Epidemiology and molecular characterization of avian influenza A viruses H5N1 and H3N8 subtypes in poultry farms and live bird markets in Bangladesh

Avian influenza virus (AIV) remains a global threat, with waterfowl serving as the primary reservoir from which viruses spread to other hosts. Highly pathogenic avian influenza (HPAI) H5 viruses continue to be a devastating threat to the poultry industry and an incipient threat to humans. A cross-sectional study was conducted in seven districts of Bangladesh to estimate the prevalence and subtypes (H3, H5, and H9) of AIV in poultry and identify underlying risk factors and phylogenetic analysis of AIVs subtypes H5N1 and H3N8. Cloacal and oropharyngeal swab samples were collected from 500 birds in live bird markets (LBMs) and poultry farms. Each bird was sampled by cloacal and oropharyngeal swabbing, and swabs were pooled for further analysis. Pooled samples were analyzed for the influenza A virus (IAV) matrix (M) gene, followed by H5 and H9 molecular subtyping using real-time reverse transcription-polymerase chain reaction (rRT-PCR). Non-H5 and Non-H9 influenza A virus positive samples were sequenced to identify possible subtypes. Selected H5 positive samples were subjected to hemagglutinin (HA) and neuraminidase (NA) gene sequencing. Multivariable logistic regression was used for risk factor analysis. We found that IAV M gene prevalence was 40.20% (95% CI 35.98-44.57), with 52.38%, 46.96%, and 31.11% detected in chicken, waterfowl, and turkey, respectively. Prevalence of H5, H3, and H9 reached 22%, 3.4%, and 6.9%, respectively. Waterfowl had a higher risk of having AIV (AOR: 4.75), and H5 (AOR: 5.71) compared to chicken; more virus was detected in the winter season than in the summer season (AOR: 4.93); dead birds had a higher risk of AIVs and H5 detection than healthy birds, and the odds of H5 detection increased in LBM. All six H5N1 viruses sequenced were clade 2.3.2.1a-R1 viruses circulating since 2015 in poultry and wild birds in Bangladesh. The 12 H3N8 viruses in our study formed two genetic groups that had more similarity to influenza viruses from wild birds in Mongolia and China than to previous H3N8 viruses from Bangladesh. The findings of this study may be used to modify guidelines on AIV control and prevention to account for the identified risk factors that impact their spread.

Prevalence, intensity, and impacts of non-cutaneous lesions of lumpy skin disease among some infected cattle flocks in Nile Delta governorates, Egypt

Lumpy skin disease (LSD) is one of the major viral diseases still causing great economic losses among breeding flocks of Egypt. This study was designed to focus light on non-cutaneous lesions (prevalence, intensity, and impacts) among necropsied LSD infected cattle. We selected some dairy and beef flocks (Frisian breed) located in 3 governorates (Sharkia, Dakahlia, and Kaloubia) in Nile delta, Egypt, in the period from January 2019 to January 2020 for our survey study. The case history of farms declared no previous vaccination of examined farms. The clinical signs, morbidity, and mortality rates were recorded. Average morbidity and mortality percentage were 22.28% and 6.59%, respectively. PCR for specimens from liver, kidneys, heart, lungs, testis, udder, trachea, and lymph node indicates presence of amplicon capripoxvirus gene product at molecular weight size 192 bp. Postmortem lesions of necropsied and emergency slaughtered were recorded. The main detectable histopathology lesions among the infected animals were orchitis (75%), mastitis in immature and lactating udder (66.66%), and necrotic hepatitis (77.77%), disseminated vasculitis (61.11), glomerulonephritis (55.55), myocardial degeneration (50%), and serous atrophy of coronary fats (38.88%), lymphadenitis (88.88%), necrosis and depleted lymphoid tissue of spleen (38.88%), necrotic myositis (77.77%), tracheitis (16.66%), and pneumonia (interstitial bronchopneumonia) (44.44%) besides intra-cytoplasmic inclusions bodies in skin (33.33%). It could be concluded that higher mortalities of LSD may be due to systemic infection of infected animals which had great impact on economic losses among breeding flocks.

Influenza A viruses in birds and humans: Prevalence, molecular characterization, zoonotic significance and risk factors' assessment in poultry farms

This study aimed to investigate the prevalence of influenza A viruses in birds and humans residing in the same localities of Sharkia Province, Egypt and the risk factors' assessment in poultry farms. A total of 100 birds comprised of 50 chickens, 25 ducks and 25 wild egrets were sampled. Swab samples were collected from 65 people (50 poultry farm workers and 15 hospitalized patients). All samples were screened for the presence of influenza A viruses using isolation and molecular assays. Avian influenza viruses were only detected in chicken samples (18%) and molecularly confirmed as subtype H5. The infection rate was higher in broilers (40%) than layers (8.6%). Influenza A (H1) pdm09 virus was detected in a single human case (1.54%). All the isolated AI H5 viruses were clustered into clade (2.2.1.2) and shared a high similarity rate at nucleotides and amino acid levels. In addition, they had a multi-basic amino acid motif (ـــPQGEKRRKKR/GLFـــ) at the H5 gene cleavage site that exhibited point mutations. Chicken breed, movement of workers from one flock to another, lack of utensils' disinfection and the introduction of new birds to the farm were significant risk factors associated with highly pathogenic AI H5 virus infection in poultry farms (p ≤ 0.05). Other factors showed no significant association. The HPAI H5 viruses are still endemic in Egypt with continuous mutation. Co-circulation of these viruses in birds and pdm09 viruses in humans raises alarm for the emergence of reassortant viruses that are capable of potentiating pandemics.