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Two-year surveillance of tilapia lake virus (TiLV) reveals its wide circulation in tilapia farms and hatcheries from multiple districts of Bangladesh

Debnath PP, Delamare-Deboutteville J, Jansen MD, Phiwsaiya K, Dalia A, Hasan MA, et al.

J Fish Dis, 2020 Nov;43(11):1381-1389.
PMID: 32851674 DOI: 10.1111/jfd.13235

Tilapia lake virus (TiLV) is an emerging pathogen in aquaculture, reportedly affecting farmed tilapia in 16 countries across multiple continents. Following an early warning in 2017 that TiLV might be widespread, we executed a surveillance programme on tilapia grow-out farms and hatcheries from 10 districts of Bangladesh in 2017 and 2019. Among farms experiencing unusual mortality, eight out of 11 farms tested positive for TiLV in 2017, and two out of seven tested positive in 2019. Investigation of asymptomatic broodstock collected from 16 tilapia hatcheries revealed that six hatcheries tested positive for TiLV. Representative samples subjected to histopathology confirmed pathognomonic lesions of syncytial hepatitis. We recovered three complete genomes of TiLV from infected fish, one from 2017 and two from 2019. Phylogenetic analyses based on both the concatenated coding sequences of 10 segments and only segment 1 consistently revealed that Bangladeshi TiLV isolates formed a unique cluster within Thai clade, suggesting a close genetic relation. In summary, this study revealed the circulation of TiLV in 10 farms and six hatcheries located in eight districts of Bangladesh. We recommend continuing TiLV-targeted surveillance efforts to identify contaminated sources to minimize the countrywide spread and severity of TiLV infection.

Matched MeSH terms: Orthomyxoviridae Infections/epidemiology
Serological and molecular surveillance for influenza A virus in dogs and their human contacts in Oyo State, Nigeria

Daodu OB, Adebiyi AI, Oluwayelu DO

Trop Biomed, 2019 Dec 01;36(4):1054-1060.
PMID: 33597474

Evidence of influenza A virus (IAV) infection in dogs, a major companion animal of humans, suggests the possibility that they may constitute a new source for transmission of novel influenza viruses to humans. The potential public health risk posed by this possibility of interspecies spread of IAV between dogs and humans necessitated surveillance for the virus in dogs and their human contacts. Sera from 239 asymptomatic pet and hunting dogs in Oyo state, Nigeria were screened for anti-IAV nucleoprotein antibodies using competitive enzyme-linked immunosorbent assay (ELISA) while haemagglutination inhibiting (HI) antibodies in the positive sera were detected using influenza virus H3 and H5 subtypespecific antigens. Suspensions prepared from 239 and 39 nasal swabs from dogs and human contacts, respectively were tested for presence of the highly conserved IAV matrix gene by reverse transcriptase-polymerase chain reaction (RT-PCR). Only 4 (1.7%) of the 239 sera tested were positive by the ELISA. The HI test confirmed the presence of H3 influenza virus subtype-specific antibodies in one (25.0%) of the 4 ELISA-positive sera with a titre of 1:128 while none was positive for H5 subtype-specific antibodies. All the nasal swabs assayed by RT-PCR were negative for IAV nucleic acid. The detection of IAV antibodies in pet and hunting dogs in this study, although at a low rate, suggests that these dogs could play a crucial role in the zoonotic transmission of influenza viruses especially considering the close interaction between them and their human contacts. Continuous surveillance for IAV among dog populations in Oyo State (and Nigeria) is therefore advocated to facilitate early detection of infection or emergence of novel influenza virus strains that could be potentially harmful to humans and or animals.

Matched MeSH terms: Orthomyxoviridae Infections/epidemiology
Detection of Tilapia Lake Virus in Egyptian fish farms experiencing high mortalities in 2015

Nicholson P, Fathi MA, Fischer A, Mohan C, Schieck E, Mishra N, et al.

J Fish Dis, 2017 Dec;40(12):1925-1928.
PMID: 28590067 DOI: 10.1111/jfd.12650
Matched MeSH terms: Orthomyxoviridae Infections/epidemiology
Molecular Epidemiology of a novel re-assorted epidemic strain of equine influenza virus in Pakistan in 2015-16

Khan A, Mushtaq MH, Ahmad MUD, Nazir J, Farooqi SH, Khan A

Virus Res, 2017 08 15;240:56-63.
PMID: 28757141 DOI: 10.1016/j.virusres.2017.07.022

