Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.

Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1–3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China5. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans. Phylogenetic and metagenomic analyses of the complete viral genome of a new coronavirus from the family Coronaviridae reveal that the virus is closely related to a group of SARS-like coronaviruses found in bats in China.

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A new coronavirus associated with human respiratory disease in China.

In March 2003, a novel coronavirus (SARS-CoV) was discovered in association with cases of severe acute respiratory syndrome (SARS). The sequence of the complete genome of SARS-CoV was determined, and the initial characterization of the viral genome is presented in this report. The genome of SARS-CoV is 29,727 nucleotides in length and has 11 open reading frames, and its genome organization is similar to that of other coronaviruses. Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closely related to any of the previously characterized coronaviruses.

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Characterization of a novel coronavirus associated with severe acute respiratory syndrome.

rpd3 is a computer program for statistical identification and characterization of historical recombination events. Given a set of aligned nucleotide sequences, rpd3 will rapidly analyze these with a range of powerful non-parametric recombination detection methods (including bootscan, maxchi, chimaera, 3seq, geneconv, siscan, phylpro and visrd; Boni et al., 2007; Gibbs et al., 2000; Lemey et al., 2009; Padidam et al., 1999, Posada and Crandall, 2001; Weiller, 1998). It will provide a detailed breakdown of recombination breakpoint locations, and the identities of recombinant and parental sequences. For further downstream analyses, the program enables users to save edited sequence alignments with (i) recombinant sequences removed; (ii) recombinationally derived tracts of sequence removed; or (iii) recombinant sequences split into their constituent parts.

An important strength of rdp3 that makes it applicable to a variety of recombination analysis problems is that, unlike many other recombination detection programs such as simplot (Lole et al., 1999), dual brothers (Minin et al., 2005), jphmm (Schultz et al., 2006) or scueal (Kosakovsky et al., 2009), it does not screen predefined sets of potentially recombinant (or query) sequences against other predefined sets of non-recombinant (or reference) sequences. rdp3 instead treats every sequence within an input alignment as a potential recombinant and systematically screens large numbers of sequence triplets and/or quartets to identify sets of three or four sequences that contain a recombinant and two sequences resembling its parents. Such an approach means that rdp3 can simultaneously detect the entire scope of recombination evident within a dataset (i.e. not just that occurring between the reference strains or species) enabling its use in the characterization of complex recombinants such as those derived through recombination between parental sequences that were themselves recombinant. The drawback of such a flexible, exploratory framework is that it can often be difficult to assess the uncertainty associated with inferred recombination patterns. However, with its wide range of cross-checking tools, rpd3 is complementary to probabilistic recombination analysis approaches.

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RDP3: a flexible and fast computer program for analyzing recombination

Three human coronaviruses are known to exist: human coronavirus 229E (HCoV-229E), HCoV-OC43 and severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV). Here we report the identification of a fourth human coronavirus, HCoV-NL63, using a new method of virus discovery. The virus was isolated from a 7-month-old child suffering from bronchiolitis and conjunctivitis. The complete genome sequence indicates that this virus is not a recombinant, but rather a new group 1 coronavirus. The in vitro host cell range of HCoV-NL63 is notable because it replicates on tertiary monkey kidney cells and the monkey kidney LLC-MK2 cell line. The viral genome contains distinctive features, including a unique N-terminal fragment within the spike protein. Screening of clinical specimens from individuals suffering from respiratory illness identified seven additional HCoV-NL63-infected individuals, indicating that the virus was widely spread within the human population.

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Identification of a new human coronavirus

According to World Health Organization estimates, India will have the greatest number of human immunodeficiency virus (HIV)-infected individuals of any country by the end of this decade (1, 6). High rates of sexually transmitted diseases, rapidly increasing seroprevalence in female commercial sex workers, and inadequate facilities for HIV testing, counseling, and prevention are the major contributing factors in the recent explosive increases in the numbers of HIV infections (5, 6, 24, 29). While antiretroviral drugs have reduced mortality from AIDS in developed nations, their effect will be negligible elsewhere due to their cost. For most communicable diseases, vaccines offer the most cost-effective control strategy. It is likely that development of a vaccine for HIV will require knowledge of the viral variants being transmitted in the target population. Despite India’s impending predominance in the worldwide pandemic, little is known of the genetic diversity of HIV-1 in India.

