key: cord-0697775-zdv0ilti authors: Nandagopal, Murugan; R, Sagaya Jansi title: COVID-19: An Update on the Epidemiological, Genomic Origin, Phylogenetic study, India centric to Worldwide current status date: 2020-04-21 journal: nan DOI: 10.1101/2020.04.17.20070284 sha: 113a089943756936936add58f2b22048306f7c57 doc_id: 697775 cord_uid: zdv0ilti The pandemic spread of novel coronavirus, (SARS-CoV-2) causing CoronaVirus Infectious Diseases (COVID-19) emerged into a global threat for human life causing serious death rates and economic crunch all over the globe. As on April 17, 2020 at 2:00am CEST, there include a total of 2,034,802 confirmed cases for Corona and 1,35,163 deaths worldwide have been reported which includes 212 countries, areas or territories reported by World Health Organization (WHO), in which USA tops 6,32,781 confirmed cases (28,221 deaths) followed by Italy 1,65,155 (21,647 deaths), Spain 1,77,633 (18,579 deaths) and China 84,149 (4,642 deaths). This study aims to compare the genomic nature of SARS-CoV-2 genome reported from Wuhan, China with two Indian isolate genome reported by ICMR-NIV, India. Further Phylogenetic studies performed with coronavirus infecting non-human species like Bats, Duck, and sparrow were compared with Indian and other country whole genome sequences of SARS-CoV2 using MegaX and traced out the association between the human coronavirus with the other species viral genome. In addition, epidemiological reports on COVID-19 among Worldwide and India centric data were compared between April 7, 2020 to April 17, 2020 global data and the number of active cases were increased dramatically in this 10 days period studied, highlighted in the current study. Totally 211 countries, territories or area have been affected by the novel pathogenic Human CoronaVirus (HCoV). The novel coronavirus was officially renamed as "SARS-CoV-2" from "2019-nCoV" by 11 th February 2020. The disease caused by SARS-CoV-2 was called "CoronaVirus Infectious Disease 2019" (COVID-19) by WHO. COVID-19 has been declared as a Public Health Emergency of International Concern by the WHO [1] . The virus belongs to Coronaviridae family which consists of single-stranded, non-segmented positive-sense RNA genome of size approximately 26-32 kb [2] [3] . To date, six known HCoVs have been identified, namely HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV); except SARS and MERS, other four were universally dispersed in the human population and causes common cold infections among one-third of human populations [4] [5] . Two serious coronavirus disease outbreaks occurred in the past two decades. First is SARS in 2003, originated from Southern China and spread to more than 30 countries and all major continents, resulted in more than 8000 human infections and 774 deaths [6] [7] . The second include MERS in 2012 genetically different from SARS-CoV but infected 2,249 people in 27 countries with 35% case fatality [8] [9] [10] . The current COVID-19 entirely made the globe into lockdown status with the highest death rates and infected rates changing dynamically every day. The beginning of SARS-CoV-2 was linked to a cluster of patients with pneumonia of unknown aetiology connected to a local Huanan South China Seafood Market in Wuhan, Hubei Province, China in December 2019 [11] . It is now emerged as pandemic condition and World Health Organization (WHO) report as on April 17, 2020 at 2:00am CEST, there include a total of 2,034,802 confirmed cases for Corona and 1,35,163 deaths worldwide which includes 212 countries, areas or territories with cases [1] WHO region wise data in Fig.1A -B. The fuss about the source of the virus and its intermediate host is still not yet confirmed. However, so far, there are still controversies about the source of the virus and its intermediate host [3] . The evolutionary analysis shows that the present strain of coronavirus is more similar to Bat coronavirus isolate RaTG13 (GenBank No.: MN996532.1), with 96.2% nucleotide homology in the whole genome [12] [13] [14] . Other groups suggest that pangolin, mink, snake, turtle may be potential intermediate hosts for the virus but not conclusively [3, [15] [16] [17] [18] . In India, from January 25 to 31, 2020 three cases were shown to be positive for . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint . https://doi.org/10.1101/2020.04.17.20070284 doi: medRxiv preprint Whereas, all the other human affecting coronavirus genome from China, Wuhan, Brazile, . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint . https://doi.org/10.1101/2020.04. 