The year started in the United States with a mild flu season but ended up being marked by deadly outbreaks of fungal meningitis, West Nile virus and Hantavirus.

Tainted steroid medication has been cited as the cause of the meningitis outbreak that killed 39 people.

Weather contributed to the worst outbreak of West Nile virus since 2003 and an unusual outbreak of Hantavirus in California's Yosemite National Park.

Transmitted by infected mice, Hantavirus is a severe, sometimes fatal syndrome that affects the lungs. West Nile can cause encephalitis or meningitis, infection of the brain and spinal cord or their protective covering.

As of December 11, 5,387 cases of West Nile virus had been reported in 48 states, resulting in 243 deaths, the CDC said in its final 2012 update on the outbreak. The 2003 outbreak left 264 dead from among nearly 10,000 reported cases.

A large number of cases this year occurred in Texas, Louisiana and Mississippi where there are large mosquito populations.

CDC and state officials have said that rainfall in the spring and record high summer temperatures contributed to the severity of the outbreak by affecting mosquito populations, which transmit the disease by biting humans and animals.

Health officials said that only a small percentage of cases of West Nile virus are reported because most people have no symptoms and about 20 percent have mild symptoms such as aches and fever. One in 150 people with West Nile virus develop other illnesses such as meningitis and encephalitis.

The biggest outbreak in nearly two decades of Hantavirus, which emerges in dry and dusty environments, cropped up during the summer in 1,200-square-mile (3,100-square-km) Yosemite National Park, killing three of 10 infected visitors.

The National Park issued warnings to 22,000 people who may have been exposed to the rare disease, and 91 Curry Village cabins in the park were closed in late August.

In early September, a 78-year-old judge named Eddie Lovelace was rushed to a hospital in Nashville, Tennessee. Thought to have had a stroke, he died a few days later.

After a large outbreak of fungal meningitis was linked to tainted steroid injections, Lovelace's cause of death was revised. He became the first documented death in a meningitis outbreak that has infected 620 people and killed 39 in 19 states.

The New England Compounding Center in Framingham, Massachusetts, was closed after investigators found that it had shipped thousands of fungus-tainted vials of methylprednisolone acetate to medical facilities around the United States. The steroid was typically used to ease back pain.

More than 14,000 people were warned that they may have had an injection of the tainted steroid. Doctors continue to see new cases of spinal infections related to the steroid, and cases of achnoiditis, an inflammation of nerve roots in the spine.

The outbreak led two Democratic lawmakers in the U.S. House of representatives to introduce legislation to increase government oversight of compounded drugs.

And what lies ahead in 2013?

"While there are some trends we can predict, the most reliable trend is that the next threat will be unpredictable," said Centers for Disease Control and Prevention (CDC) Director Thomas Frieden.

More from NBCNews.com health:

Obesity declining in poorer kids

Joys of hottie dating -- and other 'no, duh' studies of 2012

Which comes first: Pot smoking or psychosis?

FRESNO, Calif. -- Yosemite National Park will offer testing to all employees at the site to determine if they have ever been infected with a deadly mouse-borne virus, officials said Thursday.

The testing to be done by state health officials will be voluntary and available to all workers for the National Park Service and its concessionaire, DNC Parks and Resort, park spokesman John Quinley said. He declined to say when the testing would start.

There have been no confirmed or suspected hantavirus cases among park employees so far, Quinley said. The park did not offer the testing earlier because public health officials did not recommend it, he said.

Nine people who visited the park this summer have been infected, the majority after staying overnight at the "Signature" cabins in Curry Village. Three of those people later died.

Between 2,500 and 3,000 people work in the park every year, depending on the season. A little less than half are National Park employees, and the rest work for the concessionaire. Many workers also live in the park.

The California Department of Public Health conducted a pilot testing program on Wednesday, taking blood samples and questionnaires from 96 employees who live or work in the El Portal area of the park.

Hantavirus is carried in the feces, urine and saliva of deer mice and other rodents, and carried on airborne particles and dust.

People can be infected by inhaling the virus or by handling infected rodents. They usually develop flu-like symptoms at first, including fever, shortness of breath, chills and muscle and body aches.

The illness can take six weeks to incubate before rapid acute respiratory and organ failure.

