By Matt Dolloff, CBS Boston

BOSTON (CBS) — The Patriots defense followed up their worst performance of the season against the Seattle Seahawks with an improved effort against the San Francisco 49ers in Santa Clara on Sunday, allowing 299 total yards and sacking 49ers quarterback Colin Kaepernick five times. While it wasn’t a perfect day for the defense, it was encouraging to see them show more of a pass rush than they have most of the time in 2016.

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The Patriots defensive line saw a major shake-up as they played without Jabaal Sheard, a surprise healthy scratch who did not make the trip to Santa Clara with the team. Trey Flowers (48 snaps) continued to pick up the slack, playing more than any other defensive lineman. Rookie defensive tackle Vincent Valentine (17 snaps) has consistently played in the 20-snap range for most of the season but made his presence felt on Sunday, making a big tackle for a 4-yard loss on the 49ers’ Carlos Hyde on first-and-goal from the 3-yard line. The 49ers were held to a field goal on the drive.

Matt Patricia’s defense appeared to get more creative to generate pressure on Sunday, often bringing defensive backs down low for an extra rusher. Malcolm Butler and Patrick Chung each had a sack on Kaepernick, while Dont’a Hightower, Rob Ninkovich, and newcomer Kyle Van Noy recorded the other three.

Van Noy, acquired in a trade with the Detroit Lions, made his season debut for the Patriots after being inactive for three games, playing 29 defensive snaps. Van Noy split snaps with Shea McClellin (36), Elandon Roberts (11), and Barkevious Mingo (10) in the continued revolving door of linebackers post-Jamie Collins.

Kyle Van Noy celebrates after a sack of Colin Kaepernick of the San Francisco 49ers on November 20, 2016 in Santa Clara, California.  (Photo by Ezra Shaw/Getty Images)

Kyle Van Noy celebrates after a sack of Colin Kaepernick of the San Francisco 49ers on November 20, 2016 in Santa Clara, California. (Photo by Ezra Shaw/Getty Images)

The secondary had another up-and-down game overall but saw a marked improvement from cornerback Logan Ryan, who in a reduced role (41 snaps) mostly covered 49ers wideout Jeremy Kerley. Ryan held Kerley without a catch on six targets. Devin McCourty, Eric Rowe, Butler, and Chung each played a team-high 62 snaps.

Safety Devin McCourty said after the game that he was not surprised to see improvement from the Patriots defense, whose problem has never been effort or a desire to get better.

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“No matter what, this team always plays hard,” said McCourty. “We keep playing hard and we understand if we keep making those good plays, we’ll have energy and we’ll be able to get off the field.”

About getting off the field … the Patriots defense was also better on third down, as the 49ers were only 5-for-14 (35.7 percent) converting in that situation. But they still did not get consistently stops and big plays were once again something of an issue, as the defense allowed six plays of at least 16 yards. They had trouble covering down the field against the 49ers’ tight ends and running backs, who combined for 12 catches and 154 yards with two touchdowns.

The Patriots also, once again, failed to record a takeaway – but they got closer to making that happen, as the 49ers recovered their own offensive fumble four times. Hightower, Ninkovich, and Duron Harmon each forced a fumble.

Overall, the defense had a better gameplan and played slightly better as a unit than they did against Seattle, but are inevitably going to face much stronger competition than the 1-9 49ers in January. No matter what the defensive gameplan is for this coming Sunday at the New York Jets, McCourty knows that continued improvement is needed for the defense to get those key stops in the playoffs.

“I think last week we showed things we obviously needed to work on and need to work on fast if we want to continue to win,” said McCourty. “We did some of those things well today. But it doesn’t matter if we don’t come back next week and put in the work and do the same thing next Sunday.

“I think being here and being a veteran guy, you understand how much week-by-week you have to put in especially defensively. We do different things every week. No game plan and no game is really the same for us.”

Sheard’s situation is one to be watched in the coming weeks. Although the Patriots defense was able to show slight improvement without him on the field, you would think that Sheard will be needed to step up and play better in future games.

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Matt Dolloff is a writer for CBSBostonSports.com. Any opinions expressed do not necessarily reflect that of CBS or 98.5 The Sports Hub. Have a news tip or comment for Matt? Follow him on Twitter @mattdolloff and email him at mdolloff@985thesportshub.com.