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Distribution of COVID-19 and Phylogenetic Tree Construction of SARS-CoV-2 in Indonesia
Dergi Makalesi

Dergi Makalesi
Open Access
Kaynak :
Directory of Open Access Journals (DOAJ)
Dergi:
Journal of Pure and Applied Microbiology
Yazar(lar) :
Dora Dayu Rahma Turista , Aesthetica Islamy , Viol Dhea Kharisma , Arif Nur Muhammad Ansori
Yıl :
2020
Distribution of COVID-19 and Phylogenetic Tree Construction of SARS-CoV-2 in Indonesia Coronavirus disease 2019 ( COVID- 19) is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID- 19 has spread quickly across the world and has been declared a pandemic. Indonesia has many COVID- 19 cases, with a high mortality rate. The distribution data of COVID- 19 in Indonesia were obtained from the COVID- 19 Management Handling Unit and descriptively analyzed. covid-19
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Coronavirus disease 2019 (COVID-19) is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 has spread quickly across the world and has been declared a pandemic. Indonesia has many COVID-19 cases, with a high mortality rate. This study aimed to describe the distribution of COVID-19 in Indonesia and constructed the SARS-CoV-2 phylogenetic tree from Indonesian isolates and those from other countries, including other CoVs to determine their relationship. The distribution data of COVID-19 in Indonesia were obtained from the COVID-19 Management Handling Unit and descriptively analyzed. SARS-CoV-2 isolates were retrieved from the GenBank® (National Center of Biotechnology Information, USA) and GISAID EpiCoV™ databases and were used to construct phylogenetic trees using MEGA X software. Of the 37 provinces in Indonesia, five provinces with the highest case fatality rates were DKI Jakarta, Jawa Barat, Jawa Timur, and Banten, and the five provinces with the highest cure rate were Kepulauan Riau, Bali, Aceh, Gorontalo, and DI Yogyakarta. SARS-CoV-2 Indonesian isolates were closely related to SARS-CoV-2 isolates from other countries. The rapid and widespread distribution of SARS-CoV-2 in Indonesia was caused by the lack of compliance with territorial restrictions and dishonesty with medical personnel. These data revealed that mutations can occur during the transmission process, which can be caused by a history of travel and increased patient immunity.
DOI : 10.22207/JPAM.14.SPL1.42
Anahtar Kelimeler : covid-19, indonesia, phylogenetic tree, sars-cov-2
Cilt: 14
Sayı: suppl 1
Sayfa: 1035 - 1042
Sınıflandırma :
2
First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries
Dergi Makalesi

Dergi Makalesi
Kaynak :
Science Direct
Dergi:
International Journal of Infectious Diseases
Yayıncı:
Elsevier
Yazar(lar) :
Edgar Simulundu , Francis Mupeta , Pascalina Chanda-Kapata , Ngonda Saasa , Katendi Changula , Walter Muleya , Simbarashe Chitanga , Miniva Mwanza , Paul Simusika , Herman Chambaro , Benjamin Mubemba , Masahiro Kajihara , Duncan Chanda , Lloyd Mulenga , Sombo Fwoloshi , Aaron Lunda Shibemba , Fred Kapaya , Paul Zulu , Kunda Musonda , Mwaka Monze , Nyambe Sinyange , Mazyanga M. Liwewe , Muzala Kapinu2019a , Peter J. Chipimo , Raymond Hamoonga , Davie Simwaba , William Ngosa , Albertina N. Morales , Nkomba Kayeyi , John Tembo , Mathew Bates , Yasuko Orba , Hirofumi Sawa , Ayato Takada , King S. Nalubamba , Kennedy Malama , Victor Mukonka , Alimuddin Zumla , Nathan Kapata
Yıl :
2020
First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries
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DOI : 10.1016/j.ijid.2020.09.1480
ISSN: 1201-9712

Sınıflandırma :
3
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
Dergi Makalesi

Dergi Makalesi
Open Access
Kaynak :
Springer Nature
Dergi:
Nature Microbiology
Yayıncı:
Springer Nature
Yazar(lar) :
Maciej F. Boni , Philippe Lemey , Xiaowei Jiang , Tommy Tsan-Yuk Lam , Blair W. Perry , Todd A. Castoe , Andrew Rambaut , David L. Robertson
Konu :
Molecular evolution, Phylogenetics, SARS-CoV-2, Viral evolution
Yıl :
2020
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
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There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. We find that the sarbecoviruses—the viral subgenus containing SARS-CoV and SARS-CoV-2—undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879–1999), 1969 (95% HPD: 1930–2000) and 1982 (95% HPD: 1948–2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades. In this manuscript, the authors address evolutionary questions on the emergence of SARS-CoV-2. They find that SARS-CoV-2 is not a recombinant of any sarbecoviruses detected to date, and that the bat and pangolin sequences most closely related to SARS-CoV-2 probably diverged several decades ago or possibly earlier from human SARS-CoV-2 samples.
DOI : 10.1038/s41564-020-0771-4
ISSN: 2058-5276
Sayfa: 1-10
Sınıflandırma :
4
A cluster of COVID-19 cases in a small Italian town: a successful example of contact tracing and swab collection
Dergi Makalesi

