The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

On April 17, 2009, CDC determined that two cases of febrile respiratory illness occurring in children who resided in adjacent counties in southern California were caused by infection with a swine influenza A (H1N1) virus. The viruses from the two cases are closely related genetically, resistant to amantadine and rimantadine, and contain a unique combination of gene segments that previously has not been reported among swine or human influenza viruses in the United States or elsewhere. Neither child had contact with pigs; the source of the infection is unknown. Investigations to identify the source of infection and to determine whether additional persons have been ill from infection with similar swine influenza viruses are ongoing. This report briefly describes the two cases and the investigations currently under way. Although this is not a new subtype of influenza A in humans, concern exists that this new strain of swine influenza A (H1N1) is substantially different from human influenza A (H1N1) viruses, that a large proportion of the population might be susceptible to infection, and that the seasonal influenza vaccine H1N1 strain might not provide protection. The lack of known exposure to pigs in the two cases increases the possibility that human-to-human transmission of this new influenza virus has occurred. Clinicians should consider animal as well as seasonal influenza virus infections in their differential diagnosis of patients who have febrile respiratory illness and who 1) live in San Diego and Imperial counties or 2) traveled to these counties or were in contact with ill persons from these counties in the 7 days preceding their illness onset, or 3) had recent exposure to pigs. Clinicians who suspect swine influenza virus infections in a patient should obtain a respiratory specimen and contact their state or local health department to facilitate testing at a state public health laboratory.

Swine influenza A (H1N1) infection in two children - Southern California, March-April 2009.

The Summary of Notifiable Diseases - United States, 2011 contains the official statistics, in tabular and graphic form, for the reported occurrence of nationally notifiable infectious diseases in the United States for 2011. Unless otherwise noted, the data are final totals for 2011 reported as of June 30, 2012. These statistics are collected and compiled from reports sent by state health departments and territories to the National Notifiable Diseases Surveillance System (NNDSS), which is operated by CDC in collaboration with the Council of State and Territorial Epidemiologists (CSTE).

/pdf/summary-of-notifiable-diseases-united-states-2011-2ycpfu6g2m.pdf

Summary of Notifiable Diseases - United States, 2011.

Background Triple-reassortant swine influenza A (H1) viruses — containing genes from avian, human, and swine influenza viruses — emerged and became enzootic among pig herds in North America during the late 1990s. Methods We report the clinical features of the first 11 sporadic cases of infection of humans with triple-reassortant swine influenza A (H1) viruses reported to the Centers for Disease Control and Prevention, occurring from December 2005 through February 2009, until just before the current epidemic of swine-origin influenza A (H1N1) among humans. These data were obtained from routine national influenza surveillance reports and from joint case investigations by public and animal health agencies. Results The median age of the 11 patients was 10 years (range, 16 months to 48 years), and 4 had underlying health conditions. Nine of the patients had had exposure to pigs, five through direct contact and four through visits to a location where pigs were present but without contact. In another patient, hu...

https://www.nejm.org/doi/pdf/10.1056/NEJMoa0903812

Triple-Reassortant Swine Influenza A (H1) in Humans in the United States, 2005–2009

The Summary of Notifiable Infectious Diseases and Condition-United States, 2013 (hereafter referred to as the summary) contains the official statistics, in tabular and graphic form, for the reported occurrence of nationally notifiable infectious diseases and conditions in the United States for 2013. Unless otherwise noted, data are final totals for 2013 reported as of June 30, 2014. These statistics are collected and compiled from reports sent by U.S. state and territory, New York City, and District of Columbia health departments to the National Notifiable Diseases Surveillance System (NNDSS), which is operated by CDC in collaboration with the Council of State and Territorial Epidemiologists (CSTE). This summary is available at http://www.cdc.gov/mmwr/mmwr_nd/index.html. This site also includes summary publications from previous years.

/pdf/summary-of-notifiable-infectious-diseases-and-conditions-1h4kmx6yio.pdf

Summary of Notifiable Infectious Diseases and Conditions - United States, 2013.

In Ohio, United States, in early 2014, a deltacoronavirus was detected in feces and intestine samples from pigs with diarrheal disease. The complete genome sequence and phylogenetic analysis of the virus confirmed that the virus is closely related to a porcine deltacoronavirus (porcine coronavirus HKU15) reported in Hong Kong in 2012.

/pdf/detection-and-genetic-characterization-of-deltacoronavirus-3iyquqah9g.pdf

Detection and Genetic Characterization of Deltacoronavirus in Pigs, Ohio, USA, 2014

To the Editor: Porcine epidemic diarrhea (PED) was first reported in the United Kingdom in 1971 (1). The disease was characterized by severe enteritis, vomiting, watery diarrhea, dehydration, and a high mortality rate among swine. Subsequently, the causative agent of PED was identified as porcine epidemic diarrhea virus (PEDV), which belongs to the family Coronaviridae (2) and contains an enveloped, single-stranded positive-sense RNA genome. PEDV has been reported in many other countries, including Germany, France, Switzerland, Hungary, Italy, China, South Korea, Thailand, and Vietnam (3) and was first identified in the United States in May 2013. By the end of January of 2014, the outbreak had occurred in 23 US states, where 2,692 confirmed cases (www.aasv.org/news/story.php?id = 6989) caused severe economic losses. Recent studies have shown that all PEDV strains in the United States are clustered together in 1 clade within the subgenogroup 2a and are closely related to a strain from China, AH2012 (4,5).

