Vaccination is one of the leading methods of controlling the spread of the Avian Influenza (AI) viruses in Indonesia. The variety of circulating viruses and their ability to mutate must be followed by updating the vaccine master seed used in the field. In this study, we identified the reassortant H9N2 viruses in chicken farms that showed significant problems in decreased egg production with high mortality. The reassortant H9N2 viruses derived the PB2 gene from the H5N1 virus. The pathogenicity test results of the reassortant virus showed various clinical signs of illness, a high mortality rate (10%), and decreased egg production down to 63.12% at two weeks post-infection. In a vaccine efficacy test, the vaccinated groups showed minimally decreased egg production that started to increase to more than 80% at 4–7 weeks post-challenge. Our study showed that inactivated bivalent and monovalent reassortant H9N2 vaccines can induce antibody response, reducing the mortality and virus shedding caused by reassortant H9N2 virus infection. The reassortant H9N2 virus is a threat that requires vigilance in poultry farms and the industry. The vaccines used in this study can be one of the options for control or prevention measures on farms infected with the reassortant H9N2 viruses.

Coronavirus is a non-segmented, positive-stranded RNA virus with four main structural proteins, namely Spike (S), Membrane (M), Envelope (E), and Nucleocapsid (N) proteins. Coronavirus can cause diseases in the respiratory and digestive tract, as well as in central nervous system of animals and humans. There are four genera in the Orthocoronavirinae subfamily, including <em>Alphacoronavirus</em>, <em>Betacoronavirus, Gammacoronavirus</em>, and <em>Deltacoronavirus</em>. <em>Alphacoronavirus </em>and <em>Betacoronavirus </em>are commonly found in mammals, while <em>Gammacoronavirus </em>and <em>Deltacoronavirus </em>are found to infect  birds and mammals. Until 2018, zoonoses coronaviruses consisted of SARS-CoV and MERS-CoV. Coronavirus became worldwide concern after it was identified as the cause of the pneumonia outbreak occurred at the end of 2019 in China. The coronavirus is associated with the fish market in Wuhan, then the disease is called COVID-19 (Coronavirus Infectious Diseases-19) caused by SARS-CoV-2. Virus SARS-CoV-2 has infected &gt;1.6 million people around the world and until the end of March 2020, it caused more than 99.000 deaths including 3.512 cases with the total number of deaths to 306 in Indonesia. This paper discusses Coronavirus and scientific information related to Coronaviruses in which several variants are zoonoses.

Bats are an important reservoir of several zoonotic diseases. However, the circulation of bat coronaviruses (BatCoV) in live animal markets in Indonesia has not been reported. Genetic characterization of BatCoV was performed by sequencing partial RdRp genes. Real-time polymerase chain reaction based on nucleocapsid protein (N) gene and Enzyme-linked immunosorbent assay against the N protein were conducted to detect the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA and antibody, respectively. We identified the presence of BatCoV on Cynopterus brachyotis , Macroglossus minimus , and Rousettus amplexicaudatus . The results showed that the BatCoV included in this study are from an unclassified coronavirus group. Notably, SARS-CoV-2 viral RNA and antibodies were not detected in the sampled bats.

The covid-19 pandemic that occurred in the beginning of 2020 has affected all sectors, particularly in health and economic sectors. The Avian Influenza Virus (AIV), a zoonotic virus that have been reported endemic in Indonesia since 2003, might be affected by this condition. There is very limited information related AIV distribution and circulation due to covid-19 pandemic in Indonesia. This study aims to investigate the endemicity of the AIVs in Indonesia by conducting surveillance in several districts/cities in Central Java, West Java, Yogyakarta, and East Java Provinces during 2021. The samples were tested using the RT-PCR method and then DNA sequencing was carried out at Hemagglutinin and Matrix genes. The results of this study were obtained from 597 pool and individual samples from cloacal swabs, tracheal swabs, organs, and environmental swabs of poultry obtained from live poultry markets and poultry farms. The result revealed that 105 samples were tested positive for Influenza A (Matrix). Furthermore, AIV subtype-specific reverse transcription polymerase chain reaction (RT-PCR) from 105 samples tested positive for Influenza A showed that 4 samples tested positive for subtype H5 (3.8%), 4 samples tested positive for subtype H9 (3.8%), 8 samples tested positive for subtype H3 (7.6%), and no samples was found positive for subtype H10. The results showed that the AIV subtype H5N1 still circulating in Indonesia, interestingly the H3 subtype was found to be the predominant virus in this study. Influenza virus subtype H3 has a very diverse host range from birds to various mammalian species including pigs, horses, and dogs, and causes sporadic outbreaks in marine mammals. After the emergence of the A/Hong Kong/1968 (H3N2) pandemic virus, it became endemic and caused annual seasonal epidemics in humans. In China, Influenza virus subtype H3 has had a lineage in domestic poultry and has several subtypes that are H3N2, H3N3, H3N6, and H3N8, which have been isolated from domestic poultry globally. The infection of Influenza virus H3 Subtype can cause mild to severe disease. Experimental studies have also shown that the H3N8 subtype virus originating from poultry can replicate in the respiratory tract of mice, indicating that H3 isolates pose a threat of zoonotic infection. Therefore, the monitoring of H3 subtype AIVs and other AIVs subtype raised great concerns related to the potential threat to animal and human health and poses a potential risk to public health.