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The software giant and Andrey N. Sabelnikov, who admits he wrote the code used in malware that infected thousands of computers, reach a settlement in related lawsuit.
Researchers use specially crafted code to direct infected computers to their servers instead of servers run by the criminals who have been using the botnet to distribute spam.
New variants resurrect the malware four months after Microsoft and Kaspersky Lab took down the original, which was capable of sending nearly 4 billion spam e-mails each day.
St. Petersburg, Russia-based Andrey N. Sabelnikov says he is "absolutely not guilty" of participating in the creation of the huge spam network that Microsoft shut down last September.
Software giant accuses a St. Petersburg, Russia, resident of writing malware to control and nurture the botnet, which infected 41,000 computers worldwide.
A Czech resident is accused of operating a botnet that infected tens of thousands of computers, serving spam and harvesting data. This is the third botnet Microsoft has taken down using the same legal and technical measures.
Discovery leads to investigation and disruption of Nitol botnet and attempt to shut down subdomains linked to more than 500 types of malware.
Botnet was responsible for 18 billion spam messages a day -- about 18 percent of the world's spam -- experts tell The New York Times.
The pair, who are linked to a malware network that stole more than $100 million, are already in custody in the U.K.
At an event Wednesday morning in Washington, D.C., industry representatives will announce plans to fight back against botnets, which have become the Internet's leading security threat.