In the state of Ohio, the first PED case was identified in June of 2013; since then, hundreds of cases have been confirmed by the Animal Disease Diagnostic Laboratory of the Ohio Department of Agriculture. In January of 2014, samples from pigs with unique disease, suspected to be PED, were submitted to this laboratory. Sows were known to be infected, but piglets showed minimal to no clinical signs and no piglets had died. 

According to real-time reverse transcription PCR, all samples from the piglets were positive for PEDV. Subsequently, the full-length genome sequence of PEDV (OH851) was determined by using 19 pairs of oligonucleotide primers designed from alignments of the available genomes from PEDVs in the United States (6,7). On the basis of BLAST (http:blast.ncbi.nlm.nih.gov/Blast.cgi) searches, strain OH851 showed 99% and 97% nt identity to PEDVs currently circulating in the United States (Colorado, Iowa, Indiana, Minnesota) for the whole genome and the full-length spike (S) gene, respectively. By distinct contrast, strain OH851 showed only 89% or even lower nucleotide identity to PEDVs currently circulating in the United States in the first 1,170 nt of the S1 region. In that region, nucleotide similarity to that of a PEDV strain from China (CH/HBQX/10, {"type":"entrez-nucleotide","attrs":{"text":"JS120103","term_id":"364436861","term_text":"JS120103"}}JS120103) was 99%, suggesting that strain OH851 is a new PEDV variant. Phylogenetic analysis of the complete genome indicated that the novel OH851 PEDV is clustered with other strains of PEDV currently circulating in United States, including another stain from Ohio, OH1414 (Figure, panel A). However, phylogenetic analysis of the full-length S gene showed that strain OH851 is clustered with other strains of PEDV from China and most closely related to a PEDV strain from China, CH/HBQX/10 (8), but distantly related to other PEDV strains currently circulating in the United States and strain AH2012 (Figure, panel B). This finding strongly suggests that strain OH851 is a variant PEDV. In comparison with the S gene of other strains from the United States, the S gene of strain OH851 has 3 deletions (a 1-nt deletion at position 167, a 11-nt deletion at position 176, and a 3-nt deletion at position 416), a 6-nt insertion between positions 474 and 475, and several mutations mainly located in the first 1,170 nt of the S1 region. 



Figure

Phylogenetic tree of the whole-genome sequences of 33 strains of porcine epidemic diarrhea virus (PEDV) (A) and of spike protein nucleotide sequences of 56 strains of PEDV (B), including the new variant PEDV (OH851) and 8 PEDV strains currently circulating ...



It is highly possible that the sequence deletions, insertion, and mutations found in variant strain OH851 might have contributed to the reduced severity of the clinical disease in the piglets. More animal studies are needed to test this hypothesis. The unique deletion and insertion feature also represents a target for diagnostic assays to differentiate between currently circulating PEDV strains and new variants.

The low nucleotide identity in the 5′-end S1 region (first 1,170 nt) region and high nucleotide identity in the non-5′-end S1 region of the variant strain, compared with that of the PEDVs currently circulating in the United States, suggest that this new PEDV variant might have evolved from a recombinant event involving a strain from China. Because the new variant does not cause severe clinical disease, including death, the novel virus is a potential vaccine candidate that could protect the US swine industry from the infection caused by the virulent strain of PEDV currently circulating in United States.

New Variant of Porcine Epidemic Diarrhea Virus, United States, 2014

To understand the progression of porcine epidemic diarrhea virus infection, we inoculated gnotobiotic pigs with a newly emerged US strain, PC21A, of the virus. At 24–48 hours postinoculation, the pigs exhibited severe diarrhea and vomiting, fecal shedding, viremia, and severe atrophic enteritis. These findings confirm that strain PC21A is highly enteropathogenic.

/pdf/pathology-of-us-porcine-epidemic-diarrhea-virus-strain-pc21a-4qtwhd2546.pdf

Pathology of US porcine epidemic diarrhea virus strain PC21A in gnotobiotic pigs.

Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene.

Four types of porcine epidemic diarrhea virus (PEDV) variants with a large deletion in the spike protein were detected, together with the original US PEDV, from pig fecal and oral fluid samples collected during 2016-2017 in the US. Two of the variants are similar to those identified in Japan: one contains a 194-aa deletion, the same as PEDV variant TTR-2/JPN/2014, while the other contains a 204-aa deletion, the same as PEDV variant JKa-292/CS1de204. Two new S1 NTD-del PEDV variants were found: one contains a 201-aa deletion located at residues 30-230 and the other contains a 202-aa deletion located at residues 24-225 of the S protein. This is the first report on coinfection of S1 NTD-del PEDV variants and the original US PEDV strain in US pigs, indicating that PEDV continues to evolve in pigs and might be responsible for disease pattern changes.

/pdf/new-variants-of-porcine-epidemic-diarrhea-virus-with-large-4u2ojx2yn7.pdf

Yan Zhang

Papers

Detection and Genetic Characterization of Deltacoronavirus in Pigs, Ohio, USA, 2014

New Variant of Porcine Epidemic Diarrhea Virus, United States, 2014

Pathology of US porcine epidemic diarrhea virus strain PC21A in gnotobiotic pigs.

Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene.

New variants of porcine epidemic diarrhea virus with large deletions in the spike protein, identified in the United States, 2016-2017.