The tests for employees will cover all past infections, said Danielle Buttke, veterinary epidemiologist with the National Park Service. People who have been infected at any time in their lives and developed antibodies will test positive, but the test does not pinpoint time of the infection, or where the person was infected, she said.

The goal of the testing, which was proposed by public health officials, is to further the understanding of the rare virus. Park and public health officials hope to learn more about why no park employees have thus far been struck with the disease, even though many could have been exposed to it, Buttke said.

Officials also hope to learn whether there are any people who had the infection but never developed symptoms of the disease. And they plan to evaluate training or knowledge gaps employees might have about the disease.

It's possible that no employees have contracted hantavirus because they have received training about the illness and take more precautions because they are more aware of the risks than park visitors, Buttke said. Employees also don't stay in visitor facilities overnight, she said.

During the outbreak this summer, park officials say they sent all employee emails about the virus while increasing training and holding meetings about the disease.

Another reason for lack of worker infections could be the rarity of the disease. Previous studies of people who directly handle mice found that only a few had hantavirus antibodies, meaning few were infected by the disease during their careers, said Barbara Knust, an epidemiologist with the Centers for Disease Control and Prevention.

In rare cases, people who did develop antibodies never had any symptoms.

"We think it's actually quite rare that people get infected," Knust said. "And in most cases, people who do get infected with hantavirus show symptoms."

Employees tested in Wednesday's pilot program included maintenance and facilities workers, who open park buildings in the spring.

The effort included questions about employees' work activities and living environment; if and when they were exposed to mice; and what they remembered about hantavirus training.

While individual test results will remain confidential, overall results from the pilot testing could be available sometime next month. 

• Yosemite officials trap, kill mice after hantavirus outbreak
• Yosemite closes cabins after hantavirus deaths

By Ronnie Cohen
Reuters

U.S. health officials have sent warnings to 39 other countries that their citizens who stayed in Yosemite National Park tent cabins this summer may have been exposed to a deadly mouse-borne hantavirus, a park service epidemiologist said on Tuesday.

Of the 10,000 people thought to be at risk of contracting hantavirus pulmonary syndrome from their stays in Yosemite between June and August, some 2,500 live outside the United States, Dr. David Wong told Reuters in an interview.

Wong said U.S. Department of Health and Human Services officials notified 39 countries over the weekend, most of them in the European Union, that their residents may have been exposed to the deadly virus.

The lung disease has so far killed two men and sickened four other people, all U.S. citizens, prompting the U.S. Centers for Disease Control and Prevention to issue a health alert.

Officials are concerned that more Yosemite visitors could develop the lung disease in the next month or so. Most of the victims identified so far were believed to have been infected while staying in one of 91 "Signature" tent-style cabins in the park's popular Curry Village camping area.

There is no cure for the disease, but early detection through blood tests greatly increases survival rates.

"I want people to know about this so they take it seriously," Wong said. "We're doing our due diligence to share the information."

Last week, park officials shut down the insulated "Signature" tent cabins after finding deer mice, which carry the disease and can burrow through holes the size of pencil erasers, infesting the double walls.

Officials are continuing to investigate additional possible cases of the disease, which has killed 64 Californians and about 590 Americans since it was identified in 1993, Wong said.

Early symptoms include headache, fever, muscle aches, shortness of breath and coughing. The virus may incubate for up to six weeks after exposure and can lead to severe breathing difficulties and death.

Experts say hantavirus, which kills 36 percent of those it infects, has never been known to be transmitted between humans.

Four of those known to be infected at Yosemite this summer slept in the insulated tent cabins. One slept elsewhere in Curry Village, located in a valley beneath the iconic Half Dome rock formation, and the sixth case remains under investigation.

One man from northern California and another from Pennsylvania died, while three victims have recovered and a fourth remains hospitalized, the state Department of Public Health said.

Nearly 4 million people visit Yosemite each year, attracted to the park's dramatic scenery and hiking trails. Roughly 70 percent of those visitors congregate in Yosemite Valley, where Curry Village is located.

Hantavirus is carried in viral particles inhaled from rodent feces and urine. People also can be infected by eating contaminated food, touching contaminated surfaces or being bitten by infected rodents.

Hantavirus previously infected two Yosemite visitors, one in 2000 and another in 2010, but at higher elevations.

Ben Margot / AP

At least five hantavirus infections have been linked to the tent cabins in Yosemite's Curry Village.

