Keterkaitan antara pandemi covid-19 dengan eksploitasi alam

Pemanfaatan sumber daya alam tidak sepenuhnya mengedepankan prinsip lingkungan, padahal ekosistem memiliki keanekaragaman hayati termasuk virus berbahaya yang bersifat zoonosis. Kemunculan pandemi Covid-19 dipercaya akibat zoonosis yang menyebar dan menginfeksi jutaan manusia. Penelitian ini dilakukan untuk menganalisis keterkaitan antara pandemi dengan eksploitasi alam, menggunakan metode literatur review dari artikel, dokumen pemerintah, laporan lembaga, working paper, serta informasi resmi WHO dan Satgas Covid-19 RI. Terbukti ada keterkaitan antara pandemi Covid-19 dengan eksploitasi alam. Eksploitasi mempersempit habitat dan menekan kehidupan, organisme merespons dengan ekspansi mencari habitat baru yang sering kali lebih dekat dengan manusia. Eksploitasi memfasilitasi satwa liar sebagai host alami atau perantara virus zoonosis. Hasil analisis homolog SARS-CoV-2 memiliki kemiripan genom lengkap 93,7%, ORF1ab 96,5%, protein N 96,9%, dan spike protein 92,86% dengan coronavirus dari kelelawar (Rhinolophus affinis Horsfield, 1823). Spesies ini tersebar di Asia Selatan dan Tenggara, dipercaya sebagai obat tradisional penyakit pernafasan. Penggunaan satwa liar sebagai obat harus dibatasi, karena dalam praktiknya banyak perdagangan satwa liar secara ilegal yang berisiko zoonosis dan berpotensi memunculkan epidemi maupun pandemi. Hal ini dapat ditanggulangi apabila stabilitas ekosistem dijaga dan tersedia habitat yang proporsional untuk organisme lain, sehingga terjadi interaksi yang harmonis dan berkelanjutan.

SARS-CoV-2 Spike Affinity and Dynamics Exclude the Strict Requirement of an Intermediate Host

SARS-CoV-2 proximal origin is still unclear, limiting the possibility of foreseeing other spillover events with pandemic potential. Here we propose an evolutionary model based on the thorough dissection of SARS-CoV-2 and RaTG13 - the closest bat ancestor - spike dynamics, kinetics and binding to ACE2. Our results indicate that both spikes share nearly identical, high affinities for Rhinolophus affinis bat and human ACE2, pointing out to negligible species barriers directly related to receptor binding. Also, SARS-CoV-2 spike shows a higher degree of dynamics and kinetics optimization that favors ACE2 engagement. Therefore, we devise an affinity-independent evolutionary process that likely took place in R. affinis bats and limits the eventual involvement of other animal species in initiating the pandemic to the role of vector.

Identity and Similarity Percentages of SARS-CoV-2 Proteins Can Be Used as Indicators of the Virus Origin

There are three types of proteins in the coronaviruses; nonstructural, structural and accessory proteins. The coronaviruses proteins are essential for the viral replication and for the binding, invasion and regulation of the host cells metabolism and immunity. This article investigated the amino acid sequence similarity and identity percentages of 10 proteins present in SARS-CoV-2, SARS-CoV and the Rhinolophus affinis bat coronavirus (BatCoV RaTG13). The investigated proteins were 1ab polyprotein, spike protein, orf3a, envelope protein, membrane protein, orf6, orf7a, orf7b, orf8, and ncleocapsid protein. The online sequence alignment service of The European Molecular Biology Open Software Suite (EMBOSS) was used to determine the similarity and identity percentages of the three viruses proteins. The results showed that the similarity and identity percentages of the SARS-CoV-2 and BatCoV RaTG13 proteins are above 95% while the identity and similarity percentages of the SARS-CoV-2 and SARS-CoV are above 38%. The proteins of the SARS-CoV-2 and the BatCoV RaTG13 are of high identity and similarity percentages compared to those of the SARS-CoV-2 and the SARS-CoV.

The Rhinolophus affinis bat ACE2 and multiple animal orthologs are functional receptors for bat coronavirus RaTG13 and SARS-CoV-2

Bat coronavirus (CoV) RaTG13 shares the highest genome sequence identity with SARS-CoV-2 among all known coronaviruses, and also uses human angiotensin converting enzyme 2 (hACE2) for virus entry. Thus, SARS-CoV-2 is thought to have originated from bat. However, whether SARS-CoV-2 emerged from bats directly or through an intermediate host remains elusive. Here, we found that Rhinolophus affinis bat ACE2 (RaACE2) is an entry receptor for both SARS-CoV-2 and RaTG13, although RaACE2 binding to the receptor binding domain (RBD) of SARS-CoV-2 is markedly weaker than that of hACE2. We further evaluated the receptor activities of ACE2s from additional 16 diverse animal species for RaTG13, SARS-CoV, and SARS-CoV-2 in terms of S protein binding, membrane fusion, and pseudovirus entry. We found that the RaTG13 spike (S) protein is significantly less fusogenic than SARS-CoV and SARS-CoV-2, and seven out of sixteen different ACE2s function as entry receptors for all three viruses, indicating that all three viruses might have broad host rages. Of note, RaTG13 S pseudovirions can use mouse, but not pangolin ACE2, for virus entry, whereas SARS-CoV-2 S pseudovirions can use pangolin, but limited for mouse, ACE2s enter cells. Mutagenesis analysis revealed that residues 484 and 498 in RaTG13 and SARS-CoV-2 S proteins play critical roles in recognition of mouse and human ACE2. Finally, two polymorphous Rhinolophous sinicus bat ACE2s showed different susceptibilities to virus entry by RaTG13 and SARS-CoV-2 S pseudovirions, suggesting possible coevolution. Our results offer better understanding of the mechanism of coronavirus entry, host range, and virus-host coevolution.

