Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas and supports their taxonomic reunification along with Stenotrophomonas and Pseudoxanthomonas

Here we report the emergence of variant lineage B.1.1.523 that contains a set of mutations including 156_158del, E484K and S494P in Spike protein. E484K and S494P are known to significantly reduce SARS-CoV-2 neutralization by convalescent and vaccinee sera and are considered as mutations of concern. Lineage B.1.1.523 has presumably originated in Russian Federation and spread across European countries with the peak of transmission in April / May 2021. The B.1.1.523 lineage has now been reported from 27 countries.

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SARS-CoV-2 Infection in One Cat and Three Dogs Living in COVID-19-Positive Households in Madrid, Spain

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.779341 ◽

2021 ◽

Vol 8 ◽

Author(s):

Guadalupe Miró ◽

Javier Regidor-Cerrillo ◽

Rocio Checa ◽

Carlos Diezma-Díaz ◽

Ana Montoya ◽

...

Keyword(s):

Clinical Signs ◽

Nasal Discharge ◽

Virus Shedding ◽

Clinical Exam ◽

Reverse Transcription Pcr ◽

Infection Dynamics ◽

Variant Lineage ◽

Biochemical Profiles ◽

Alpha Variant ◽

Complete Blood Counts

In this study, we describe SARS-CoV-2 infection dynamics in one cat and three dogs from households with confirmed human cases of COVID-19 living in the Madrid Community (Spain) at the time of expansion (December 2020 through June 2021) of the alpha variant (lineage B.1.1.7). A thorough physical exam and nasopharyngeal, oropharyngeal, and rectal swabs were collected for real-time reverse-transcription PCR (RT-qPCR) SARS-CoV-2 testing on day 0 and in successive samplings on days 7, 14, 21, and 47 during monitoring. Blood was also drawn to determine complete blood counts, biochemical profiles, and serology of the IgG response against SARS-CoV-2. On day 0, the cat case 1 presented with dyspnea and fever associated with a mild bronchoalveolar pattern. The dog cases 2, 3, and 4 were healthy, but case 2 presented with coughing, dyspnea, and weakness, and case 4 exhibited coughing and bilateral nasal discharge 3 and 6 days before the clinical exam. Case 3 (from the same household as case 2) remained asymptomatic. SARS-CoV-2 detection by RT-qPCR showed that the cat case 1 and the dog case 2 exhibited the lowest cycle threshold (Ct) (Ct < 30) when they presented clinical signs. Viral detection failed in successive samplings. Serological analyses revealed a positive IgG response in cat case 1 and dog cases 3 and 4 shortly after or simultaneously to virus shedding. Dog case 2 was seronegative, but seroconverted 21 days after SARS-CoV-2 detection. SARS-CoV-2 genome sequencing was attempted, and genomes were classified as belonging to the B.1.1.7 lineage.

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First detection of an Italian human-to-cat outbreak of SARS-CoV-2 Alpha variant – lineage B.1.1.7

One Health ◽

10.1016/j.onehlt.2021.100295 ◽

2021 ◽

pp. 100295

Author(s):

Roberto Zoccola ◽

Chiara Beltramo ◽

Gabriele Magris ◽

Simone Peletto ◽

Pierluigi Acutis ◽

...

Keyword(s):

Variant Lineage ◽

Alpha Variant

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Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York

Nature ◽

10.1038/s41586-021-03908-2 ◽

2021 ◽

Vol 597 (7878) ◽

pp. 703-708 ◽

Cited By ~ 3

Author(s):

Medini K. Annavajhala ◽

Hiroshi Mohri ◽

Pengfei Wang ◽

Manoj Nair ◽

Jason E. Zucker ◽

...