About 10,000 people who stayed in tent cabins at Yosemite National Park over the summer may be at risk for hantavirus, the U.S. Centers for Disease Control and Prevention said on Friday in a health advisory. 

"People who stayed in the tents between June 10 and Aug. 24 may be at risk of developing (hantavirus) in the next six weeks," the CDC said in the release.

Earlier, two more Yosemite National Park visitors were found with a mouse-borne virus blamed for the deaths of two people, bringing the total number of infections to six, state health officials said.

The new discoveries were made during the agency's investigation into cases of hantavirus pulmonary syndrome at the famed park, California Department of Public Health Anita Gore spokeswoman said.

The infections spurred park officials to close 91 tent cabins at Curry Village in Yosemite Valley, where five of the six infections occurred. Gore said one of the infected people may have been in another area of the park.

"Our investigation is trying to determine which area of the park that person visited," she said.

Over the past three weeks, two people have died of hantavirus pulmonary syndrome after staying in cabins at Curry Village in Yosemite Valley.

Park officials said the double-walled design of the cabins that were closed Tuesday made it easy for mice to nest between the walls. The disease is carried in the feces, urine and saliva of deer mice and other rodents.

The illness begins as flu-like symptoms, including including headache, fever, muscle ache, shortness of breath and cough. Initial symptoms may appear up to six weeks after exposure and can lead to severe breathing difficulties and death.  

Although there is no cure for hantavirus, treatment after early detection through blood tests can save lives. The virus, which has never been known to be transmitted between humans, kills 38 percent of those it infects.

"The earlier it's caught and supportive care is given, the better the survival rate," said Dr. Vicki Kramer, chief of vector-borne diseases at the state Public Health Department.

Dr. Charles Chiu, an infectious disease specialist at the University of California, San Francisco, said he made a habit of airing out his tent-cabin before occupying it as a precaution against possible virus-carrying dust particles when he stayed in Curry Village a few years ago.

But even Chiu said he was surprised to learn that a hantavirus had killed two people and stricken others who slept in the same structures this summer.

"It wasn't something even I had thought of at the time," Chiu, who studies hantavirus, told Reuters.

Five of the people who fell ill are known to have stayed in the tent cabins in June or July, and warnings have gone out to visitors who stayed in Curry Village in June, July or August.

The hantavirus outbreak occurred despite efforts by park officials to step up protection efforts last April. A 2010 report from the state health department warned park officials that rodent inspection efforts should be increased after a visitor to the Tuolumne Meadows area of the park fell ill.

The new hantavirus policy, enacted April 25, was designed to provide a safe place, "free from recognized hazards that may cause serious physical harm or death."

It came after the state report revealed that 18 percent of mice trapped for testing at various locations around the park were positive for hantavirus.

"Inspections for rodent infestations and appropriate exclusion efforts, particularly for buildings where people sleep, should be enhanced," it said.

Melanie Norall of Palo Alto, California, is monitoring her 8-year-old daughter's every sniffle. They stayed in a cabin outside Yosemite's north entrance at the end of July and awoke to mice scurrying and eating nuts out of their luggage.

In 2009, the park installed the 91 new, higher-end cabins to replace some that had been closed or damaged after parts of Curry Village, which sits below the 3,000-foot Glacier Point promontory, were determined to be in a rock-fall hazard zone.

The new cabins have canvas exteriors and drywall or plywood inside, with insulation in between. Park officials found this week when they tried to shore up some of the cabins that mice had built nests in the walls.

The deer mice most prone to carrying the virus can squeeze through holes just one-quarter-inch in diameter. They are distinguished from solid-colored house mice by their white bellies and gray and brown bodies.

The park sent warning emails and letters Wednesday to another 1,000 people who stayed in tent cabins, after officials found that a computer glitch had stopped the notices from going out with the original 1,700 warnings Monday. The warning says anyone with flu-like symptoms or respiratory problems should seek immediate medical attention.

In 2011, half of the 24 U.S. hantavirus cases ended in death. But since 1993, when the virus first was identified, the average death rate is 36.39 percent, according to the Centers for Disease Control.

The vast majority of hantavirus victims are young and middle-age adults, Chiu said, probably because they are mostly likely to engage in activities that would readily expose them, such as chopping and carrying fire wood or sweeping the floors.