BACKGROUND: A widespread epidemic of equine influenza (EI) occurred in nonvaccinated equine population across multiple districts in Khyber Pakhtunkhwa Province of Pakistan during 2015-2016.
OBJECTIVES AND METHODS: An epidemiological surveillance study was conducted from Oct 2015 to April 2016 to investigate the outbreak. EI virus strains were isolated in embryonated eggs from suspected equines swab samples and were subjected to genome sequencing using M13 tagged segment specific primers. Phylogenetic analyses of the nucleotide sequences were concluded using Geneious. Haemagglutinin (HA), Neuraminidase (NA), Matrix (M) and nucleoprotein (NP) genes nucleotide and amino acid sequences of the isolated viruses were aligned with those of OIE recommended, FC-1, FC-2, and contemporary isolates of influenza A viruses from other species.
RESULTS: HA and NA genes amino acid sequences were very similar to Tennessee/14 and Malaysia/15 of FC-1 and clustered with the contemporary isolates recently reported in the USA. Phylogenetic analysis showed that these viruses were mostly identical (with 99.6% and 97.4% nucleotide homology) to, and were reassortants containing chicken/Pakistan/14 (H7N3) and Canine/Beijing/10 (H3N2) like M and NP genes. Genetic analysis indicated that A/equine/Pakistan/16 viruses were most probably the result of several re-assortments between the co-circulating avian and equine viruses, and were genetically unlike the other equine viruses due to the presence of H7N3 or H3N2 like M and NP genes.
CONCLUSION: Epidemiological data analysis indicated the potential chance of mixed, and management such as mixed farming system by keeping equine, canine and backyard poultry together in confined premises as the greater risk factors responsible for the re-assortments. Other factors might have contributed to the spread of the epidemic, including low awareness level, poor control of equine movements, and absence of border control disease strategies.

Matched MeSH terms: Orthomyxoviridae Infections/epidemiology
Diversity of influenza A viruses retrieved from respiratory disease outbreaks and subclinically infected herds in Spain (2017-2019)

Sosa Portugal S, Cortey M, Tello M, Casanovas C, Mesonero-Escuredo S, Barrabés S, et al.

Transbound Emerg Dis, 2021 Mar;68(2):519-530.
PMID: 32619306 DOI: 10.1111/tbed.13709

The present study was aimed to assess the diversity of influenza A viruses (IAV) circulating in pig farms in the Iberian Peninsula. The study included two different situations: farms suffering respiratory disease outbreaks compatible with IAV (n = 211) and randomly selected farms without overt respiratory disease (n = 19). Initially, the presence of IAV and lineage determination was assessed by qRT-PCR using nasal swabs. IAV was confirmed in 145 outbreaks (68.7%), mostly in nurseries (53/145; 36.5%). Subtyping by RT-qPCR was possible in 94 of those cases being H1avN2hu (33.6%), H1avN1av (24.3%) and H1huN2hu (18.7%), the most common lineages. H3huN2hu and H1pdmN1pdm represented 7.5% and 6.5% of the cases, respectively. As for the randomly selected farms, 15/19 (78.9%) were positive for IAV. Again, the virus was mostly found in nurseries and H1avN2hu was the predominant lineage. Virus isolation in MDCK cells was attempted from positive cases. Sixty of the isolates were fully sequenced with Illumina MiSeq®. Within those 60 isolates, the most frequent genotypes had internal genes of avian origin, and these were D (19/60; 31.7%) and A (11/60; 18.3%), H1avN2hu and H1avN1av, respectively. In addition, seven previously unreported genotypes were identified. In two samples, more than one H or N were found and it was not possible to precisely establish their genotypes. A great diversity was observed in the phylogenetic analysis. Notably, four H3 sequences clustered with human isolates from 2004-05 (Malaysia and Denmark) that were considered uncommon in pigs. Overall, this study indicates that IAV is a very common agent in respiratory disease outbreaks in Spanish pig farms. The genetic diversity of this virus is continuously expanding with clear changes in the predominant subtypes and lineages in relatively short periods of time. The current genotyping scheme has to be enlarged to include the new genotypes that could be found in the future.

Matched MeSH terms: Orthomyxoviridae Infections/epidemiology
Seroprevalence and risk factors for influenza A viruses in pigs in Peninsular Malaysia

Suriya R, Hassan L, Omar AR, Aini I, Tan CG, Lim YS, et al.

