A scary virus is sweeping Saudi Arabia. Six million religious pilgrims are about to descend on the country from across the world. The result could be disastrous.

When the Black Death exploded in Arabia in the 14th century, killing an estimated third of the population, it spread across the Islamic world via infected religious pilgrims. Today, the Middle East is threatened with a new plague, one eponymously if not ominously named the Middle East respiratory syndrome (MERS-CoV, or MERS for short). This novel coronavirus was discovered in Jordan in March 2012, and as of June 26, there have been 77 laboratory-confirmed infections, 62 of which have been in Saudi Arabia; 34 of these Saudi patients have died.

Although the numbers -- so far -- are small, the disease is raising anxiety throughout the region. But officials in Saudi Arabia are particularly concerned.

This fall, millions of devout Muslims will descend upon Mecca, Medina, and Saudi Arabia's holy sites in one of the largest annual migrations in human history. In 2012, approximately 6 million pilgrims came through Saudi Arabia to perform the rituals associated with umrah, and this number is predicted to rise in 2013. Umrah literally means "to visit a populated place," and it's the very proximity that has health officials so worried. In Mecca alone, millions of pilgrims will fulfill the religious obligation of circling the Kaaba. And having a large group of people together in a single, fairly confined space threatens to turn the holiest site in Islam into a massive petri dish.

The disease is still mysterious. Little is understood about how it is transmitted and even less regarding its origins. But we do know that MERS is deadly, with a mortality rate of about 55 percent -- a remarkably higher lethality than that posed by its close cousin, the severe acute respiratory syndrome (SARS) virus, which in 2003 terrified travelers across the globe but posed a fatality rate of only 9.6 percent. The MERS coronavirus is new to our species, so mild and asymptomatic infections seem to be rare, but the human immune response to infection is itself so extreme that it can prove deadly in some cases.

The outbreak of avian-origin influenza A (H7N9) virus in eastern China^1,2 has reminded the world of the imminent threat of unexpected pathogens, including an "old" virus, influenza. Recent conversation has centered on H5N1, H9N2, H7N3, and H7N7, but never before had we considered H7N9 to be the cause of outbreaks of human infection or the next possible pandemic. Maybe we have to take a closer look at the possibility of reassortment among any of the 16 hemagglutinins and 9 neuraminidases subtypes, and even within the newly identified bat-derived, influenza-like virus H17N10.^3,4

A new coronavirus, called human coronavirus Erasmus Medical Center (hCoV-EMC) (with a recent proposed new name as Middle East respiratory syndrome coronavirus, or MERS-CoV in abbreviation), has caused alarm in the Middle East, as human infection was first reported in March 2012.⁵ In one year, as of May 12, 2013, there have been 34 cases, with 18 fatalities in total (www.who.org). More importantly, human-to-human transmission has been reported, with second-generation infections in France and the UK in those individuals who have had close contact with patients with a history of travel to the Middle East.

Less publicized but equally significant, the recently emerged severe fever with thrombocytopenia syndrome virus (SFTSV) expanded its geographic spectrum in 2012 - 2013, from China to the USA, and now to Japan.

SFTSV-induced disease was first suspected in China in 2009, and the virus was isolated and confirmed in 2011.⁶ SFTSV is a new member of the genus Phlebovirus, with over 70 known members in the genus, which is in the family Bunyaviridae. Although the phlebovirus has been found in Africa and Europe for many years, SFTSV is the first-ever virus of this type isolated in China.^6,7,8,9,10 The virus is known as the Heartland virus after the name of the place (Heartland, Missouri) where the virus was first isolated in the USA. The Heartland virus is phylogenetically distinct from SFTSV isolated in China, although similar clinical manifestations have been observed.⁹

Researchers have discovered a new virus in patients in Vietnam suffering from severe brain infections, a team of scientists reported today in mBio, the journal of the American Society for Microbiology.