17.20070284 doi: medRxiv preprint Australia were closely related and they were adjacent to Bat coronavirus (MN996532.1, EF065511.1, MN611520.1), civet coronavirus AY572038.1 as a secondary neighborhood close to the human coronavirus next to bat virus. Though it is not conclusive, the coronavirus from sparrow and white-eye are more close to Indian isolates, which indicates they may be associated with the patients from other species of animal sources. The emergence and rapid spread of COVID-19 signifies a perfect epidemiological storm. COVID-19 a member of the genus Betacoronavirus, subgenus -Sarbecovirus as like SARS-CoV, but MERS-CoV belongs to Merbecovirus (subgenus) [12, [23] [24] . The RaTG13 is 96% identical to COVID-19 at the nucleotide level, but the receptor binding domain (RBD) is only 85% similar and shared only one of the six critical amino acid residues [25] . Still, the COVID-19 RBD for human ACE2 receptor found to be strong and functional [26] which armor the virus towards human respiratory system. Research Group of South China Agricultural University analyzed more than 1,000 metagenomic samples, and they found 70% of pangolins were positive for the coronavirus. In addition, virus isolate from pangolin shared 99% sequence similarity with the current infected human strain SARS-CoV-2 [27] and they addressed pangolins may be one of the intermediate hosts for SARS-CoV-2 later they were embrassed to be a miscommunication of data reported [28] Infact, only 90% genome were homology to SARS-CoV-2 genome and Coronavirus from Pangolins. This incidence was a best example, how the scientific and public media were exaggerating the data without solid evident. Inspite, the 96% identity of SARS-CoV-2 with the Bat coronavirus presumes, they are very closely related to SARSCoV-2, in virtual this likely represents more than 20 years of RNA sequence evolution, whcih may occure if the molecular clock emerges at an uncertain rate if there was strong adaptive evolution of the virus in humans [25] . Available bat coronavirus genome was studied from Yunnan province, over 1,500 km from Wuhan. There are few bat coronaviruses from Hubei province, and those that have been sequenced are . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint . Inspite of all the effort taken all over the world, USA has been affected to the highest level in the world, where 6,32,781 confirmed cases and 28,221deaths were reported as on April Although Germany position to be 4 th as per the confirmed cases, but the number of death reported till date was lower compared to other countries, which made it as 9 th position. The complete country wise cumulative confirmed cases and cumulative deaths between April 7 th 2020 and April 17 th 2020 was calculated and the percentage wise confirmed cases and death rate in 10 days was calculated and shown in the Continued testing of people, irrespective of symptoms and travel history is the need of time to scrutinize the asymptomatic carrier people among the group of population, will cut down the number of death rate. This April 2020 plays major role in the steady death toll increase among various countries mentioned above. Early diagnosis, appropriate treatment, containment zone formation, Quarantine the people with symptoms may help us to flat the rate of infection and death rate. Fig. 5A -C. Representation of major country wise confirmed case fold change and Death fold change between April 7, 2020 to April 17, 2020 (10 days) as per WHO report [1] . . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint . https://doi.org/10.1101/2020.04. 17.20070284 doi: medRxiv preprint The pandemic COVID-19 outbreak may have handful different endings. If nature or God give us the luck, the most favourable scenario would be COVID-19 unconsciously petering out as was the case with SARS in 2003. The second chance would be like MERS which, continue sporadically pop up over the years. The third one in worst scenario, it may create more deaths over the year as the sinister path like 1918 Spanish influenza over a decade [30] . Let the nature and future determine it. The dynamic increase of number of confirmed cases and genome sequences from all over the world made us to register the various conditions as on April 1 st week, 2020. Every one hour, the world wide data has been updated in various resources like WHO, John Hopkins website, Worldometer. In this context, our study from 2 Indian isolate provided us the trace for infection source and the spread rate increases the point mutation, which may either reduce the virulent or increase the pathogenicity of novel coronavirus, SARS-CoV-2 mediated COVID-19 which needs further study. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.04.17.20070284 doi: medRxiv preprint Table 4 : Representative of complete country wise cumulative confirmed cases and cumulative deaths between April 7 th 2020 and April 17 th 2020 was calculated and the percentage wise confirmed cases and death rate in 10 days were shown in 7 parts (30 countries in each part), Totally 211 countries/areas or regions were given as per WHO report on April 17, 2020 [1] World Health Organization. Coronavirus disease(COVID-2019) situation reports. WHO; 2020 Origin and evolution of pathogenic coronaviruses Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species. Infection, Genetics and Evolution Human coronaviruses: What do they cause? 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