeces, liver | Chambaro et al. (2021) | |||
| Bile | Amorim et al. (2018) | |||
| Bile, bladder, faeces, liver, lymph nodes, plasma, tonsils | Leblanc et al. (2010) | |||
| Diaphragm, faeces, liver | Chelli et al. (2021) | |||
| Not reported, serum | de Souza et al. (2012) | |||
| Blood, rectum swabs | Khounvisith et al. (2018) | |||
| Liver | Feurer et al. (2018) | |||
| Caecum content, liver, serum | Boxman et al. (2022) | |||
| Liver | Temmam et al. (2013) | |||
| Liver | Rose et al. (2011) | |||
| Liver | Motoya et al. (2019) | |||
| Bile, liver | Casas et al. (2011) | |||
| Liver | Pellerin et al. (2022) | |||
| Bile | Zhang et al. (2018) | |||
| Faeces, liver | Forero et al. (2017) | |||
| Blood, liver | Bigoraj et al. (2021) | |||
| Blood | Boxman et al. (2017) | |||
| Faeces, plasma | Leblanc et al. (2007) | |||
| Liver | Wang et al. (2023) | |||
| Liver, swab slaughter line | Milojević et al. (2019) | |||
| Pork liver surface | Li et al. (2011) | |||
| Herpesviridae | Enveloped (linear) dsDNA | Porcine cytomegalovirus (PCMV) | Lung | Tajima and Kawamura (1998) |
| Orthomyxoviridae | Enveloped segmented ssRNA‐ | Influenza A (H1N1, pandemic strain 2009) | Lung | Paladino et al. (2017) |
| Nasal swab | Perera et al. (2013) | |||
| Blood | Nokireki et al. (2013) | |||
| Nasal swabs | Chen et al. (2021) | |||
| Lung | Olaniyi et al. (2020) | |||
| Nasal swabs | Rose et al. (2013) | |||
| Nasal swabs | Takemae et al. (2017) | |||
| Nasal swabs | Baudon et al. (2018) | |||
| Serum/nasal swab | Baudon et al. (2015) | |||
| Nasal swabs/tracheal swab | Cheung et al. (2022) | |||
| H7N2 influenza virus | Lung | Kwon et al. (2011) | ||
| H1N2 influenza virus | Nasal swabs | Qiao et al. (2014) | ||
| Influenza virus | Nasal swabs | Osoro et al. (2019) | ||
| Nasal/faecal swabs pools | Hause et al. (2016a) | |||
| Lung | De Conti et al. (2021) | |||
| Tracheal swab | Meseko et al. (2018) | |||
| Tracheal swab | Amorim et al. (2013) | |||
| Nasal swabs | Ducatez et al. (2015) | |||
| Swine influenza virus (SIV) | Lung | Kwon et al. (2011) | ||
| Lung | Florez et al. (2018) | |||
| Lung | Hillen et al. (2014) | |||
| Nasal swabs | Papatsiros et al. (2015) | |||
| Nasal swabs | Oladipo et al. (2013) | |||
| Nasal swabs | Baudon et al. (2018) | |||
| Spray‐dried porcine plasma | Blázquez et al. (2022) | |||
| Paramyxoviridae | Enveloped ssRNA‐ | Porcine parainfluenza virus type 1 (PPIV‐1) | Assorted tissue, bronchoalveolar lavage, lung, nasal swabs, nasal turbinate, oral fluid, respiratory swab | Park et al. (2019) |
| Parvoviridae | Non‐enveloped (linear) ssDNA | Bocavirus | Faeces, lymph nodes, nasopharyngeal swab, serum | Lau et al. (2011) |
| Inguinal lymph node, spleen, submandibular lymph node, tonsils | Liu et al. (2014) | |||
| Liver | Da Silva et al. (2020) | |||
| Nasal/faecal swabs pools | Hause et al. (2016a) | |||
| Porcine boca‐like virus (PBo‐likeV) | Tonsils | Saekhow et al. (2015) | ||
| Hokovirus | Nasal/faecal swabs pools | Hause et al. (2016a) | ||