Keyword(s):

New York ◽

New York City ◽

Monoclonal Antibodies ◽

Viral Evolution ◽

The United States ◽

Sharp Rise ◽

Rapid Spread ◽

Variant Lineage ◽

Antibody Resistance ◽

Therapeutic Monoclonal Antibodies

AbstractSARS-CoV-2 infections have surged across the globe in recent months, concomitant with considerable viral evolution1–3. Extensive mutations in the spike protein may threaten the efficacy of vaccines and therapeutic monoclonal antibodies4. Two signature spike mutations of concern are E484K, which has a crucial role in the loss of neutralizing activity of antibodies, and N501Y, a driver of rapid worldwide transmission of the B.1.1.7 lineage. Here we report the emergence of the variant lineage B.1.526 (also known as the Iota variant5), which contains E484K, and its rise to dominance in New York City in early 2021. This variant is partially or completely resistant to two therapeutic monoclonal antibodies that are in clinical use and is less susceptible to neutralization by plasma from individuals who had recovered from SARS-CoV-2 infection or serum from vaccinated individuals, posing a modest antigenic challenge. The presence of the B.1.526 lineage has now been reported in all 50 states in the United States and in many other countries. B.1.526 rapidly replaced earlier lineages in New York, with an estimated transmission advantage of 35%. These transmission dynamics, together with the relative antibody resistance of its E484K sub-lineage, are likely to have contributed to the sharp rise and rapid spread of B.1.526. Although SARS-CoV-2 B.1.526 initially outpaced B.1.1.7 in the region, its growth subsequently slowed concurrently with the rise of B.1.1.7 and ensuing variants.

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Reinfections in COVID-19 Patients: Impact of Virus Genetic Variability and Host Immunity

Vaccines ◽

10.3390/vaccines9101168 ◽

2021 ◽

Vol 9 (10) ◽

pp. 1168

Author(s):

Aisha Fakhroo ◽

Hebah A. AlKhatib ◽

Asmaa A. Al Thani ◽

Hadi M. Yassine

Keyword(s):

Social Life ◽

Protective Immunity ◽

Host Factors ◽

Severe Illness ◽

Rapid Decline ◽

Rapid Spread ◽

Antibody Titers ◽

Variant Lineage ◽

Humoral Responses ◽

Induced Immunity

The COVID-19 pandemic is still posing a devastating threat to social life and economics. Despite the modest decrease in the number of cases during September–November 2020, the number of active cases is on the rise again. This increase was associated with the emergence and spread of the new SARS-CoV-2 variants of concern (VOCs), such as the U.K. (B1.1.7), South Africa (B1.351), Brazil (P1), and Indian (B1.617.2) strains. The rapid spread of these new variants has raised concerns about the multiple waves of infections and the effectiveness of available vaccines. In this review, we discuss SARS-CoV-2 reinfection rates in previously infected and vaccinated individuals in relation to humoral responses. Overall, a limited number of reinfection cases have been reported worldwide, suggesting long protective immunity. Most reinfected patients were asymptomatic during the second episode of infection. Reinfection was attributed to several viral and/or host factors, including (i) underlying immunological comorbidities; (ii) low antibody titers due to the primary infection or vaccination; (iii) rapid decline in antibody response after infection or vaccination; and (iv) reinfection with a different SARS-CoV-2 variant/lineage. Infections after vaccination were also reported on several occasions, but mostly associated with mild or no symptoms. Overall, findings suggest that infection- and vaccine-induced immunity would protect from severe illness, with the vaccine being effective against most VOCs.

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High prevalence of SARS-CoV-2 B.1.1.7 (UK variant) and the novel B.1.525 lineage in Oyo State, Nigeria

10.1101/2021.04.09.21255206 ◽

2021 ◽

Author(s):

Egon A Ozer ◽

Lacy M Simons ◽

Olubusuyi M Adewumi ◽

Adeola A Fowotade ◽

Ewean C Omoruyi ◽

...

Keyword(s):