The virus was detected in 28 of 644 patients who had severe brain infections and none of 122 patients who had non-infectious brain disorders, according to researchers at the Oxford University Clinical Research Unit, Wellcome Trust South East Asia Major Overseas Programme and the Academic Medical Center, University of Amsterdam. It's tentatively called CyCV-VN and is part of a group of viruses known as Circoviridae known to circulate in animals such as birds and pigs, they said.

Swimming has been banned at a former blue flag beach in Co Cork due to excessive E.coli levels while the public has been warned of "potential risks" at three other bathing spots, including two current blue flag beaches.

Cork County Council was forced to prohibit swimming at Fountainstown beach, 23km south of Cork City.

A previous recipient of the coveted EU-approved symbol, the council did not make an application this year for Fountainstown to retain its blue flag status due to stricter bathing water criteria.

Recent tests showed Fountainstown had more than double the EU permitted levels of E.coli.

However, advisory notices have also been placed at three beaches in West Cork - Barleycove in the Mizen peninsula, The Warren at Rosscarbery and Tragumna near Skibbereen.

A mysterious group of viruses known for their circular genome has been detected in patients with severe disease on two continents. In papers published independently this week, researchers report the discovery of agents called cycloviruses in Vietnam and in Malawi. The studies suggest that the viruses - one of which also widely circulates in animals in Vietnam - could be involved in brain inflammation and paraplegia, but further studies are needed to confirm a causative link.

The discovery in Vietnam grew out of a frustrating lack of information about the causes of some central nervous system (CNS) infections such as encephalitis and meningitis, which can be fatal or leave lasting damage. "There are a lot of severe cases in the hospitals here, and very often we can't come to a diagnosis," says H. Rogier van Doorn, a clinical virologist with the Oxford University Clinical Research Unit in the Hospital for Tropical Diseases, Ho Chi Minh City. Extensive diagnostic tests turn up pathogens in only about half of patients with such infections, he says. Van Doorn and colleagues in Vietnam and at the University of Amsterdam's Academic Medical Center hoped that they might uncover new pathogens using a powerful new technique called next-generation sequencing.

The group sequenced all the genetic material in cerebrospinal fluid (CSF) samples taken from more than 100 patients with undiagnosed CNS infections. One sample batch returned a promising lead: a viral sequence belonging to the Circoviridae family.

Probing the original patient samples, the scientists ferreted out the sequence in two of the samples - one from an adult and one from a child. Next, they expanded their search, testing samples from an additional 642 patients with CNS infections using a sensitive polymerase chain reaction (PCR) test developed to specifically target the detected sequence. Roughly 4% of the samples tested positive, the team reported in mBio on Tuesday. Whole-genome sequencing confirmed that the virus, which the scientists have dubbed CyCV-VN, for cyclovirus-Vietnam, is novel; it belongs to a genus within the Circoviridae family called cycloviruses.

In the largest outbreak ever reported in the U.S. of blastomycosis, a fungal infection with flulike symptoms, 55 people in central Wisconsin became sick in 2010.

The fungus that causes blastomycosis is commonly found in soil, but exactly what triggered the spike in cases in Marathon County remains a mystery, according to a new report from the Centers for Disease Control and Prevention and Wisconsin health officials.

Unlike a blastomycosis outbreak in a neighboring Wisconsin county in 2006, in which a pile of waste in a large yard was the likely source, the culprit in this episode remains elusive.

"We didn't find evidence for a single source in the environment that could explain all the cases," said Kaitlin Benedict, an epidemiologist with the CDC's Mycotic Diseases Branch, who was involved in the research.

"We think there were probably multiple 'hot spots' for the fungus in several different neighborhoods."

It's also unclear why infection rates among Asians, particularly those of Hmong descent, were about 12 times higher than non-Asians, the report said.

Some 45 percent of people affected by the outbreak were of Hmong ethnicity. This group is originally from Southeast Asia, but many of those who became sick in the outbreak had been living in Wisconsin for more than a decade, according to the report.

The large number of cases among the Hmong was one of the most surprising things about this outbreak, Benedict said.