Transcriptome sequencing of cochleae from constant-frequency and frequency-modulated echolocating bats

Echolocating bats are fascinating for their ability to ‘see’ the world in the darkness. Ultrahigh frequency hearing is essential for echolocation. In this study we collected cochlear tissues from constant-frequency (CF) bats (two subspecies of Rhinolophus affinis, Rhinolophidae) and frequency-modulated (FM) bats (Myotis ricketti, Vespertilionidae) and applied PacBio single-molecule real-time isoform sequencing (Iso-seq) technology to generate the full-length (FL) transcriptomes for the three taxa. In total of 10103, 9676 and 10504 non-redundant FL transcripts for R. a. hainanus, R. a. himalayanus and Myotis ricketti were obtained respectively. These data present a comprehensive list of transcripts involved in ultrahigh frequency hearing of echolocating bats including 26342 FL transcripts, 24833 of which are annotated by public databases. No further comparative analyses were performed on the current data in this study. This data can be reused to quantify gene or transcript expression, assess the level of alternative splicing, identify novel transcripts and improve genome annotation of bat species.

To understand well on the source of COVID-19: Rhinolophus affinis-2

At the beginning of the epidemic, most of the research done in Wuhan showed that the first patients worked or visited a seafood market in Wuhan. It was thought to have originated from snakes first, and later studies showed that it has something to do with bats. As the epidemic progresses, this virus infection has been shown to be transmitted from person to person through droplets and by placing hands on the face that come into contact with contaminated floors. The virus can be found in patients' respiratory secretions 1-2 days before the onset of clinical symptoms and two weeks after disease symptoms.

Enlaces zoonóticos del coronavirus SARS-COV-2

<p>El 11 de marzo del 2020, la Organización Mundial de la Salud (OMS) declaró al COVID-19 como una enfermedad pandémica. Al 21 de abril del 2020, se han registrado a nivel mundial en 210 países y territorios, 2.528.396 casos positivos y 174.547 fallecidos por SARS-CoV-2/COVID-19. Se ha sugerido que la enfermedad puede transmitirse en forma zoonótica de animales a humanos. El objetivo del presente trabajo de revisión fue analizar lo publicado con relación al enlace zoonótico del COVID-19. El SARS-CoV-2 posee una estrecha relación con un coronavirus de murciélago, que fue identificado en Rhinolophus affinis Horsfield, 1823, en la provincia de Yunnan en China, donde se inició el COVID-19. Un análisis exhaustivo de las relaciones mamífero-hospedero-virus ha demostrado que los murciélagos albergan una proporción significativamente mayor de virus zoonóticos que otras órdenes de mamíferos. El pangolín Manis javanica Desmarest, 1822, es el principal sospechoso de ser el hospedero intermediario debido que, al compararse su material genético viral con el del SARS-CoV-2, mostró una alta similitud. En relación a los animales domésticos, se ha descubierto que hurones y gatos son susceptibles a la infección. En cambio, se replica mal en perros, y los cerdos, pollos y patos no son susceptibles al SARS-CoV-2. De igual forma, no hay evidencia certera que sugiera que los animales domésticos infectados tengan un papel en la propagación del COVID-19 a los humanos.</p><p>Palabras clave: enfermedad viral, COVID19, fauna silvestre, gato, murciélago, pangolín, zoonosis</p><p> </p><p><strong>ABSTRACT </strong></p><p>On March 11, 2020, the World Health Organization (WHO) declared COVID-19 as a pandemic illness. As of April 21, 2020, 2,528,396 positive cases and 174,547 deaths from SARS-CoV-2 / COVID-19 have been registered worldwide in 210 countries and territories. It has been suggested that the disease can be transmitted zoonotically from animals to humans. The objective of this review work was to analyze what was published in relation to the zoonotic link of COVID-19. SARS-CoV-2 is closely related to a bat coronavirus, which was identified in Rhinolophus affinis Horsfield, 1823, in China's Yunnan province, where COVID-19 was started. A comprehensive analysis of mammal-host-virus relationships has shown that bats harbor a significantly higher proportion of zoonotic viruses than other orders of mammals. The pangolin Manis javanica Desmarest, 1822, is the main suspect of being the intermediate host, because when comparing its viral genetic material with that of SARS-CoV-2 it showed a high similarity. In relation to domestic animals, ferrets and cats have been found to be susceptible to infection. In contrast, it replicates poorly in dogs, and SARS-CoV-2 is not susceptible in pigs, chickens, and ducks. Similarly, there is no accurate evidence to suggest that infected pets have a role in the spread of COVID-19 to humans.</p><p>Key words: bat, cat, pangolin, viral disease, wildlife, zoonosis</p>