Immune Escape ◽

Sequence Data ◽

Rapid Expansion ◽

Viral Population ◽

The Novel ◽

Global Pandemic ◽

High Prevalence ◽

Variant Lineage ◽

Recent Origin ◽

Relative Rarity

The spread of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), has resulted in a global pandemic that has claimed the lives of millions of people. Genomic surveillance of the virus has proven to be a critical tool for tracking the emergence and spread of variants with increased transmission or immune evasion potential. Despite the global distribution of infection, differences in viral genomic surveillance capabilities between countries and regions have resulted in gaps in our understanding of the viral population dynamics underlying the pandemic. Nigeria, despite having the largest population of any country in Africa, has had relatively little SARS-CoV-2 sequence data made publicly available. In this study, we report the whole-genome sequences of 74 SARS-CoV-2 isolates collected from individuals in Oyo State, Nigeria over the first two weeks of January 2021. Forty-six of the isolates belong to the B.1.1.7 ″UK variant″ lineage. Comparison to available regional and global sequences suggest that the B.1.1.7 isolates in Nigeria are primarily monophyletic, possibly representing a singular successful introduction into the country. The majority of the remaining isolates (17 of 74) belong to the B.1.525 lineage, which contains multiple spike protein mutations, including the E484K mutation associated with potential immune escape. Indeed, Nigeria has the highest reported frequency of this lineage despite its relative rarity worldwide. Phylogenetic analysis of the B.1.525 isolates in this study relative to other local and global isolates suggested a recent origin and rapid expansion of this lineage in Nigeria, with the country serving as a potential source for this lineage in other outbreaks. These results demonstrate the importance of genomic surveillance for identifying SARS-CoV-2 variants of concern in Nigeria and in other undersampled regions across the globe.

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Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas with Stenotrophomonas and Pseudoxanthomonas as misclassified relatives

10.1101/2021.08.22.457248 ◽

2021 ◽

Author(s):

Kanika Bansal ◽

Sanjeet Kumar ◽

Amandeep Kaur ◽

Anu Singh ◽

Prabhu B. Patil

Keyword(s):

Comparative Studies ◽

Gc Content ◽

Taxonomic Status ◽

Gene Clusters ◽

Insect Vector ◽

Phenotypic Data ◽

Specific Host ◽

Variant Lineage ◽

A Minor

AbstractGenus Xanthomonas is a group of phytopathogens which is phylogenetically related to Xylella, Stenotrophomonas and Pseudoxanthomonas following diverse lifestyles. Xylella is a lethal plant pathogen with highly reduced genome, atypical GC content and is taxonomically related to these three genera. Deep phylo-taxono-genomics reveals that Xylella is a variant Xanthomonas lineage that is sandwiched between Xanthomonas species. Comparative studies suggest the role of unique pigment and exopolysaccharide gene clusters in the emergence of Xanthomonas and Xylella clades. Pan genome analysis identified set of unique genes associated with sub-lineages representing plant associated Xanthomonas clade and nosocomial origin Stenotrophomonas. Overall, our study reveals importance to reconcile classical phenotypic data and genomic findings in reconstituting taxonomic status of these four genera.Significance StatementXylella fastidiosa is a devastating pathogen of perennial dicots such as grapes, citrus, coffee, and olives. The pathogen is transmitted by an insect vector to its specific host wherein the infection leads to complete wilting of the plants. The genome of X. fastidiosa is extremely reduced both in terms of size (2Mb) and GC content (50%) when compared with its relatives such as Xanthomonas, Stenotrophomonas, and Pseudoxanthomonas that have higher GC content (65%) and larger genomes (5Mb). In this study, using systematic and in-depth genome-based taxonomic and phylogenetic criteria along with comparative studies, we assert the need of unification of Xanthomonas with its misclassified relatives (Xylella, Stenotrophomonas and Pseudoxanthomonas). Interestingly, Xylella revealed itself as a minor lineage embedded within two major Xanthomonas lineages comprising member species of different hosts.

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Air travel-related outbreak of multiple SARS-CoV-2 variants

10.1101/2021.07.22.21260854 ◽

2021 ◽

Author(s):