Dergi Makalesi
Kaynak :
Science Direct
Dergi:
Clinical Microbiology and Infection
Yayıncı:
Elsevier
Yazar(lar) :
F. Valent , T. Gallo , E. Mazzolini , C. Pipan , A. Sartor , M. Merelli , G. Bontempo , S. Marzinotto , F. Curcio , C. Tascini
Yıl :
2020
A cluster of COVID-19 cases in a small Italian town: a successful example of contact tracing and swab collection
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DOI : 10.1016/j.cmi.2020.04.028
ISSN: 1198-743X
Sayı: 8
Cilt: 26
Sayfa: 1112-1114
Sınıflandırma :
Viroloji %83
5
Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)?
Dergi Makalesi

Dergi Makalesi
Open Access
Kaynak :
Directory of Open Access Journals (DOAJ)
Dergi:
PLoS Pathogens
Yazar(lar) :
Ping Liu , Jing-Zhe Jiang , Xiu-Feng Wan , Yan Hua , Linmiao Li , Jiabin Zhou , Xiaohu Wang , Fanghui Hou , Jing Chen , Jiejian Zou , Jinping Chen
Yıl :
2020
The outbreak of a novel corona Virus Disease 2019 ( COVID- 19) in the city of Wuhan, China has resulted in more than 1.7 million laboratory confirmed cases
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The outbreak of a novel corona Virus Disease 2019 (COVID-19) in the city of Wuhan, China has resulted in more than 1.7 million laboratory confirmed cases all over the world. Recent studies showed that SARS-CoV-2 was likely originated from bats, but its intermediate hosts are still largely unknown. In this study, we assembled the complete genome of a coronavirus identified in 3 sick Malayan pangolins. The molecular and phylogenetic analyses showed that this pangolin coronavirus (pangolin-CoV-2020) is genetically related to the SARS-CoV-2 as well as a group of bat coronaviruses but do not support the SARS-CoV-2 emerged directly from the pangolin-CoV-2020. Our study suggests that pangolins are natural hosts of Betacoronaviruses. Large surveillance of coronaviruses in pangolins could improve our understanding of the spectrum of coronaviruses in pangolins. In addition to conservation of wildlife, minimizing the exposures of humans to wildlife will be important to reduce the spillover risks of coronaviruses from wild animals to humans.
DOI : 10.1371/journal.ppat.1008421
Cilt: 16
Sayı: 5
Sayfa: e1008421
Sınıflandırma :
6
Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins
Dergi Makalesi

Dergi Makalesi
Open Access
Kaynak :
Springer Nature
Dergi:
Nature
Yayıncı:
Springer Nature
Yazar(lar) :
Kangpeng Xiao , Junqiong Zhai , Yaoyu Feng , Niu Zhou , Xu Zhang , Jie-Jian Zou , Na Li , Yaqiong Guo , Xiaobing Li , Xuejuan Shen , Zhipeng Zhang , Fanfan Shu , Wanyi Huang , Yu Li , Ziding Zhang , Rui-Ai Chen , Ya-Jiang Wu , Shi-Ming Peng , Mian Huang , Wei-Jun Xie , Qin-Hui Cai , Fang-Hui Hou , Wu Chen , Lihua Xiao , Yongyi Shen
Konu :
SARS-CoV-2, SARS virus, Viral infection
Yıl :
2020
The current outbreak of coronavirus disease-2019 ( COVID- 19) poses unprecedented challenges to global health1.
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The current outbreak of coronavirus disease-2019 (COVID-19) poses unprecedented challenges to global health1. The new coronavirus responsible for this outbreak—severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—shares high sequence identity to SARS-CoV and a bat coronavirus, RaTG132. Although bats may be the reservoir host for a variety of coronaviruses3,4, it remains unknown whether SARS-CoV-2 has additional host species. Here we show that a coronavirus, which we name pangolin-CoV, isolated from a Malayan pangolin has 100%, 98.6%, 97.8% and 90.7% amino acid identity with SARS-CoV-2 in the E, M, N and S proteins, respectively. In particular, the receptor-binding domain of the S protein of pangolin-CoV is almost identical to that of SARS-CoV-2, with one difference in a noncritical amino acid. Our comparative genomic analysis suggests that SARS-CoV-2 may have originated in the recombination of a virus similar to pangolin-CoV with one similar to RaTG13. Pangolin-CoV was detected in 17 out of the 25 Malayan pangolins that we analysed. Infected pangolins showed clinical signs and histological changes, and circulating antibodies against pangolin-CoV reacted with the S protein of SARS-CoV-2. The isolation of a coronavirus from pangolins that is closely related to SARS-CoV-2 suggests that these animals have the potential to act as an intermediate host of SARS-CoV-2. This newly identified coronavirus from pangolins—the most-trafficked mammal in the illegal wildlife trade—could represent a future threat to public health if wildlife trade is not effectively controlled. A newly identified coronavirus found in Malayan pangolins shares considerable sequence identity with SARS-CoV-2, which suggests that the latter may have originated from a recombination event involving SARS-related coronaviruses from bats and pangolins.
DOI : 10.1038/s41586-020-2313-x
ISSN: 1476-4687
Cilt: 583
Sayı: 7815
Sayfa: 286-289
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