| Porcine parvovirus | Heart | Streck et al. (2013) | ||
| Tonsils | Streck et al. (2013) | |||
| Tonsils | Saekhow et al. (2015) | |||
| Fetuses at abattoir | Mengeling et al. (1991) | |||
| Follicular fluid | Pogranichniy et al. (2008) | |||
| Kidney | Ghosh et al. (2018) | |||
| Liver | Da Silva et al., 2020 | |||
| Nasal/faecal swabs pools | ||||
| Spray‐dried porcine plasma | Blázquez et al. (2022) | |||
| Porcine parvovirus 1 (PPV1) | Blood, lung | Thuy et al. (2021) | ||
| Porcine parvovirus 2 (PPV2) | Heart | Streck et al. (2013) | ||
| Tonsils | Streck et al. (2013) | |||
| Tonsils | Saekhow et al. (2015) | |||
| Blood | Thuy et al. (2021) | |||
| Lung | Thuy et al. (2021) | |||
| Porcine parvovirus 3 (PPV3) | Tonsils | Streck et al. (2013) | ||
| Tonsils | Saekhow et al. (2015) | |||
| Blood | Thuy et al. (2021) | |||
| Lung | Thuy et al. (2021) | |||
| Porcine parvovirus 4 (PPV4) | Tonsils | Streck et al. (2013) | ||
| Tonsils | Saekhow et al. (2015) | |||
| Lung | Thuy et al. (2021) | |||
| Porcine parvovirus 7 (PPV7) | Lung | Chen et al. (2018) | ||
| Picobirnaviridae | Non‐enveloped segmented dsRNA | Picobirnavirus | Nasal/faecal swabs pools | Hause et al. (2016a) |
| Picornaviridae | Non‐enveloped ssRNA+ | Encephalomyocarditis virus (EMCV) | Faeces | Machnowska et al. (2014) |
| Enterovirus | Nasal/faecal swabs pools | Hause et al. (2016a) | ||
| Foot‐and‐mouth‐disease virus (FMDV) | Heart | Sharmila and Sherikar (2005) | ||
| Kobuvirus | Nasal/faecal swabs pools | Hause et al. (2016a) | ||
| Parecho‐like virus | Nasal/faecal swabs pools | Hause et al. (2016a) | ||
| Pasivirus | Nasal/faecal swabs pools | Hause et al. (2016a) | ||
| Sapelovirus | Nasal/faecal swabs pools | Hause et al. (2016a) | ||
| Intestinal content | Swati et al. (2020) | |||
| Senecavirus A | Nasal/faecal swabs pools | Hause et al. (2016b) | ||
| Nasal/faecal swabs pools | Hause et al. (2016b) | |||
| Senecavirus A SVA‐GD5‐2018, SVA‐GDSZ‐2018 | Lymph nodes | Jiang et al. (2021) | ||
| Teschovirus | Nasal/faecal swabs pools | Hause et al. (2016a) | ||
| Intestinal content | John et al. (2022) | |||
| Swab slaughter line (bleeding) | Jones and Muehlhauser (2017a) | |||
| unclassified Picornavirales | Posavirus | Nasal/faecal swabs pools | Hause et al. (2016a) | |
| Reoviridae | Non‐enveloped segmented dsRNA | Porcine rotavirus (RV) | Swab slaughter line (bleeding) | Jones and Muehlhauser (2017b) |
| Rotavirus group A (GARV) | Faeces | Machnowska et al. (2014) | ||
| Rotaviruses | Faeces | Halaihel et al. (2010) | ||
| Tobaniviridae | Enveloped ssRNA+ | Torovirus | Nasal/faecal swabs pools | Hause et al. (2016a) |
*
‘Quasi‐enveloped’ viruses (Feng et al., 2014) are viruses historically considered as non‐enveloped due to the features displayed at excretion and in the environment that, however, circulate in the bloodstream of an infected subject in a membrane‐cloaked form. This attribute has been described, among others, in Hepatitis E virus (Takahashi et al., 2010).