Vijaykrishna Dhanasekaran ◽

Kimberly M Edwards ◽

Ruopeng Xie ◽

Haogao Gu ◽

Dillon C Adam ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Hong Kong ◽

Opportunistic Infections ◽

Positive Sample ◽

Onset Date ◽

New Delhi ◽

Nomenclature System ◽

Variant Lineage ◽

And Control ◽

Acid Test

Background. A large cluster of 59 cases were linked to a single flight with 146 passengers from New Delhi to Hong Kong in April 2021. This outbreak coincided with early reports of exponential pandemic growth in New Delhi, which reached a peak of >400,000 newly confirmed cases on 7 May 2021. Methods. Epidemiological information including date of symptom onset, date of positive-sample detection, and travel and contact history for individual cases from this flight were collected. Whole genome sequencing was performed, and sequences were classified based on the dynamic Pango nomenclature system. Maximum-likelihood phylogenetic analysis compared sequences from this flight alongside other cases imported from India to Hong Kong on 26 flights between June 2020 and April 2021, as well as sequences from India or associated with India-related travel from February to April 2021, and 1,217 reference sequences. Results. Sequence analysis identified six lineages of SARS-CoV-2 belonging to two variants of concern (Alpha and Delta) and one variant of public health interest (Kappa) involved in this outbreak. Phylogenetic analysis confirmed at least three independent sub-lineages of Alpha with limited onward transmission, a superspreading event comprising 37 cases of Kappa, and transmission of Delta to only one passenger. Additional analysis of another 26 flights from India to Hong Kong confirmed widespread circulation of all three variants in India since early March 2021. Conclusions. The broad spectrum of disease severity and long incubation period of SARS-CoV-2 pose a challenge for surveillance and control. As illustrated by this particular outbreak, opportunistic infections of SARS-CoV-2 can occur irrespective of variant lineage, and requiring a nucleic acid test within 72 hours of departure may be insufficient to prevent importation or in-flight transmission.

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SARS-CoV-2 Lambda Variant Remains Susceptible to Neutralization by mRNA Vaccine-elicited Antibodies and Convalescent Serum

10.1101/2021.07.02.450959 ◽

2021 ◽

Author(s):

Takuya Tada ◽

Hao Zhou ◽

Belinda M Dcosta ◽

Marie I Samanovic ◽

Mark J Mulligan ◽

...

Keyword(s):

Monoclonal Antibody ◽

Antibody Therapy ◽

Spike Protein ◽

World Health ◽

South American ◽

Novel Mutations ◽

Therapeutic Monoclonal Antibody ◽

Variant Lineage ◽

Health Organization ◽

Antibody Cocktail

The SARS-CoV-2 lambda variant (lineage C.37) was designated by the World Health Organization as a variant of interest and is currently increasing in prevalence in South American and other countries. The lambda spike protein contains novel mutations within the receptor binding domain (L452Q and F490S) that may contribute to its increased transmissibility and could result in susceptibility to re-infection or a reduction in protection provided by current vaccines. In this study, the infectivity and susceptibility of viruses with the lambda variant spike protein to neutralization by convalescent sera and vaccine-elicited antibodies was tested. Virus with the lambda spike had higher infectivity and was neutralized by convalescent sera and vaccine-elicited antibodies with a relatively minor 2.3-3.3-fold decrease in titer on average. The virus was neutralized by the Regeneron therapeutic monoclonal antibody cocktail with no loss of titer. The results suggest that vaccines in current use will remain protective against the lambda variant and that monoclonal antibody therapy will remain effective.

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Detection of SARS-CoV-2 RNA in Bivalve Mollusks by Droplet Digital RT-PCR (dd RT-PCR)

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph19020943 ◽

2022 ◽

Vol 19 (2) ◽

pp. 943

Author(s):

Andrea Mancusi ◽

Federico Capuano ◽

Santa Girardi ◽

Orlandina Di Maro ◽

Elisabetta Suffredini ◽

...

Keyword(s):

Municipal Sewage ◽

Bivalve Mollusks ◽

Human Pathogens ◽

Rt Pcr ◽

Campania Region ◽

Variant Lineage ◽

Alpha Variant ◽

Bivalve Shellfish ◽

Positive Results ◽

Over Time

Bivalve shellfish are readily contaminated by human pathogens present in waters impacted by municipal sewage, and the detection of SARS-CoV-2 in feces of infected patients and in wastewater has drawn attention to the possible presence of the virus in bivalves. The aim of this study was to collect data on SARS-CoV-2 prevalence in bivalve mollusks from harvesting areas of Campania region. A total of 179 samples were collected between September 2019 and April 2021 and were tested using droplet digital RT-PCR (dd RT-PCR) and real-time RT-PCR. Combining results obtained with different assays, SARS-CoV-2 presence was detected in 27/179 (15.1%) of samples. A median viral concentration of 1.1 × 102 and 1.4 × 102 g.c./g was obtained using either Orf1b nsp14 or RdRp/gene E, respectively. Positive results were unevenly distributed among harvesting areas and over time, positive samples being more frequent after January 2021. Partial sequencing of the spike region was achieved for five samples, one of which displaying mutations characteristic of the Alpha variant (lineage B.1.1.7). This study confirms that bivalve mollusks may bioaccumulate SARS-CoV-2 to detectable levels and that they may represent a valuable approach to track SARS-CoV-2 in water bodies and to monitor outbreak trends and viral diversity.

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