Natural infection of Delta mutant of SARS‐CoV‐2 in Asiatic lions of India

Karikalan, M.; Chander, V; Mahajan, S.; Deol, P.; Agrawal, R. K.; Nandi, S.; Rai, S K; Mathur, A.; Pawde, A.; Singh, K P; Sharma, G K

doi:10.1111/tbed.14290

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Natural infection of Delta mutant of SARS‐CoV‐2 in Asiatic lions of India

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Author(s): M. Karikalan ¹ , V. Chander ¹ , S. Mahajan ¹ , P. Deol ¹ , R. K. Agrawal ¹ , S. Nandi ¹ , S. K. Rai ² , A. Mathur ³ , A. Pawde ¹ , K. P. Singh ¹ , G. K. Sharma ¹ ^,

Publication date (Electronic): 26 August 2021

Journal: Transboundary and Emerging Diseases

Publisher: John Wiley and Sons Inc.

Keywords: COVID‐19, Delta mutant, lions, SARS‐CoV‐2

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Abstract

The current pandemic caused by a novel coronavirus (SARS‐CoV‐2) has underlined the importance of emerging diseases of zoonotic importance. Along with human beings, several species of wild and pet animals have been demonstrated to be infected by SARS‐CoV‐2, both naturally and experimentally. In addition, with constant emergence of new variants, the species susceptibility might further change which warrants intensified screening efforts. India is a vast and second most populated country, with a habitat of a very diverse range of animal species. In this study we place on record of SARS‐CoV‐2 infections in three captive Asiatic lions. Detailed genomic characterization revealed involvement of Delta mutant (Pango lineage B.1.617.2) of SARS‐CoV‐2 at two different locations. Interestingly, no other feline species enclosed in the zoo/park were found infected. The epidemiological and molecular analysis will contribute to the understanding of the emerging mutants of SARS‐CoV‐2 in wild and domestic animals.

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The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker … (2009)

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk

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A Novel Coronavirus from Patients with Pneumonia in China, 2019

Na Zhu, Dingyu Zhang, Wenling Wang … (2020)

Summary In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed a clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that infect humans. Enhanced surveillance and further investigation are ongoing. (Funded by the National Key Research and Development Program of China and the National Major Project for Control and Prevention of Infectious Disease in China.)

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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2009)

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk

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Author and article information

Contributors

G. K. Sharma:

ORCID: https://orcid.org/0000-0002-9996-9422

gaurvet@gmail.com

Journal

Journal ID (nlm-ta): Transbound Emerg Dis

Journal ID (iso-abbrev): Transbound Emerg Dis

Journal ID (doi): 10.1111/(ISSN)1865-1682

Journal ID (publisher-id): TBED

Title: Transboundary and Emerging Diseases

Publisher: John Wiley and Sons Inc. (Hoboken )

ISSN (Print): 1865-1674

ISSN (Electronic): 1865-1682

Publication date (Electronic): 26 August 2021

Publication date PMC-release: 26 August 2021

Electronic Location Identifier: 10.1111/tbed.14290

Affiliations

[ ¹ ] CADRAD ICAR‐Indian Veterinary Research Institute Izatnagar Bareilly Uttar Pradesh India

[ ² ] Lion Safari Park Etawah Uttar Pradesh India

[ ³ ] Nahargarh Biological Park Jaipur Rajasthan India

Author notes

[*] [* ] Correspondence

Dr Gaurav Sharma, IVRI, ICAR, CADRAD, IVRI Izatnagar, Uttar Pradesh, Bareilly, Uttar Pradesh 243122, India.

Email: gaurvet@ 123456gmail.com

Author information

V. Chander https://orcid.org/0000-0002-6168-9556

S. Mahajan https://orcid.org/0000-0001-7671-4251

G. K. Sharma https://orcid.org/0000-0002-9996-9422

Article

Publisher ID: TBED14290

DOI: 10.1111/tbed.14290

PMC ID: 8447162

PubMed ID: 34404118

SO-VID: 539f0673-158c-4e78-8845-c7ab7844b946

License:

This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.