"This is the first known report of Asians being disproportionately affected" by the fungal illness, she said, adding that previous studies have shown high blastomycosis rates among African-Americans in other U.S. states.

The report was published online (June 3) in the journal Clinical Infectious Diseases.

The squirrels were found in campgrounds near Palomar Mountain

Editor's Note: County officials issued a correction to their news release on Thursday. The squirrels were found at Cedar Grove Campground and Doane Valley Campground.

Three squirrels with plague have been discovered at two campgrounds near Palomar Mountain.

San Diego County Department of Environmental Health officials urged hikers and campers to take simple precautions Wednesday to make sure they don't come into contact with squirrels or their fleas, which can spread plague, a disease caused by bacteria that can make people very sick and even kill them without quick treatment.

"It's not unusual for us to find plague in our area and there really are simple things people can do to protect themselves," said environmental health director Jack Miller. "The big thing is to avoid contact with squirrels and the fleas they carry. If you're camping, set your tents up away from squirrel burrows. If you're hiking, don't feed squirrels and don't let your kids play with them."

The health ministry decided June 14 to withdraw its recommendation for a vaccination to protect girls against cervical cancer after hundreds complained about possible side effects, including long-term pain and numbness.

The Ministry of Health, Labor and Welfare is not suspending the use of the vaccination, but it has instructed local governments not to promote the use of the medicine while studies are conducted on the matter.

"The decision (not to recommend the vaccination) does not mean that the vaccine itself is problematic from the viewpoint of safety," said Mariko Momoi, vice president of the International University of Health and Welfare, who headed a ministry task force looking into the matter.

"By implementing investigations, we want to offer information that can make the people feel more at ease."

It is rare for the ministry to withdraw a recommendation for a vaccine that is used regularly by local governments and is spelled out in a law.

Girls can still receive the vaccination for free, although medical institutions must now inform them beforehand that the ministry does not recommend it.

MERS-CoV, sometimes called nCoV (novel coronavirus), was first characterized in 2012 by Prof Ali Mohamed Zaki. That first case was a 60-year old male with suspected viral pneumonia. Prof. Zaki ran the usual respiratory viral tests which were negative so he sent a sample to virus hunters at Erasmus Medical Centre in The Netherlands. In the interim Prof Zaki tried a broad-spectrum "pan-coronavirus" RT-PCR method and got a positive result.

Members of the subfamily Coronavirinae that infect humans currently include the respiratory coronaviruses HCoV-OC43 (a betaCoV), HCoV-229E (alphaCoV), HCoV-NL63 (alphaCoV), SARS-CoV (betaCoV), MERS-CoV and HCoV-HKU1 (both betaCoV).

Quick numbers

As of 06^th June; FluTrackers, CIDRAP, WHO

• Total human cases of MERS-CoV: 55^a
• Total deaths attributed to infection with MERS-CoV: 33
• Current Case Fatality Rate (CFR^d): 61%

^a Data from FluTrackers, WHO and the European CDC.
^b This uses numbers based on publicly available data which may lack detail. This number gives you an idea of our understanding at the moment. To be pedantic and use only the number of discharges as the denominator for the CFR is most useful at the end of an outbreak/epidemic/pandemic, but not so much when data-in-hand is poor during the beginning.

It is being reported that commercial labs are applying for patents on the Novel Coronavirus that is currently killing 50% of the people who contract it.

The World Health Organisation (WHO) has urged countries with possible cases of novel coronavirus to share information.

The move comes after Saudi Arabia said the development of diagnostic tests had been delayed by patent rights on the NCoV virus by commercial laboratories.

Twenty-two deaths and 44 cases have been reported worldwide since 2012, the WHO says.

NCoV is from the same family of viruses as the one that caused Severe Acute Respiratory Syndrome (Sars).

An outbreak of Sars in 2003 killed about 770 people. However, NCoV and Sars are distinct from each other, the WHO says.

The virus first emerged in Saudi Arabia, which is where most cases have since arisen.