The HIV-1 sequence database is growing exponentially, but the distribution of submitted sequences is not representative of the worldwide picture. Subtype C has been reported in nearly every region affected by HIV-1 (11, 23, 28) and predominates in India, and it also causes 74% of infections in southern Africa and 96% of infections in northern Africa (11, 18, 32). Given the combined population of India and the other regions affected, subtype C is likely to be the most commonly transmitted HIV-1 subtype worldwide. In contrast, 7% of the available HIV-1 sequence data is from subtype C-infected individuals (37), and of the 46 completely sequenced HIV-1 genomes (excluding multiple derivatives of HIV-1LAI), only two are of subtype C, one from a 1992 Brazilian sample and the other from a 1986 Ethiopian sample (37). In November 1997, an analysis of cross-clade epitope variation (9) excluded the C clade from evaluation of p24gag epitopes because of a lack of sequence data, whereas there was sufficient data to analyze subtypes A, B, D, F, G, and H (no HIV-1 harboring a subtype E gag gene has been found). Further sequence data from subtype C is needed, but the past approach of generating data from small subgenomic amplicons is no longer sufficient.

Recent developments have made full-genome characterization of HIV-1 isolates both important and feasible. First, the recognition of intersubtype recombination in a significant proportion of HIV-1 sequences (44, 45) has led to detection of mosaic genomes in many regions of the world affected by multiple subtypes (14, 17, 31). Subtypes A, B, and C in India have been reported (4, 22, 30, 31, 59), but mosaic HIV-1 there has not been reported. The existence of such recombinants makes characterization of variants by analyzing subgenomic segments incomplete. Second, immune responses to vaccines based on single genes such as env have been limited (13), and attention is being shifted toward multivalent vaccines that incorporate other gene products. Third, interactions among discontinuous regions of the genome, such as between the long terminal repeat (LTR) and pol (26), can be detected only when such regions can be analyzed from the same template.

In an effort to characterize subtype C virus genomes being transmitted currently in India, viral isolates were obtained from individuals with seroincident infections in India. Three of the isolates (collected in 1994 and 1995) were known to be non-syncytium inducing (NSI) and therefore resembled viruses transmitted through unprotected sexual contact, which account for 75 to 85% of new infections (2, 15, 61). These isolates were cloned, and nearly full-length genomic sequences were determined. Detailed sequence analysis was performed, as was an analysis of variation in characterized cytotoxic T lymphocyte (CTL) epitopes.

https://jvi.asm.org/content/jvi/73/1/152.full.pdf

Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination

ABSTRACT Q-type C2H2 zinc finger proteins (ZFPs) play a role in plant stress response. Overexpression of individual ZFPs enhances tolerance to abiotic stresses such as drought or salt. Overexpression of ZFP, Zat18 enhances tolerance to drought, whereas plants with lower amounts are less resilient. The effect of Zat18 loss on gene expression has not been characterized. Overexpression of an ortholog of Zat18 in potato, StZFP2 enhances tolerance to infestation by Manduca sexta. This work focuses on two Zat18 mutant lines, a knockout and knockdown. The two lines differ in response to infestation. Typically, a chewing insect induces the jasmonic acid (JA) pathway. While infestation induces JA pathway genes, Zat18 mutant lines downregulate abscisic acid signaling and induce ethylene signaling genes ERF1 and EBF2 as well as salicylic acid response gene NPR3. Knockdown Zat18, cause far more changes in the infestation response compared with Col-0 or the Zat18 knockout line.

https://www.tandfonline.com/doi/pdf/10.1080/17429145.2021.2024285?needAccess=true

Nicole G. Novak

Papers

Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination

The response to cabbage looper infestation in Arabidopsis is altered by lowering levels of Zat18 a Q-type C2H2 zinc finger protein