Zoonoses Public Health, 2008 Sep;55(7):342-51.
PMID: 18667027 DOI: 10.1111/j.1863-2378.2008.01138.x

Following a series of H5N1 cases in chickens and birds in a few states in Malaysia, there was much interest in the influenza A viruses subtypes that circulate among the local pig populations. Pigs may act as a mixing vessel for avian and mammal influenza viruses, resulting in new reassorted viruses. This study investigated the presence of antibodies against influenza H1N1 and H3N2 viruses in pigs from Peninsular Malaysia using Herdcheck Swine Influenza H1N1 and H3N2 Antibody Test Kits. At the same time, the presence of influenza virus was examined from the nasal swabs of seropositive pigs by virus isolation and real time RT-PCR. The list of pig farms was obtained from the headquarters of the Department of Veterinary Services, Malaysia, and pig herds were selected randomly from six of 11 states in Peninsular Malaysia. A total of 727 serum and nasal swab samples were collected from 4- to 6-month-old pigs between May and August 2005. By ELISA, the seroprevalences of swine influenza H1N1 and H3N2 among pigs were 12.2% and 12.1% respectively. Seropositivity for either of the virus subtypes was detected in less than half of the 41 sampled farms (41.4%). Combination of both subtypes was detected in 4% of all pigs and in 22% of sampled farms. However, no virus or viral nucleic acid was detected from nasal samples. This study identified that the seropositivity of pigs to H1N1 and H3N2 based on ELISA was significantly associated with factors such as size of farm, importation or purchase of pigs, proximity of farm to other pig farms and the presence of mammalian pets within the farm.

Matched MeSH terms: Orthomyxoviridae Infections/epidemiology
Fulltext Using routine surveillance data to estimate the epidemic potential of emerging zoonoses: application to the emergence of US swine origin influenza A H3N2v virus

Cauchemez S, Epperson S, Biggerstaff M, Swerdlow D, Finelli L, Ferguson NM

PLoS Med, 2013;10(3):e1001399.
PMID: 23472057 DOI: 10.1371/journal.pmed.1001399

BACKGROUND: Prior to emergence in human populations, zoonoses such as SARS cause occasional infections in human populations exposed to reservoir species. The risk of widespread epidemics in humans can be assessed by monitoring the reproduction number R (average number of persons infected by a human case). However, until now, estimating R required detailed outbreak investigations of human clusters, for which resources and expertise are not always available. Additionally, existing methods do not correct for important selection and under-ascertainment biases. Here, we present simple estimation methods that overcome many of these limitations.
METHODS AND FINDINGS: Our approach is based on a parsimonious mathematical model of disease transmission and only requires data collected through routine surveillance and standard case investigations. We apply it to assess the transmissibility of swine-origin influenza A H3N2v-M virus in the US, Nipah virus in Malaysia and Bangladesh, and also present a non-zoonotic example (cholera in the Dominican Republic). Estimation is based on two simple summary statistics, the proportion infected by the natural reservoir among detected cases (G) and among the subset of the first detected cases in each cluster (F). If detection of a case does not affect detection of other cases from the same cluster, we find that R can be estimated by 1-G; otherwise R can be estimated by 1-F when the case detection rate is low. In more general cases, bounds on R can still be derived.
CONCLUSIONS: We have developed a simple approach with limited data requirements that enables robust assessment of the risks posed by emerging zoonoses. We illustrate this by deriving transmissibility estimates for the H3N2v-M virus, an important step in evaluating the possible pandemic threat posed by this virus. Please see later in the article for the Editors' Summary.

Matched MeSH terms: Orthomyxoviridae Infections/epidemiology
Fulltext Isolation and characterization of equine influenza virus (H3N8) from an equine influenza outbreak in Malaysia in 2015

Toh X, Soh ML, Ng MK, Yap SC, Harith N, Fernandez CJ, et al.

Transbound Emerg Dis, 2019 Sep;66(5):1884-1893.
PMID: 31059176 DOI: 10.1111/tbed.13218

Equine influenza is a major cause of respiratory infections in horses and can spread rapidly despite the availability of commercial vaccines. In this study, we carried out molecular characterization of Equine Influenza Virus (EIV) isolated from the Malaysian outbreak in 2015 by sequencing of the HA and NA gene segments using Sanger sequencing. The nucleotide and amino acid sequences of HA and NA were compared with representative Florida clade 1 and clade 2 strains using phylogenetic analysis. The Florida clade 1 viruses identified in this outbreak revealed numerous amino acid substitutions in the HA protein as compared to the current OIE vaccine strain recommendations and representative strains of circulating Florida sub-lineage clade 1 and clade 2. Differences in HA included amino acids located within antigenic sites which could lead to reduced immune recognition of the outbreak strain and alter the effectiveness of vaccination against the outbreak strain. Detailed surveillance and genetic information sharing could allow genetic drift of equine influenza viruses to be monitored more effectively on a global basis and aid in refinement of vaccine strain selection for EIV.

Matched MeSH terms: Orthomyxoviridae Infections/epidemiology
Emerging viral diseases

Nichol ST, Arikawa J, Kawaoka Y

Proc Natl Acad Sci U S A, 2000 Nov 07;97(23):12411-2.
PMID: 11035785
Matched MeSH terms: Orthomyxoviridae Infections/epidemiology*