"The message should not be you should stop camping. The important thing is general awareness of this disease and to avoid wild rodents in general," Chiu said.

The Associated Press and Reuters contributed to this report

More hantavirus news:

Yosemite closes cabins after hantavirus deaths 

Hantavirus cluster worries officials

Centers for Disease Control and Prevention

Deer mice, such as this one, can carry the hantavirus, which is now responsible for the deaths of two visitors to Yosemite National Park.

The hantavirus that has killed two California park visitors and infected two others has been known to science for only 20 years. It’s so rare that health officials say it’s unusual and worrying for there to be more than one case at a time in the same place.

National Park Service officials have taken the unusual step of cautioning 1,700 people who stayed in tented cabins at California’s Yosemite park this summer. The hantavirus can take weeks to start making people sick, so victims may not realize when and where they were infected. It kills about a third of its victims, and there’s no good treatment, making it highly dangerous.

The virus was so mystifying when it was first reported in 1993 that it was called the Sin Nombre virus – Spanish for “the virus without a name.” The first known victim was a strapping young New Mexico man who died despite efforts to save him. Others followed, the victims suffocating as their lungs failed or dying of kidney failure. The cases were clustered in the “Four Corners” region, where Arizona, New Mexico, Colorado and Utah come together.

Disease investigators trapped thousands of rodents in their search for the carrier and finally found the deer mouse was the host. The virus, it turned out, was related to a mystery virus that killed U.S. troops during the Korean War and that wasn’t identified until 1976.

It was named hantavirus after the Han river in South Korea. The virus doesn’t harm the mice, and they shed it in their urine and feces. It survives being dried out, and most of the victims appear to have been infected when cleaning or working in dusty buildings that had been closed up – perhaps allowing the mice to nest in it. Hikers and people who sleep outdoors on the ground are also susceptible.

The Centers for Disease Control and Prevention gets about 20 reports a year of hantavirus, says Barbara Knust, of the CDC’s viral special pathogens branch. This year doesn’t look unusual in terms of numbers, she says, but a cluster of four cases in one place is.

“It’s a concern because it is a park where lots of people visit and also it is unusual for more than one hantavirus case to occur in any one location,” Knust said in a telephone interview. “We think the likely reason is that it is an area with a lot of deer mice … and which also has a lot of visitors.”

People are infected when they breathe in dust contaminated with rodent droppings or urine. The Park Service is cautioning people who stayed in "Signature Tent Cabins" at Curry Village in the park. The cabins, with flexible fabric sides, are attractive places for rodents to nest.

“Just having a situation where there is some kind of a mouse infestation and some kind of activity that might stir up the air, or opening a building that might have been closed for a while” can expose people to the virus, Knust said.

“Since hantavirus pulmonary syndrome was first identified in 1993, there have been approximately 60 cases in California and 587 cases nationally,” the National Park Service said in a statement.

There’s no specific treatment for hantavirus infection. Knust said people with serious illness may need help breathing and people showing symptoms need to get to a hospital right away. Infected people are not contagious to other people.  

The National Institutes of Health says symptoms at first look like flu, and include chills, headache or muscle aches and fever. Symptoms progress to dry cough and shortness of breath, which can in turn lead to acute respiratory distress syndrome, kidney failure and dangerously low blood pressure. Patients may need oxygen or a breathing tube, and a generic antiviral drug called ribavirin may help prevent the worst symptoms although it’s not a cure.

The CDC has advice for people working in areas where deer mice might have nested.

• When opening an unused cabin, shed or other building, open all the doors and windows, leave the building and allow the space to air out for 30 minutes.
• Spray the surfaces, carpet and other areas with a disinfectant. Leave the building for another 30 minutes.
• Spray mouse nests and droppings with a 10 percent solution of chlorine bleach or similar disinfectant. Allow it to sit for 30 minutes. Using rubber gloves, place the materials in plastic bags. Seal the bags and throw them in the trash or an incinerator. Dispose of gloves and cleaning materials in the same way.
• Wash all potentially contaminated hard surfaces with a bleach or disinfectant solution. Avoid vacuuming until the area has been thoroughly decontaminated. Then, vacuum the first few times with enough ventilation.

Related links:

Second Yosemite visitor dies of rodent-borne illness

West Nile virus outbreak affects 1,100

New pig flu spreads to people at state fairs